Sequence numbers correspond to the following labels:

1. • T0104 Hypothetical protein HI0065, Haemophilus influenzae
2. • gi|1176349|sp|P44492|YJEE_HAEIN_1:157 HYPOTHETICAL PROTEIN HI0065 (Haemophilus influenzae)
   • gi|1074243|pir||H64141 hypothetical protein HI0065 - Haemophilus influenzae (strain Rd KW20) (Haemophilus influenzae)
   • gi|1573014|gb|AAC21743.1| (U32692) conserved hypothetical protein [Haemophilus influenzae Rd] (Haemophilus influenzae Rd)
3. • gi|401636|sp|P31805|YJEE_ECOLI_1:151 HYPOTHETICAL 16.9 KDA PROTEIN IN PSD-AMIB INTERGENIC REGION (URF2) (Escherichia coli)
   • gi|1361143|pir||S56393 hypothetical 16.9K protein (psd-amiB intergenic region) - Escherichia coli (Escherichia coli)
   • gi|304913|gb|AAA20096.1| (L19346) urf2 [Escherichia coli] (Escherichia coli)
   • gi|537009|gb|AAA97064.1| (U14003) urf2 of GenBank Accession Number L19346 [Escherichia coli] (Escherichia coli)
   • gi|1790610|gb|AAC77125.1| (AE000489) orf, hypothetical protein [Escherichia coli] (Escherichia coli)
4. • gi|7225682|gb|AAF40894.1|_4:149 (AE002401) conserved hypothetical protein [Neisseria meningitidis MC58] (Neisseria meningitidis MC58)
5. • gi|7380656|emb|CAB85246.1|_4:149 (AL162757) conserved hypothetical protein [Neisseria meningitidis] (Neisseria meningitidis)
6. • gi|6226431|sp|O05515|YDIB_BACSU_1:152 HYPOTHETICAL 17.9 KDA PROTEIN IN PHOB-GROES INTERGENIC REGION (Bacillus subtilis)
   • gi|7450018|pir||C69786 conserved hypothetical protein ydiB - Bacillus subtilis (Bacillus subtilis)
   • gi|1945107|dbj|BAA19715.1| (D88802) E. coli hypothetical protein; P31805 (267) [Bacillus subtilis] (Bacillus subtilis)
   • gi|2632904|emb|CAB12410.1| (Z99107) similar to hypothetical proteins [Bacillus subtilis] (Bacillus subtilis)
7. • gi|7450019|pir||H72229_1:152 conserved hypothetical protein - Thermotoga maritima (strain MSB8) (Thermotoga maritima)
   • gi|4982205|gb|AAD36699.1|AE001806_9 (AE001806) conserved hypothetical protein [Thermotoga maritima] (Thermotoga maritima)
8. • gi|7190852|gb|AAF39625.1|_1:142 (AE002349) conserved hypothetical protein [Chlamydia muridarum] (Chlamydia muridarum)
9. • gi|6226350|sp|P74415|Y257_SYNY3_4:143 HYPOTHETICAL 17.7 KDA PROTEIN SLL0257 (Synechocystis PCC6803)
   • gi|7450017|pir||S76256 hypothetical protein - Synechocystis sp. (strain PCC 6803) (Synechocystis sp.)
   • gi|1653602|dbj|BAA18515.1| (D90914) hypothetical protein [Synechocystis sp.] (Synechocystis sp.)
10. • gi|7450025|pir||H71502_1:145 probable (ATPase or kinase) - Chlamydia trachomatis (serotype D, strain UW3/Cx) (Chlamydia trachomatis)
    • gi|3328975|gb|AAC68139.1| (AE001324) (ATPase or Kinase) [Chlamydia trachomatis] (Chlamydia trachomatis)
11. • gi|6226308|sp|Q9ZED0|Y013_RICPR_4:136 HYPOTHETICAL PROTEIN RP013 (Rickettsia prowazekii)
    • gi|7450020|pir||F71708 hypothetical protein RP013 - Rickettsia prowazekii (Rickettsia prowazekii)
    • gi|3860584|emb|CAA14485.1| (AJ235270) unknown [Rickettsia prowazekii] (Rickettsia prowazekii)
12. • gi|2496467|sp|Q50706|YY22_MYCTU_18:165 HYPOTHETICAL 18.2 KDA PROTEIN RV3422C (Mycobacterium tuberculosis)
    • gi|7477616|pir||C70738 hypothetical protein Rv3422c - Mycobacterium tuberculosis (strain H37RV) (Mycobacterium tuberculosis)
    • gi|1449365|emb|CAB01034.1| (Z77165) hypothetical protein Rv3422c [Mycobacterium tuberculosis] (Mycobacterium tuberculosis)
13. • gi|2496468|sp|Q49864|YY22_MYCLE_6:154 HYPOTHETICAL 17.6 KDA PROTEIN U229F (Mycobacterium leprae)
    • gi|2145802|pir||S72986 hypothetical protein B229_C2_205 - Mycobacterium leprae (Mycobacterium leprae)
    • gi|467118|gb|AAA17300.1| (U00020) u229f; match to 16.9 kd E.coli protein in amiB region (yjeE); B229_C2_205 [Mycobacterium leprae] (Mycobacterium leprae)
14. • gi|6226476|sp|O52749|YJEE_ANASP_12:151 HYPOTHETICAL 17.9 KDA PROTEIN (Anabaena PCC7120)
    • gi|2896025|gb|AAC03104.1| (AF046871) unknown [Anabaena PCC7120] (Anabaena PCC7120)
15. • gi|6226403|sp|O83845|Y875_TREPA_2:130 HYPOTHETICAL PROTEIN TP0875 (Treponema pallidum)
    • gi|7450022|pir||A71271 conserved hypothetical protein TP0875 - syphilis spirochete (Treponema pallidum subsp. pallidum)
    • gi|3323187|gb|AAC65838.1| (AE001257) conserved hypothetical protein [Treponema pallidum] (Treponema pallidum)
16. • gi|7471517|pir||E75283_10:143 conserved hypothetical protein - Deinococcus radiodurans (strain R1) (Deinococcus radiodurans)
    • gi|6460164|gb|AAF11897.1|AE002066_1 (AE002066) conserved hypothetical protein [Deinococcus radiodurans] (Deinococcus radiodurans)
17. • gi|7450024|pir||B72052_1:131 yjee hypothetical protein - Chlamydia pneumoniae (strain CWL029) (Chlamydophila pneumoniae)
    • gi|4376956|gb|AAD18796.1| (AE001648) YjeE hypothetical protein [Chlamydophila pneumoniae] (Chlamydophila pneumoniae)
    • gi|7189025|gb|AAF37975.1| (AE002172) conserved hypothetical protein [Chlamydophila pneumoniae AR39] (Chlamydophila pneumoniae AR39)
18. • gi|6226477|sp|O86788|YJEE_STRCO_2:138 HYPOTHETICAL 15.8 KDA PROTEIN SC6G4.25 (Streptomyces coelicolor)
    • gi|7480504|pir||T35576 probable ATP/GTP binding protein - Streptomyces coelicolor (Streptomyces coelicolor)
    • gi|3449259|emb|CAA20403.1| (AL031317) putative ATP /GTP binding protein [Streptomyces coelicolor A3(2)] (Streptomyces coelicolor A3(2))
19. • gi|6226401|sp|O67011|Y843_AQUAE_7:127 HYPOTHETICAL PROTEIN AQ_843 (Aquifex aeolicus)
    • gi|7450021|pir||H70372 conserved hypothetical protein aq_843 - Aquifex aeolicus (Aquifex aeolicus)
    • gi|2983396|gb|AAC06981.1| (AE000710) hypothetical protein [Aquifex aeolicus] (Aquifex aeolicus)
20. • gi|2801652|gb|AAB97417.1|_6:123 (AF042096) unknown [Bradyrhizobium japonicum] (Bradyrhizobium japonicum)
21. • gi|6226340|sp|O51204|Y186_BORBU_4:128 HYPOTHETICAL PROTEIN BB0186 (Borrelia burgdorferi)
    • gi|7450023|pir||B70123 conserved hypothetical protein BB0186 - Lyme disease spirochete (Borrelia burgdorferi)
    • gi|2688077|gb|AAC66574.1| (AE001129) conserved hypothetical protein [Borrelia burgdorferi] (Borrelia burgdorferi)
22. • gi|7463982|pir||D64609_6:124 conserved hypothetical protein HP0716 - Helicobacter pylori (strain 26695) (Helicobacter pylori)
    • gi|2313840|gb|AAD07766.1| (AE000584) conserved hypothetical protein [Helicobacter pylori 26695] (Helicobacter pylori 26695)
23. • gi|7464783|pir||H71905_6:123 hypothetical protein jhp0654 - Helicobacter pylori (strain J99) (Helicobacter pylori)
    • gi|4155206|gb|AAD06230.1| (AE001497) putative [Helicobacter pylori J99] (Helicobacter pylori J99)
24. • gi|6968130|emb|CAB72945.1|_16:130 (AL139076) putative ATP /GTP-binding protein [Campylobacter jejuni] (Campylobacter jejuni)
25. • gi|2589001|dbj|BAA23276.1|_23:93 (AB004097) ORF4 [Hyphomicrobium methylovorum] (Hyphomicrobium methylovorum)
26. • gi|2828193|sp|P30621|MOXR_METEX_14:84 MOXR PROTEIN (MXAR PROTEIN) (Methylobacterium extorquens)
    • gi|1771259|emb|CAA69191.1| (Y07864) mxaR [Methylobacterium extorquens] (Methylobacterium extorquens)
27. • gi|6324833|ref|NP_014902.1|_183:256 ATPase; component of the 26S proteasome cap subunit; Rpt4p (Saccharomyces cerevisiae)
    • gi|2506090|sp|P53549|SUG2_YEAST PROBABLE 26S PROTEASE SUBUNIT SUG2 (PROTEASOMAL CAP SUBUNIT) (Saccharomyces cerevisiae)
    • gi|2133163|pir||S67156 26S proteasome regulatory particle chain RPT4 - yeast (Saccharomyces cerevisiae) (Saccharomyces cerevisiae)
    • gi|1420585|emb|CAA99481.1| (Z75167) ORF YOR259c [Saccharomyces cerevisiae] (Saccharomyces cerevisiae)
    • gi|1931623|gb|AAB51594.1| (U93262) proteasome cap subunit [Saccharomyces cerevisiae] (Saccharomyces cerevisiae)
28. • gi|1147800|gb|AAA85134.1|_183:256 (U43720) Sug2p [Saccharomyces cerevisiae] (Saccharomyces cerevisiae)
29. • gi|266551|sp|P29901|MOXR_PARDE_8:78 MOXR PROTEIN (Paracoccus denitrificans)
    • gi|94691|pir||D41377 moxR protein - Paracoccus denitrificans (Paracoccus denitrificans)

              10        20        30        40        50        60     
              |         |         |         |         |         |     
   1 MESLTQYIPDEFSMLRFGKKFAEILLKLHTEKAIMVYLNGDLGAGKTTLTRGMLQGIGHQ...GN
   2 MESLTQYIPDEFSMLRFGKKFAEILLKLHTEKAIMVYLNGDLGAGKTTLTRGMLQGIGHQ...GN
   3 MMNRVIPLPDEQATLDLGERVAKAC-----DGATVIYLYGDLGAGKTTFSRGFLQALGHQ...GN
   4 LPSISRFLADEAATLDLGAAWSSRL-----NAPLVIYLEGDLGAGKTTLTRGILRGLGHQ...GA
   5 LPSISRFLADEAATLDLGAAWSSRL-----NAPLVIYLEGDLGAGKTTLTRGILRGLGHQ...GA
   6 MKQLKWRTVNPEETKAIAKLTAAFA-----KPGDVLTLEGDLGAGKTTFTKGFAEGLGIT...RI
   7 MRHLRFENLTEEQLKRLAKILTENL-----KGGEVVILSGNLGAGKTTFVKGMIRAIGLDe..KM
   8 MGRYRRVTDSCEETIDLAAKLGHLL-----IPGMVVLLSGDYGAGKTEFVRGIVQGFLGEtavGQ
   9 -NSMEFFLPDLNATDQWGQQLAQQL-----PLGTIILLQGDLGAGKTSLVQGLGRGLGIT...GE
  10 MGRYRRVTHSCEETIDLATRVGRDL-----TLGMVVLLSGDYGSGKTEFVRGIVQGFLGEaavDQ
  11 -------LNSKKETKNFAKLFAQNL-----KPNDIVLLNGDLGAGKTFFCREIIKHFCGKn..TN
  12 -GGGTATLPRVEDTLTLGSRLGEQL-----CAGDVVVLSGPLGAGKTVLAKGIAMAMDVE...GP
  13 LRSGAVICERVEDTVALGSRLGEQL-----RAGDVVVLSGPLGAGKTVLAKGIAVAMDVD...GP
  14 ---TKIFLADKESTLNLGILLGETL-----TAGSVILLEGDLGAGKTTLVQGLGKGLSIT...EP
  15 ----RCVSRSAQDTARWGTVVGRLL-----EEGSVVVLQGALAAGKTCFVKGLALGLGIQ...EE
  16 --GERRLLRGVDEQRALGAALARAL-----APGSVLFLEGELGAGKTTLTQGLLAALGFD...GH
  17 MGRYRRVSHSSQETLLLGTELGQVL-----VPGAVLLLFGDYGAGKTEFVRGIVSGYLGDtiaEE
  18 --------------RELGRRLAKLL-----RAGDLVMLSGELGAGKTTLTRGLGEGLGVR...GA
  19 -----VILESEEDTYKLAEEIAQLL-----KGSEVICLRGTLGAGKTTFVKALAKALKVKnp.SA
  20 --TFSVALHNETATAQLMADLALLV-----GPGDVITLTGDLGAGKTAAARAMIRYLADDea.LE
  21 ------EFKSEKKMINFSKSFFYPL-----PIGKIFVLSGDMGSGKTSFLKGLALNLGIS...-Y
  22 --------------DELDKVAAAIL---KDDFKGVVLLKGVVGSGKTTLVQACLKHLGLD...IQ
  23 --------------DELDKVAAAIL---KDDFKGVVLLKGVVGSGKTTLVQACLKHLGLD...IQ
  24 ----------------------QIM-----PKEGVVLLQGDLASGKTSLVQAWVKFLGLD...VR
  25 WRARALEFEGEVGRAIVGQERAIRLLVIAVFARGHVLLEGDVGVGKTTLLRAVAHALGGS...YE
  26 WRDAAARFEREIAKAVVGQDRAIRLLTIAIFARGHVMLEGDVGVGKTTLLRAVARGLGGA...YE
  27 IGGLTEQIRELREVIELPLKNPEIFQRVGIKPPKGVLLYGPPGTGKTLLAKAVAATIG-A...NF
  28 IGGLTEQIRELREVIELPLKNPEIFQRVGIKPPKGVLLYGPPGTGKTLLAKAVAATIG-A...NF
  29 WHARFRDAEAALNGVVLGQARTIRLLLISALCRGHVLLAGDVGTGKTTLLRAMARALGGP...YG


            70             80        90       100             110      
            |              |         |         |               |      
   1 VKSPTYTLVEEY...N..IAGKMIYHFDLYRLADPEELEFMGIRDYF.NTD.....SICLIEWS.
   2 VKSPTYTLVEEY...N..IAGKMIYHFDLYRLADPEELEFMGIRDYF.NTD.....SICLIEWS.
   3 VKSPTYTLVEPY...T..LDNLMVYHFDLYRLADPEELEFMGIRDYF.AND.....AICLVEWP.
   4 VKSPTYAIVESY...P..LERFTLHHFDLYRFSFPEEWEDAGLDELF.AAN.....SVCLIEWP.
   5 VKSPTYAIVESY...P..LERFTLHHFDLYRFSFPEEWEDAGLDELF.AAN.....SVCLIEWP.
   6 VNSPTFTIIKEY...N..DGVLPLYHMDVYRMED--ESEDLGLDEYF.HGQ.....GVCLVEWA.
   7 VKSPTFTLMNVY...-..PGLKTIYHLDLYRLQDTDFLSLDVEDILE.DED.....GIMVVEWG.
   8 VASPSFSLLHVY...E..AMGRRVCHYDLYRLETMHVKSGEGLFQDA.EEE.....DLICVEWP.
   9 IVSPTFTIVNEY...R..EGKMPLYHLDLYRLNTLEVEYLYPEQYWQ.GEDfpl..GITAVEWP.
  10 VASPSFALLHVY...E..AGGRRVCHYDLYRLETMDIKNGADLFQDA.EEE.....DLICVEWP.
  11 IISPTFNLLQIY...K..TPKFNIYHYDMYRIKSPEEIYELGFEEAL.NGN.....-LILIEWS.
  12 ITSPTFVLARMHrprR..PGTPAMVHVDVYRLLDHNSADLLSELDSL.DLDtdledAVVVVEWG.
  13 VISPTYVLARVHlprR..LGTPAMIHVDVYRLLDHRDADLVGELDSL.DLDtdlaeAVVVMEWG.
  14 IVSPTFTLINEY...T..EGRIPLYHLDLYRLEPQEVLSLNLEIYWE.GIEiip..GIVAIEWS.
  15 ITSPTFTLLAVY...-..HGRLTLYHMDVYRLASLEDFFDIGAQECV.YGT.....GVCVIEWG.
  16 VTSPTYALMQLY...P..ASAGQVLHVDAYRVRDVAELYEMDLDELI.AGS.....RLSVIEWG.
  17 VASPSFSILHVY...G..NEPKRLCHYDLYRIDQKNQEY---IFQDA.EED.....DVLCIEWA.
  18 VTSPTFVIARVH...PslGDGPPLVHVDAYRLSGGLDEMEDLDLDVS.LSD.....SVIVVEWG.
  19 VRSPTFTLVNEY...E..TDKGKLIHIDLYRVPDFDYSEFIG-----.--E.....GILAVEWE.
  20 VPSPTFTLVQGY...E..LPPFPVMHADLYRVEDESELEEIGCRRCS.DAT.....-LVLIEWP.
  21 FTSPTYNIVNVY...D..FINFKFYHIDLYRVSSLEEFELVGGLEILmDLD.....SIIAIEWP.
  22 ATSPTFSLMHAY...-..--SESVFHYDFY-MHDLKACLELGMLECL.LEK.....GIHFVEWGd
  23 ATSPTFSLMHAY...-..--SESVFHYDFY-MRDLETCLELGMLECL.LEK.....GIHFVEWGd
  24 VDSPTFSTMQKY...E..NHDICIYHYDIY-QEGLEGLLANGLFENF.FEK.....GLHLVEWGg
  25 RVEGTIDLM---...-..-----------------------------.---.....--------.
  26 RVEGTVDMM---...-..-----------------------------.---.....--------.
  27 IFSPASGIVDKY...I..-----------------------------.---.....--------.
  28 IFSPASGIVDKY...I..-----------------------------.---.....--------.
  29 RVEGTVDLL---...-..-----------------------------.---.....--------.


        120          130         140       150        
         |            |           |         |        
   1 EKGQGILPEAD...ILVNIDYY..DDARNIELIAQTNLGKNIISAFSN
   2 EKGQGILPEAD...ILVNIDYY..DDARNIELIAQTNLGKNIISAFS-
   3 QQGTGVLPDPD...VEIHIDYQ..AQGREARVSAVSSAGELLLARL--
   4 QQGGEFTPPAD...ITATLTHD..GDGRKCLLTAHTERGRE-------
   5 QQGGEFTPPAD...ITATLTHD..GGGRKCLLTAHTERGRE-------
   6 HLIEEQLPQER...LQIVIKRAg.DDEREITFTAVGNRYEMLCEELSR
   7 DLFDGFWPEDS...IKVKIEIA..DESHRNVEILIPEEVNFLVEKIE-
   8 EVV-NLLPQFRks.VCVHMCLL..ADSQREVVI---------------
   9 ERL-PQLPSQY...LQIQLCHQ..GEGRSIALTA--------------
  10 EAV-NLLPQFRks.VCVQMRSL..TDAQREVSIGVT------------
  11 EIIKHLLTPPL...IEVNLKVL..DNNKRLCSIHK-------------
  12 EGLAERLSQRH...LDVRLERV..SHSDTRIATWSW------------
  13 AGLAECLAARH...LDIRLERV..RYSDVRIATWQW------------
  14 ERM-PYKPSTY...INVLLTYG..DEGSRQAEITPF------------
  15 ERVASELPEYT...VTISLRVL..ADGNR-------------------
  16 EGLYADYPQAP...IYLFEHVE..GDPETRR-----------------
  17 DRL----PKPR...FCDTI---..----NIYITMQTN-----------
  18 EGKVEELTEDR...LRLRIDRAvgDTADEVRHVTVTGLGERW------
  19 ERD----KPCD...IILEIEIL..DENKRK------------------
  20 ERARRRCPR--...--------..------------------------
  21 QIALSIVPKDRl..FSLTFKIV..G-----------------------
  22 EKLEKILKKYD...LAIKVVEV..KTEST-------------------
  23 EKLEKILKKYD...LAIKVVEI..KTES--------------------
  24 ENLKKTLMKFGistIQIKISIK..DDKRK-------------------
  25 -----------...--------..------------------------
  26 -----------...--------..------------------------
  27 -----------...--------..------------------------
  28 -----------...--------..------------------------
  29 -----------...--------..------------------------