Query 039905
Match_columns 168
No_of_seqs 40 out of 42
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 03:13:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039905.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039905hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00554 FAS1 Four repeated 99.7 3E-17 6.4E-22 117.0 5.6 89 46-139 1-97 (99)
2 PF02469 Fasciclin: Fasciclin 99.5 1.9E-14 4E-19 105.8 3.6 115 22-139 2-127 (128)
3 COG2335 Secreted and surface p 98.9 4E-09 8.6E-14 87.7 7.0 123 9-140 48-181 (187)
4 KOG1437 Fasciclin and related 95.6 0.044 9.6E-07 53.5 7.6 93 40-141 537-642 (682)
5 KOG1437 Fasciclin and related 87.9 0.66 1.4E-05 45.6 4.2 119 18-140 380-507 (682)
6 PF07691 PA14: PA14 domain; I 74.9 7.8 0.00017 28.5 4.9 68 88-167 51-119 (145)
7 smart00758 PA14 domain in bact 74.0 11 0.00024 27.9 5.5 34 88-121 49-82 (136)
8 PF11181 YflT: Heat induced st 43.7 12 0.00026 27.5 1.0 19 6-24 7-25 (103)
9 PF00712 DNA_pol3_beta: DNA po 34.7 14 0.0003 27.4 0.2 44 73-117 69-112 (120)
10 COG0848 ExbD Biopolymer transp 32.4 76 0.0016 25.0 4.0 56 63-118 23-79 (137)
11 KOG0996 Structural maintenance 30.4 17 0.00038 38.2 0.1 70 62-135 141-221 (1293)
12 PF01345 DUF11: Domain of unkn 26.2 65 0.0014 21.8 2.4 21 99-121 45-65 (76)
13 PF00498 FHA: FHA domain; Int 26.1 1.2E+02 0.0026 19.6 3.6 22 99-120 31-53 (68)
14 PHA02097 hypothetical protein 25.9 61 0.0013 22.6 2.1 23 110-133 37-59 (59)
15 cd05830 Sortase_D_5 Sortase D 23.3 1.3E+02 0.0028 23.0 3.8 36 78-122 58-94 (137)
16 CHL00029 rpl36 ribosomal prote 23.3 33 0.00071 20.3 0.4 9 153-161 17-25 (26)
17 TIGR01022 rpmJ_bact ribosomal 22.7 34 0.00074 22.0 0.4 11 152-162 16-26 (37)
18 cd04909 ACT_PDH-BS C-terminal 22.6 47 0.001 21.6 1.1 18 7-24 51-68 (69)
19 KOG0245 Kinesin-like protein [ 22.0 1E+02 0.0022 32.7 3.7 45 100-144 514-558 (1221)
20 PF04203 Sortase: Sortase fami 21.9 1E+02 0.0022 22.6 2.9 45 68-122 44-90 (128)
21 COG4863 Uncharacterized protei 21.3 63 0.0014 30.5 1.9 36 110-146 323-358 (439)
No 1
>smart00554 FAS1 Four repeated domains in the Fasciclin I family of proteins, present in many other contexts.
Probab=99.69 E-value=3e-17 Score=117.00 Aligned_cols=89 Identities=28% Similarity=0.437 Sum_probs=78.3
Q ss_pred EEEeeCChhhhcccCC------hh-hHHHHHhhcccCcccccccccCCCCCceeccCCCCceEEEEecCC-cceEEcceE
Q 039905 46 TFLMPNDEKLSEVVAT------PE-HLHDFILSHSIPTVLLNNNLLHFPNGTLVPSSQPGRMLSMTNSGK-LGTYVNNAR 117 (168)
Q Consensus 46 T~faP~D~als~~~~~------~~-~~~~~Ll~H~VP~~l~~~~L~~fp~Gt~vPT~l~g~~ItVTn~g~-~~l~lNnV~ 117 (168)
|+|||+|+||++.... .+ .+..+|++|++|..+...+|.. |..++|.. |..|+|+..++ +.+++||++
T Consensus 1 TvfaP~d~Af~~~~~~~~~~l~~~~~l~~ll~~Hiv~~~~~~~~l~~---~~~~~Tl~-g~~l~v~~~~~~~~i~in~~~ 76 (99)
T smart00554 1 TVFAPTDEAFQKLPPGTLNSLLADPKLKNLLLYHVVPGRLSSADLLN---GGTLPTLA-GSKLRVTRSGDSGTVTVNGAR 76 (99)
T ss_pred CEeCcCHHHHHhcCHHHHHHHhCCHHHHHHHHhcEeCceEcHHHhcc---CCccccCC-CCEEEEEEeCCCCeEEEcceE
Confidence 8999999999886431 12 6789999999999999999986 88999987 99999999985 699999999
Q ss_pred ecCCCcccCCeeEEeccccccc
Q 039905 118 LVNFNVWMNSQLKSHGISSSIT 139 (168)
Q Consensus 118 I~~Pdl~~n~~I~~HGId~vL~ 139 (168)
|+.||+..+. -++|+||+||.
T Consensus 77 v~~~di~~~n-Gvih~Id~vL~ 97 (99)
T smart00554 77 IVEADIAATN-GVVHVIDRVLL 97 (99)
T ss_pred EEECCEecCC-eEEEEECceeC
Confidence 9999999876 79999999983
No 2
>PF02469 Fasciclin: Fasciclin domain; InterPro: IPR000782 The FAS1 (fasciclin-like) domain is an extracellular module of about 140 amino acid residues. It has been suggested that the FAS1 domain represents an ancient cell adhesion domain common to plants and animals []; related FAS1 domains are also found in bacteria []. The crystal structure of FAS1 domains 3 and 4 of fasciclin I from Drosophila melanogaster (Fruit fly) has been determined, revealing a novel domain fold consisting of a seven-stranded beta wedge and at least five alpha helices; two well-ordered N-acetylglucosamine groups attached to a conserved asparagine are located in the interface region between the two FAS1 domains []. Fasciclin I is an insect neural cell adhesion molecule involved in axonal guidance that is attached to the membrane by a GPI-anchored protein. FAS1 domains are present in many secreted and membrane-anchored proteins. These proteins are usually GPI anchored and consist of: (i) a single FAS1 domain, (ii) a tandem array of FAS1 domains, or (iii) FAS1 domain(s) interspersed with other domains. Proteins known to contain a FAS1 domain include: Fasciclin I (4 FAS1 domains). Human TGF-beta induced Ig-H3 (BIgH3) protein (4 FAS1 domains), where the FAS1 domains mediate cell adhesion through an interaction with alpha3/beta1 integrin; mutation in the FAS1 domains result in corneal dystrophy []. Volvox major cell adhesion protein (2 FAS1 domains) []. Arabidopsis fasciclin-like arabinogalactan proteins (2 FAS1 domains) []. Mammalian stabilin protein, a family of fasciclin-like hyaluronan receptor homologues (7 FAS1 domains)[]. Human extracellular matrix protein periostin (4 FAS1 domains). Bacterial immunogenic protein MPT70 (1 FAS1 domain) []. The FAS1 domains of both human periostin (Q15063 from SWISSPROT) and BIgH3 (Q15582 from SWISSPROT) proteins were found to contain vitamin K-dependent gamma-carboxyglutamate residues []. Gamma-carboxyglutamate residues are more commonly associated with GLA domains (IPR000294 from INTERPRO), where they occur through post-translational modification catalysed by the vitamin K-dependent enzyme gamma-glutamylcarboxylase.; PDB: 1O70_A 1W7D_A 1W7E_A 1NYO_A 1X3B_A 2VXP_A.
Probab=99.48 E-value=1.9e-14 Score=105.81 Aligned_cols=115 Identities=19% Similarity=0.236 Sum_probs=82.5
Q ss_pred cHHHHHHHHHHHhcC-CCCCCCCceEEEeeCChhhhccc--------CChhhHHHHHhhcccCcccccccccCCCCCcee
Q 039905 22 SYHEFVVLLKMIIAS-SNPLQSTAVTFLMPNDEKLSEVV--------ATPEHLHDFILSHSIPTVLLNNNLLHFPNGTLV 92 (168)
Q Consensus 22 gY~~~a~lL~ml~~s-~~~~~~~~lT~faP~D~als~~~--------~~~~~~~~~Ll~H~VP~~l~~~~L~~fp~Gt~v 92 (168)
+|+.|+.+|+...-. .+....+..|+|||+|+|+++.. .+.+.+.++|++|+||..+..++|..- ++.+
T Consensus 2 ~~s~f~~~l~~~~l~~~l~~~~~~~TvfaP~d~a~~~~~~~~~~~~~~~~~~l~~~l~~hiv~~~~~~~~l~~~--~~~~ 79 (128)
T PF02469_consen 2 DLSTFSRLLEQAGLADLLNDSDGNYTVFAPTDDAFQKLSQETNSSLADSKEQLKSLLKYHIVPGSITSSDLRNG--KQTL 79 (128)
T ss_dssp TTHHHHHHHHHTTCHHHHGCSSSSEEEEEE-HHHHHHSHHHHHHHHHTHHHHHHHHHHHTEEES---HCHHHCH--HEEE
T ss_pred CHHHHHHHHHHcCCHHHHhcCCCCEEEEEECHHHHHhccccccchhhhhhhhHhhhhhhEEEcCceehhhhccc--cccc
Confidence 355566555532111 01012246999999999997652 156778999999999999988776654 4789
Q ss_pred ccCCCCceEEEEec-CCcceEEcc-eEecCCCcccCCeeEEeccccccc
Q 039905 93 PSSQPGRMLSMTNS-GKLGTYVNN-ARLVNFNVWMNSQLKSHGISSSIT 139 (168)
Q Consensus 93 PT~l~g~~ItVTn~-g~~~l~lNn-V~I~~Pdl~~n~~I~~HGId~vL~ 139 (168)
+|.+.|..+.|+.. +++.+++|| ++|+.+|+..+. -++|.||+||.
T Consensus 80 ~t~~~g~~~~v~~~~~~~~~~v~~~a~i~~~~~~~~n-G~ih~id~vL~ 127 (128)
T PF02469_consen 80 ETLLNGQPLRVSSSPSNGTIYVNGKARIVKSDIEASN-GVIHIIDDVLI 127 (128)
T ss_dssp EBSSTTCEEEEEEEGGTTEEEECCEEEESEEEEEESS-EEEEEESS-TS
T ss_pred eeccCCCEEEEEEEecCCceEecCceEEEeCCEEeCC-EEEEEECceEC
Confidence 99999999999999 567999999 999999986554 67799999973
No 3
>COG2335 Secreted and surface protein containing fasciclin-like repeats [Cell envelope biogenesis, outer membrane]
Probab=98.89 E-value=4e-09 Score=87.68 Aligned_cols=123 Identities=20% Similarity=0.245 Sum_probs=88.4
Q ss_pred ccHHHHHHHHhhccHHHHHHHHHHHhcC-CCCCCCCceEEEeeCChhhhccc--------C--ChhhHHHHHhhcccCcc
Q 039905 9 TDLETAVAETRAKSYHEFVVLLKMIIAS-SNPLQSTAVTFLMPNDEKLSEVV--------A--TPEHLHDFILSHSIPTV 77 (168)
Q Consensus 9 ~dl~~A~~~lr~~gY~~~a~lL~ml~~s-~~~~~~~~lT~faP~D~als~~~--------~--~~~~~~~~Ll~H~VP~~ 77 (168)
.||.+.+. .+..|.+++.+++-.... ++ .-.++.|+|+|+|+||++.. . +...+...|.||+|++.
T Consensus 48 ~~iV~~a~--~~~~f~tl~~a~~aa~Lv~~L-~~~gp~TVFaPtn~AFa~lp~~T~~~Ll~pen~~~L~~iLtYHVv~Gk 124 (187)
T COG2335 48 ADIVESAA--NNPSFTTLVAALKAAGLVDTL-NETGPFTVFAPTNEAFAKLPAGTLDALLKPENKPLLTKILTYHVVEGK 124 (187)
T ss_pred hHHHHHHc--cCcchHHHHHHHHhhhhHHHh-cCCCCeEEecCCHHHHHhCChhHHHHHhCccchhhhheeeEEEEEcCc
Confidence 34444433 555677776666521111 11 12346999999999998874 2 44556678899999999
Q ss_pred cccccccCCCCCceeccCCCCceEEEEecCCcceEEcceEecCCCcccCCeeEEecccccccc
Q 039905 78 LLNNNLLHFPNGTLVPSSQPGRMLSMTNSGKLGTYVNNARLVNFNVWMNSQLKSHGISSSITC 140 (168)
Q Consensus 78 l~~~~L~~fp~Gt~vPT~l~g~~ItVTn~g~~~l~lNnV~I~~Pdl~~n~~I~~HGId~vL~~ 140 (168)
++-.+|.. +..+ +.+.|.+++|.-.++ +++||+++++-+|+=. +-=++|=||.||.-
T Consensus 125 ~~~~~l~~---~~~v-~t~~G~~~~i~~~~~-~~~Vn~a~v~~~di~a-~NgvIhvID~Vl~P 181 (187)
T COG2335 125 ITAADLKS---SGSV-KTVQGADLKIKVTGG-GVYVNDATVTIADINA-SNGVIHVIDKVLIP 181 (187)
T ss_pred ccHHHhhc---cccc-eeecCceEEEEEcCC-cEEEeeeEEEeccEec-cCcEEEEEeeeccC
Confidence 99999998 3333 357899999999988 5999999999999653 34467999999854
No 4
>KOG1437 consensus Fasciclin and related adhesion glycoproteins [Cell wall/membrane/envelope biogenesis; Extracellular structures]
Probab=95.57 E-value=0.044 Score=53.50 Aligned_cols=93 Identities=20% Similarity=0.228 Sum_probs=63.3
Q ss_pred CCCCceEEEeeCChhhhcccCC------hhhHHHHHhhcccCcccccccccCCCCCceec------cCCCCceEEEEecC
Q 039905 40 LQSTAVTFLMPNDEKLSEVVAT------PEHLHDFILSHSIPTVLLNNNLLHFPNGTLVP------SSQPGRMLSMTNSG 107 (168)
Q Consensus 40 ~~~~~lT~faP~D~als~~~~~------~~~~~~~Ll~H~VP~~l~~~~L~~fp~Gt~vP------T~l~g~~ItVTn~g 107 (168)
...++-|+|+|+|+++.+.... ...+.+||.||++|+-.- +.-|.+-- -...|..+-+..--
T Consensus 537 ~~~~~~t~fvPt~ka~~~~~~~~~~~~~~~~l~~~l~yH~v~~~~~------ls~~~~~~v~~~~k~s~~~~~~~~~~~~ 610 (682)
T KOG1437|consen 537 TPEGNYTLFVPTNKAWQKSTKDEKSLFHKKALQDFLKYHLVPGQSR------LSLGSSPYVMIQVKLSLRGDHLFFSLVN 610 (682)
T ss_pred ccCCceEEEeecccccccCCcchhhcchHHHHHHHHHhccccceee------eecccccceeeeeeEEEecccEEeeeec
Confidence 3456799999999999887543 467899999999999875 22222222 22333333333333
Q ss_pred CcceEEcceEecCCCccc-CCeeEEeccccccccc
Q 039905 108 KLGTYVNNARLVNFNVWM-NSQLKSHGISSSITCN 141 (168)
Q Consensus 108 ~~~l~lNnV~I~~Pdl~~-n~~I~~HGId~vL~~~ 141 (168)
+ ...+|-.+++.+|+|. |+ ++|-||.|+...
T Consensus 611 ~-~~~vn~e~~~~~~i~~~n~--~~h~i~~vl~p~ 642 (682)
T KOG1437|consen 611 P-RGDVNKERLVGIDIMGTNG--VVHVIDLVLKPP 642 (682)
T ss_pred c-ccceeeeeeeccceeeecc--eeEEEEEEcccC
Confidence 3 3457778999999985 44 679999888765
No 5
>KOG1437 consensus Fasciclin and related adhesion glycoproteins [Cell wall/membrane/envelope biogenesis; Extracellular structures]
Probab=87.87 E-value=0.66 Score=45.60 Aligned_cols=119 Identities=14% Similarity=0.203 Sum_probs=72.0
Q ss_pred HhhccHHHHHHHHHHHhcCCCCCCCCceEEEeeCChhhhcccCCh--hhHHHHHhhcccCcccccccccCCCCCceeccC
Q 039905 18 TRAKSYHEFVVLLKMIIASSNPLQSTAVTFLMPNDEKLSEVVATP--EHLHDFILSHSIPTVLLNNNLLHFPNGTLVPSS 95 (168)
Q Consensus 18 lr~~gY~~~a~lL~ml~~s~~~~~~~~lT~faP~D~als~~~~~~--~~~~~~Ll~H~VP~~l~~~~L~~fp~Gt~vPT~ 95 (168)
-+..--+++..++..+...+.-..++..|+|+|.|+++..-.... ...+.+|.+|.||-.+..+++.+- ++.++|.
T Consensus 380 a~e~~~st~~rlv~elgll~~L~~n~e~t~~lp~n~~fd~~~~~~~r~l~~qIL~~HII~~~~~~~~~y~~--~~~v~t~ 457 (682)
T KOG1437|consen 380 AREDEISTSMRLVAELGLLTALAPNDEATLLLPTNNLFDDLTPLESRRLAEQILYNHIIPEYLTSSSMYNG--QTTVRTL 457 (682)
T ss_pred HhcccccHHHHHHHhccceEEEcCCCceEEeeehhhhccCCChhhhHHHHHHHHHHhCcchhhhhhhhhcc--cceeecc
Confidence 344456667677765554331123334999999999997733211 125889999999999998887653 3367666
Q ss_pred CCCceEEEEecC-----CcceEEcc-eEecCCCccc-CCeeEEecccccccc
Q 039905 96 QPGRMLSMTNSG-----KLGTYVNN-ARLVNFNVWM-NSQLKSHGISSSITC 140 (168)
Q Consensus 96 l~g~~ItVTn~g-----~~~l~lNn-V~I~~Pdl~~-n~~I~~HGId~vL~~ 140 (168)
-..+-+.-+-.. .+.+.++| +.|+.-|+.. || ++|.||.|+.-
T Consensus 458 g~~~l~~fv~r~~~s~~~t~i~~~~~~~Ii~aDi~~~nG--vvH~id~vl~p 507 (682)
T KOG1437|consen 458 GKNKLLYFVYRHSVSANVTDILIGNEACIIEADISVKNG--VVHIIDRVLDP 507 (682)
T ss_pred CCeEEEEEEecccccccceeeeccceeeEEecccceecC--ceEEeeEEcCc
Confidence 555444332221 22344444 4555666653 34 46777777765
No 6
>PF07691 PA14: PA14 domain; InterPro: IPR011658 The PA14 domain forms an insert in bacterial beta-glucosidases, other glycosidases, glycosyltransferases, proteases, amidases, yeast adhesins and bacterial toxins, including anthrax protective antigen (PA). The domain also occurs in a Dictyostelium pre-spore cell-inducing factor Psi and in fibrocystin, the mammalian protein whose mutation leads to polycystic kidney and hepatic disease. The crystal structure of PA shows that this domain (named PA14 after its location in the PA20 pro-peptide) has a beta-barrel structure. The PA14 domain sequence suggests a binding function, rather than a catalytic role. The PA14 domain distribution is compatible with carbohydrate binding [].; PDB: 2XVG_A 2XVK_A 2XVL_A 2XJU_A 2XJT_A 2XJQ_A 2XJS_A 2XJV_A 2XJP_A 2XJR_A ....
Probab=74.85 E-value=7.8 Score=28.53 Aligned_cols=68 Identities=15% Similarity=0.212 Sum_probs=41.5
Q ss_pred CCceeccCCCCceEEEEecCCcceEEcceEecCCCcccCCeeEEecccccccccCCccccccchhh-hcccceEEEEEee
Q 039905 88 NGTLVPSSQPGRMLSMTNSGKLGTYVNNARLVNFNVWMNSQLKSHGISSSITCNSPISSSQSMASL-NRHGRVYQLEILY 166 (168)
Q Consensus 88 ~Gt~vPT~l~g~~ItVTn~g~~~l~lNnV~I~~Pdl~~n~~I~~HGId~vL~~~~~~~~~~~~~~~-~~~~~~~~~~~~~ 166 (168)
.|...|.---.+.+.++..+...++|||..|+.-+ .+.+ ......-..+....+ .--|+.|.++|.|
T Consensus 51 ~G~~~~~~~G~y~f~~~~~d~~~l~idg~~vid~~--~~~~----------~~~~~~~~~~~~~~v~l~~g~~y~i~i~y 118 (145)
T PF07691_consen 51 TGYFKPPETGTYTFSLTSDDGARLWIDGKLVIDNW--GNQG----------GGFFNSGPSSTSGTVTLEAGGKYPIRIEY 118 (145)
T ss_dssp EEEEEESSSEEEEEEEEESSEEEEEETTEEEEECS--CTTT----------STTTTTSBCCEEEEEEE-TT-EEEEEEEE
T ss_pred EEEEecccCceEEEEEEecccEEEEECCEEEEcCC--cccc----------ccccccccceEEEEEEeeCCeeEEEEEEE
Confidence 36666666677889999999889999999997665 2111 111111112222223 3347899999998
Q ss_pred e
Q 039905 167 Y 167 (168)
Q Consensus 167 ~ 167 (168)
.
T Consensus 119 ~ 119 (145)
T PF07691_consen 119 F 119 (145)
T ss_dssp E
T ss_pred E
Confidence 5
No 7
>smart00758 PA14 domain in bacterial beta-glucosidases other glycosidases, glycosyltransferases, proteases, amidases, yeast adhesins, and bacterial toxins.
Probab=73.95 E-value=11 Score=27.90 Aligned_cols=34 Identities=15% Similarity=0.287 Sum_probs=28.5
Q ss_pred CCceeccCCCCceEEEEecCCcceEEcceEecCC
Q 039905 88 NGTLVPSSQPGRMLSMTNSGKLGTYVNNARLVNF 121 (168)
Q Consensus 88 ~Gt~vPT~l~g~~ItVTn~g~~~l~lNnV~I~~P 121 (168)
.|...|..-.-+.+.+.+.+...++|||..|+..
T Consensus 49 ~g~i~~~~~G~y~f~~~~~~~~~l~Idg~~vid~ 82 (136)
T smart00758 49 TGYLKPPEDGEYTFSITSDDGARLWIDGKLVIDN 82 (136)
T ss_pred EEEEECCCCccEEEEEEcCCcEEEEECCcEEEcC
Confidence 4677777777799999999999999999998864
No 8
>PF11181 YflT: Heat induced stress protein YflT
Probab=43.72 E-value=12 Score=27.54 Aligned_cols=19 Identities=26% Similarity=0.426 Sum_probs=16.9
Q ss_pred CCcccHHHHHHHHhhccHH
Q 039905 6 INQTDLETAVAETRAKSYH 24 (168)
Q Consensus 6 ~n~~dl~~A~~~lr~~gY~ 24 (168)
.|+.++.+|++.|+++||.
T Consensus 7 ~~~~E~~~~I~~L~~~Gy~ 25 (103)
T PF11181_consen 7 DNEEEALSAIEELKAQGYS 25 (103)
T ss_pred CCHHHHHHHHHHHHHcCCC
Confidence 4678999999999999995
No 9
>PF00712 DNA_pol3_beta: DNA polymerase III beta subunit, N-terminal domain; InterPro: IPR022634 This entry describes the N-terminal domain of the beta chain of DNA polymerase III. This is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. The beta chain is required for initiation of replication from an RNA primer, nucleotide triphosphate (dNTP) residues being added to the 5'-end of the growing DNA chain.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0008408 3'-5' exonuclease activity, 0006260 DNA replication, 0009360 DNA polymerase III complex; PDB: 3P16_A 3RB9_B 2AWA_C 1VPK_A 2XUR_B 3Q4K_A 3BEP_A 3D1G_A 1UNN_B 3Q4J_D ....
Probab=34.66 E-value=14 Score=27.45 Aligned_cols=44 Identities=16% Similarity=0.194 Sum_probs=35.8
Q ss_pred ccCcccccccccCCCCCceeccCCCCceEEEEecCCcceEEcceE
Q 039905 73 SIPTVLLNNNLLHFPNGTLVPSSQPGRMLSMTNSGKLGTYVNNAR 117 (168)
Q Consensus 73 ~VP~~l~~~~L~~fp~Gt~vPT~l~g~~ItVTn~g~~~l~lNnV~ 117 (168)
+||+....+=++.+|.|..|-=...+..++|+ +|++.+.+++-.
T Consensus 69 ~v~ak~l~~ivk~lp~~~~I~i~~~~~~l~I~-~~~~~f~l~~~~ 112 (120)
T PF00712_consen 69 LVPAKKLFDIVKKLPDDEEITIEVEENKLTIK-SGKSRFKLPTLD 112 (120)
T ss_dssp EEEHHHHHHHHHHSSSTSEEEEEEETTEEEEE-ETTEEEEEE-BE
T ss_pred EEEhHHHHHHHHhCCCCCeEEEEEeCCEEEEE-ECCEEEEEcCCC
Confidence 57888888999999997777777778889999 777788888755
No 10
>COG0848 ExbD Biopolymer transport protein [Intracellular trafficking and secretion]
Probab=32.38 E-value=76 Score=25.00 Aligned_cols=56 Identities=9% Similarity=0.300 Sum_probs=46.4
Q ss_pred hhHHHHHhhcccCcccccccc-cCCCCCceeccCCCCceEEEEecCCcceEEcceEe
Q 039905 63 EHLHDFILSHSIPTVLLNNNL-LHFPNGTLVPSSQPGRMLSMTNSGKLGTYVNNARL 118 (168)
Q Consensus 63 ~~~~~~Ll~H~VP~~l~~~~L-~~fp~Gt~vPT~l~g~~ItVTn~g~~~l~lNnV~I 118 (168)
+=+.-+|-.=.|..|+.-.++ ..||.++.-+..-+...+.|+-++++++++|+-++
T Consensus 23 DVmLVLLiiFmvtap~~t~~i~V~LP~a~~~~~~~~~~~i~v~i~~~G~~~l~~~~v 79 (137)
T COG0848 23 DVMLVLLIIFMVTAPFITQSIKVDLPKASAKPAPQDKKPIIVSVDADGQIYLNDKPV 79 (137)
T ss_pred HHHHHHHHHHHHhhhcccccccccCCCCcCCCcCCCCCCEEEEEeCCCcEEECCccc
Confidence 445567777788888888887 89999977777788889999999999999999554
No 11
>KOG0996 consensus Structural maintenance of chromosome protein 4 (chromosome condensation complex Condensin, subunit C) [Chromatin structure and dynamics; Cell cycle control, cell division, chromosome partitioning]
Probab=30.44 E-value=17 Score=38.23 Aligned_cols=70 Identities=24% Similarity=0.350 Sum_probs=53.5
Q ss_pred hhhHHHHHh-------hcccCcccccccccCCCCCceeccCCCCceEEEEecC----CcceEEcceEecCCCcccCCeeE
Q 039905 62 PEHLHDFIL-------SHSIPTVLLNNNLLHFPNGTLVPSSQPGRMLSMTNSG----KLGTYVNNARLVNFNVWMNSQLK 130 (168)
Q Consensus 62 ~~~~~~~Ll-------~H~VP~~l~~~~L~~fp~Gt~vPT~l~g~~ItVTn~g----~~~l~lNnV~I~~Pdl~~n~~I~ 130 (168)
..-+++++. ..++.-.+.|+..+..|.|+- -.+||-.++||... .+.|++||.+..+-|| ...++
T Consensus 141 ~~klS~LIh~S~~~~~l~SCsV~vhFq~iiD~~~~~~--E~vp~s~~~ItRtA~~~NsSkY~Ingk~as~~~V--~~lLk 216 (1293)
T KOG0996|consen 141 SKKLSALIHKSDGHPNLQSCSVEVHFQKIIDKPGGTY--EVVPDSEFTITRTAFRDNSSKYYINGKEASFKDV--TKLLK 216 (1293)
T ss_pred HHHHHHHHhccCCCCCCcceeEEEeeeeeeccCCCce--eecCCCeeEEEehhhhCCCceEeECCccccHHHH--HHHHH
Confidence 344555555 234666789999999999995 56778788888763 6699999999998875 36788
Q ss_pred Eeccc
Q 039905 131 SHGIS 135 (168)
Q Consensus 131 ~HGId 135 (168)
-||||
T Consensus 217 ~~gID 221 (1293)
T KOG0996|consen 217 SHGID 221 (1293)
T ss_pred hcCCC
Confidence 89988
No 12
>PF01345 DUF11: Domain of unknown function DUF11; InterPro: IPR001434 This group of sequences is represented by a conserved region of about 53 amino acids shared between regions, usually repeated, of proteins from a small number of phylogenetically distant prokaryotes. Examples include a 132-residue region found repeated in three of the five longest proteins of Bacillus anthracis, a 131-residue repeat in a cell wall-anchored protein of Enterococcus faecalis (Streptococcus faecalis), and a 120-residue repeat in Methanobacterium thermoautotrophicum. A similar region is found in some Chlamydia trachomatis outer membrane proteins. In C. trachomatis, three cysteine-rich proteins (also believed to be lipoproteins), MOMP, OMP6 and OMP3, make up the extracellular matrix of the outer membrane []. They are involved in the essential structural integrity of both the elementary body (EB) and recticulate body (RB) phase. They are thought to be involved in porin formation and, as these bacteria lack the peptidoglycan layer common to most Gram-negative microbes, such proteins are highly important in the pathogenicity of the organism.; GO: 0005727 extrachromosomal circular DNA
Probab=26.23 E-value=65 Score=21.79 Aligned_cols=21 Identities=19% Similarity=0.300 Sum_probs=15.9
Q ss_pred ceEEEEecCCcceEEcceEecCC
Q 039905 99 RMLSMTNSGKLGTYVNNARLVNF 121 (168)
Q Consensus 99 ~~ItVTn~g~~~l~lNnV~I~~P 121 (168)
+.|+|+|.|... ..||.|..+
T Consensus 45 ytitvtN~G~~~--a~nv~v~D~ 65 (76)
T PF01345_consen 45 YTITVTNTGPAP--ATNVVVTDT 65 (76)
T ss_pred EEEEEEECCCCe--eEeEEEEEc
Confidence 678899999754 777887654
No 13
>PF00498 FHA: FHA domain; InterPro: IPR000253 The forkhead-associated (FHA) domain [] is a phosphopeptide recognition domain found in many regulatory proteins. It displays specificity for phosphothreonine-containing epitopes but will also recognise phosphotyrosine with relatively high affinity. It spans approximately 80-100 amino acid residues folded into an 11-stranded beta sandwich, which sometimes contain small helical insertions between the loops connecting the strands []. To date, genes encoding FHA-containing proteins have been identified in eubacterial and eukaryotic but not archaeal genomes. The domain is present in a diverse range of proteins, such as kinases, phosphatases, kinesins, transcription factors, RNA-binding proteins and metabolic enzymes which partake in many different cellular processes - DNA repair, signal transduction, vesicular transport and protein degradation are just a few examples.; GO: 0005515 protein binding; PDB: 1LGQ_B 1LGP_A 2CSW_A 2PIE_A 3FM8_A 3MDB_B 3GQS_B 1UHT_A 1WLN_A 3POA_A ....
Probab=26.08 E-value=1.2e+02 Score=19.60 Aligned_cols=22 Identities=27% Similarity=0.368 Sum_probs=16.6
Q ss_pred ceEEEEec-CCcceEEcceEecC
Q 039905 99 RMLSMTNS-GKLGTYVNNARLVN 120 (168)
Q Consensus 99 ~~ItVTn~-g~~~l~lNnV~I~~ 120 (168)
....|+.- +..+++|||.++..
T Consensus 31 ~~~~i~d~~s~ngt~vng~~l~~ 53 (68)
T PF00498_consen 31 GQFYIEDLGSTNGTFVNGQRLGP 53 (68)
T ss_dssp EEEEEEESSSSS-EEETTEEESS
T ss_pred eeEEEEeCCCCCcEEECCEEcCC
Confidence 56777774 56699999999887
No 14
>PHA02097 hypothetical protein
Probab=25.92 E-value=61 Score=22.58 Aligned_cols=23 Identities=17% Similarity=0.180 Sum_probs=18.1
Q ss_pred ceEEcceEecCCCcccCCeeEEec
Q 039905 110 GTYVNNARLVNFNVWMNSQLKSHG 133 (168)
Q Consensus 110 ~l~lNnV~I~~Pdl~~n~~I~~HG 133 (168)
--|+-|+++++-. --|+++-|||
T Consensus 37 ~~fi~~ikvv~~~-n~ng~~~~hg 59 (59)
T PHA02097 37 IQFIAGVKVVKDA-NYNGFELVHG 59 (59)
T ss_pred EEEeCCcEEEecC-CCCcEEEecC
Confidence 4578899988755 3589999998
No 15
>cd05830 Sortase_D_5 Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at the cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Class D sortases are further classified into subfamilies 4 and 5. This group contains a subset of Class D sortases belonging to subfamily-5 represented by Streptomyces avermitilis SAV4337. Subfamily-5 sortases recognize a nonstandard sorting signal (LAXTG) and have replaced Sortase A in some gram-postive bacteria. They may play a housekeeping role in the cell.
Probab=23.32 E-value=1.3e+02 Score=23.02 Aligned_cols=36 Identities=14% Similarity=0.106 Sum_probs=27.6
Q ss_pred cccccccCCCCCceeccCCCCceEEEEecCC-cceEEcceEecCCC
Q 039905 78 LLNNNLLHFPNGTLVPSSQPGRMLSMTNSGK-LGTYVNNARLVNFN 122 (168)
Q Consensus 78 l~~~~L~~fp~Gt~vPT~l~g~~ItVTn~g~-~~l~lNnV~I~~Pd 122 (168)
-+|.+|.++..|. .|.|++.++ -.+.|-.++++.|+
T Consensus 58 ~~F~~L~~l~~Gd---------~i~v~~~~~~~~Y~V~~~~~v~~~ 94 (137)
T cd05830 58 APFNDLDKLRPGD---------KIVVETADGWYTYVVRSSEIVLPT 94 (137)
T ss_pred cccccHhhCCCCC---------EEEEEECCeEEEEEEeEEEEECCC
Confidence 4688888888776 777877653 37889999988885
No 16
>CHL00029 rpl36 ribosomal protein L36
Probab=23.31 E-value=33 Score=20.34 Aligned_cols=9 Identities=33% Similarity=0.977 Sum_probs=7.2
Q ss_pred hhcccceEE
Q 039905 153 LNRHGRVYQ 161 (168)
Q Consensus 153 ~~~~~~~~~ 161 (168)
++|+|++|-
T Consensus 17 vrR~g~v~V 25 (26)
T CHL00029 17 IRRRGRIFV 25 (26)
T ss_pred EeecCEEEE
Confidence 688998874
No 17
>TIGR01022 rpmJ_bact ribosomal protein L36, bacterial type. Proteins found by this model occur exclusively in bacteria and organelles.
Probab=22.68 E-value=34 Score=21.96 Aligned_cols=11 Identities=27% Similarity=0.443 Sum_probs=8.6
Q ss_pred hhhcccceEEE
Q 039905 152 SLNRHGRVYQL 162 (168)
Q Consensus 152 ~~~~~~~~~~~ 162 (168)
-++|+||+|-.
T Consensus 16 vvrR~grv~Vi 26 (37)
T TIGR01022 16 IIKRKGVVRVI 26 (37)
T ss_pred EEEECCEEEEE
Confidence 47899999854
No 18
>cd04909 ACT_PDH-BS C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH). The C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH) enzyme that catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate, found in Bacillus subtilis (BS) and other Firmicutes, Deinococci, and Bacteroidetes. PDH is the first enzyme in the aromatic amino acid pathway specific for the biosynthesis of tyrosine. This enzyme is feedback-inhibited by tyrosine in B. subtilis and other microorganisms. Both phenylalanine and tryptophan have been shown to be inhibitors of this activity in B. subtilis. Bifunctional chorismate mutase-PDH (TyrA) enzymes such as those seen in Escherichia coli do not contain an ACT domain. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=22.55 E-value=47 Score=21.61 Aligned_cols=18 Identities=28% Similarity=0.309 Sum_probs=15.3
Q ss_pred CcccHHHHHHHHhhccHH
Q 039905 7 NQTDLETAVAETRAKSYH 24 (168)
Q Consensus 7 n~~dl~~A~~~lr~~gY~ 24 (168)
+++|.+++.+.|+.+||.
T Consensus 51 ~~~~~~~~~~~L~~~G~~ 68 (69)
T cd04909 51 TQEDRERAKEILKEAGYE 68 (69)
T ss_pred CHHHHHHHHHHHHHcCCc
Confidence 446889999999999985
No 19
>KOG0245 consensus Kinesin-like protein [Cytoskeleton]
Probab=22.03 E-value=1e+02 Score=32.65 Aligned_cols=45 Identities=16% Similarity=0.149 Sum_probs=39.8
Q ss_pred eEEEEecCCcceEEcceEecCCCcccCCeeEEecccccccccCCc
Q 039905 100 MLSMTNSGKLGTYVNNARLVNFNVWMNSQLKSHGISSSITCNSPI 144 (168)
Q Consensus 100 ~ItVTn~g~~~l~lNnV~I~~Pdl~~n~~I~~HGId~vL~~~~~~ 144 (168)
..|+.-..+...||||-.|..|-+...|-.++-|=|-+..||.|.
T Consensus 514 ~vtl~p~e~aetyVNGk~v~ep~qL~~GdRiilG~~H~frfn~P~ 558 (1221)
T KOG0245|consen 514 VVTLEPCEDAETYVNGKLVTEPTQLRSGDRIILGGNHVFRFNHPE 558 (1221)
T ss_pred eEEeccCCccceeEccEEcCCcceeccCCEEEEcCceeEEecCHH
Confidence 456666778899999999999999999888889999999999996
No 20
>PF04203 Sortase: Sortase family; InterPro: IPR005754 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to MEROPS peptidase family C60 (clan C-) and include the members of both subfamilies of sortases. The Staphylococcus aureus sortase is a transpeptidase that attaches surface proteins to the cell wall; it cleaves between the Gly and Thr of the LPXTG motif and catalyses the formation of an amide bond between the carboxyl-group of threonine and the amino-group of the cell-wall peptidoglycan []. Sortase homologues are found in almost all Gram-positives, a single Gram-negative (Shewanella putrefaciens) and an archaean (Methanobacterium thermoautotrophicum), where cell wall LPXTG-mediated decoration has not been reported [, ]. Surface proteins not only promote interaction between the invading pathogen and animal tissues, but also provide ingenious strategies for bacterial escape from the host's immune response. In the case of S. aureus protein A, immunoglobulins are captured on the microbial surface and camouflage bacteria during the invasion of host tissues. S. aureus mutants lacking the srtA gene fail to anchor and display some surface proteins and are impaired in the ability to cause animal infections. Sortase acts on surface proteins that are initiated into the secretion (Sec) pathway and have their signal peptide removed by signal peptidase. The S. aureus genome encodes two sets of sortase and secretion genes. It is conceivable that S. aureus has evolved more than one pathway for the transport of 20 surface proteins to the cell wall envelope. ; PDB: 2W1K_A 2OQZ_A 1RZ2_A 2OQW_A 1T2W_A 1IJA_A 1T2P_A 1T2O_C 2KID_A 3RCC_N ....
Probab=21.86 E-value=1e+02 Score=22.56 Aligned_cols=45 Identities=22% Similarity=0.311 Sum_probs=34.1
Q ss_pred HHhhcccCcccccccccCCCCCceeccCCCCceEEEEe-cCCc-ceEEcceEecCCC
Q 039905 68 FILSHSIPTVLLNNNLLHFPNGTLVPSSQPGRMLSMTN-SGKL-GTYVNNARLVNFN 122 (168)
Q Consensus 68 ~Ll~H~VP~~l~~~~L~~fp~Gt~vPT~l~g~~ItVTn-~g~~-~l~lNnV~I~~Pd 122 (168)
.|--|- -..-+|.+|..+ -+|..|.|+. .|.. .+.+-.+.++.|+
T Consensus 44 vi~GH~-~~~~~F~~L~~~---------~~gd~i~~~~~~g~~~~Y~V~~~~~v~~~ 90 (128)
T PF04203_consen 44 VIAGHN-GGGAMFSNLNKL---------KKGDEIYLTTPDGKTYEYRVTSVKIVDPD 90 (128)
T ss_dssp EEEEES-STSSTTCGGGGG---------HTT-EEEEEETSSEEEEEEEEEEEEECTT
T ss_pred EEEeCC-CCCccccccccc---------CCCCEEEEEEecCEEEEEEEEEEEEEcCC
Confidence 344454 566778888777 6888999999 5655 8999999999887
No 21
>COG4863 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.31 E-value=63 Score=30.52 Aligned_cols=36 Identities=14% Similarity=0.273 Sum_probs=30.9
Q ss_pred ceEEcceEecCCCcccCCeeEEecccccccccCCccc
Q 039905 110 GTYVNNARLVNFNVWMNSQLKSHGISSSITCNSPISS 146 (168)
Q Consensus 110 ~l~lNnV~I~~Pdl~~n~~I~~HGId~vL~~~~~~~~ 146 (168)
.+|+||.++..+| -.++-++.-|-++|+.+..|+-.
T Consensus 323 ~lf~dg~pv~ned-gm~~i~vt~g~~~v~~YrRplfr 358 (439)
T COG4863 323 YLFMDGIPVINED-GMTSIIVTQGNDDVLSYRRPLFR 358 (439)
T ss_pred EEEecCcceeCcc-ccccceeeecccchhhhhccccc
Confidence 5789999999998 45678899999999999998753
Done!