Query psy11017
Match_columns 142
No_of_seqs 91 out of 105
Neff 3.8
Searched_HMMs 46136
Date Fri Aug 16 16:02:53 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11017.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11017hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4310|consensus 100.0 6.6E-31 1.4E-35 223.9 3.5 103 5-114 141-245 (373)
2 PF03909 BSD: BSD domain ; I 99.6 1.9E-15 4.1E-20 101.0 3.7 58 45-102 2-59 (62)
3 smart00751 BSD domain in trans 99.5 1.8E-14 3.9E-19 93.3 3.3 49 51-99 3-51 (51)
4 KOG4310|consensus 99.1 1.6E-11 3.6E-16 105.6 -0.2 79 3-84 171-250 (373)
5 KOG2690|consensus 98.8 4.3E-09 9.4E-14 91.4 3.9 79 21-104 144-227 (331)
6 KOG2074|consensus 95.2 0.014 3.1E-07 54.1 2.6 37 56-92 192-228 (548)
7 PF03909 BSD: BSD domain ; I 86.8 0.25 5.5E-06 32.7 0.5 57 7-66 1-57 (62)
8 KOG2074|consensus 86.6 0.31 6.8E-06 45.5 1.2 36 57-92 116-152 (548)
9 smart00751 BSD domain in trans 58.7 5 0.00011 25.5 0.9 47 14-63 3-49 (51)
10 PRK15215 fimbriae biosynthesis 57.3 4.9 0.00011 30.2 0.8 17 73-89 22-38 (100)
11 PF03333 PapB: Adhesin biosynt 32.9 22 0.00047 26.1 0.9 20 70-89 11-30 (91)
12 KOG0073|consensus 30.3 26 0.00057 29.0 1.1 20 78-97 67-86 (185)
13 KOG1654|consensus 27.8 36 0.00079 26.3 1.4 34 65-106 39-72 (116)
14 PF09094 DUF1925: Domain of un 24.5 36 0.00079 24.6 0.8 11 87-97 2-12 (80)
15 PF00594 Gla: Vitamin K-depend 23.6 39 0.00085 21.2 0.8 10 83-92 32-41 (42)
16 PRK05590 hypothetical protein; 21.7 43 0.00094 27.2 0.9 27 71-98 8-34 (166)
17 KOG2660|consensus 21.3 53 0.0012 29.4 1.4 31 64-94 69-99 (331)
18 PF02517 Abi: CAAX protease se 20.4 59 0.0013 21.5 1.2 19 81-99 15-33 (91)
No 1
>KOG4310|consensus
Probab=99.96 E-value=6.6e-31 Score=223.92 Aligned_cols=103 Identities=35% Similarity=0.636 Sum_probs=94.5
Q ss_pred CCC--CCCCCCccccccchhHHHhhhhhhhhhhhccccccCCCCCcceeecCchhHHHHHHhhcchhhhhhchhcCcccc
Q psy11017 5 NPP--PGVDYEFDYTTQYPVAMVTLEQDKKLEHKKNFTRNPPPGVDYEFDYTTQYPVAMVTLAQDKKLEHMRFELVPATL 82 (142)
Q Consensus 5 ~pP--~gVdF~fd~~~~~pvai~~L~~D~~l~DkRnFlr~PP~g~~f~FDfd~~~~~A~aLLkeDpnL~kmR~~LVPk~i 82 (142)
+.| ||+|.+=+-.++.+ |+.| +.|+|||||+||.+++|.|+|++++++|..||++|++|.+|||.||||.+
T Consensus 141 ~n~dlPWq~l~DEElakkQ--ilaL-----SadkRNFLRDppaaan~efdfdQ~~amA~llLk~D~~LakmRFaLVPK~V 213 (373)
T KOG4310|consen 141 ANIDLPWQDLNDEELAKKQ--ILAL-----SADKRNFLRDPPAAANFEFDFDQMQAMALLLLKEDELLAKMRFALVPKLV 213 (373)
T ss_pred cCCCCCCCCCCHHHHHHHH--HHHh-----hccchhhccCCchhccccccHHHHHHHHHHHHccchHHhhhHHHhhHHHH
Confidence 345 89999988888777 4445 68999999999999999999999999999999999999999999999999
Q ss_pred hhhhhhhhhhhhHHhhhhhhhcCcccccCCCC
Q psy11017 83 NETTFWRNYFYRVSLITQYFDTSLSSIQQPVP 114 (142)
Q Consensus 83 ~Ee~FWrnYFyrV~lIkq~~~l~~~~~~~~~~ 114 (142)
+|++||+||||||+||||++.+.+.+.|+|.|
T Consensus 214 KEeqFWqNYFYRigLIkQS~laq~~~~qqpa~ 245 (373)
T KOG4310|consen 214 KEEQFWQNYFYRIGLIKQSALAQALAAQQPAA 245 (373)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCC
Confidence 99999999999999999999999988888754
No 2
>PF03909 BSD: BSD domain ; InterPro: IPR005607 The BSD domain is an about 60-residue long domain named after the BTF2-like transcription factors, Synapse-associated proteins and DOS2-like proteins in which it is found. Additionally, it is also found in several hypothetical proteins. The BSD domain occurs in one or two copies in a variety of species ranging from primal protozoan to human. It can be found associated with other domains such as the BTB domain (see PDOC50097 from PROSITEDOC) or the U-box in multidomain proteins. The function of the BSD domain is yet unknown []. Secondary structure prediction indicates the presence of three predicted alpha helices, which probably form a three-helical bundle in small domains. The third predicted helix contains neighbouring phenylalanine and tryptophan residues - less common amino acids that are invariant in all the BSD domains identified and that are the most striking sequence features of the domain []. Some proteins known to contain one or two BSD domains are listed below: Mammalian TFIIH basal transcription factor complex p62 subunit (GTF2H1). Yeast RNA polymerase II transcription factor B 73 kDa subunit (TFB1), the homologue of BTF2. Yeast DOS2 protein. It is involved in single-copy DNA replication and ubiquitination. Drosophila synapse-associated protein SAP47. Mammalian SYAP1. Various Arabidopsis thaliana (Mouse-ear cress) hypothetical proteins.; PDB: 1X3A_A 1PFJ_A 2RNR_B 2DII_A.
Probab=99.57 E-value=1.9e-15 Score=100.98 Aligned_cols=58 Identities=36% Similarity=0.615 Sum_probs=47.4
Q ss_pred CCCcceeecCchhHHHHHHhhcchhhhhhchhcCcccchhhhhhhhhhhhHHhhhhhh
Q psy11017 45 PGVDYEFDYTTQYPVAMVTLAQDKKLEHMRFELVPATLNETTFWRNYFYRVSLITQYF 102 (142)
Q Consensus 45 ~g~~f~FDfd~~~~~A~aLLkeDpnL~kmR~~LVPk~i~Ee~FWrnYFyrV~lIkq~~ 102 (142)
...+..|+.+.....+..+|.+||+|++++.+|||+.|+|++||++|||++..+++..
T Consensus 2 ~~~~~~f~~~~~~e~i~~lL~~~p~l~~~~~~lVP~~~~e~~FW~rYf~~~~~~~~~~ 59 (62)
T PF03909_consen 2 ENWDFEFDIDEQTEEIKKLLEEDPNLRKLYNELVPSKMSEEEFWKRYFYRLHKIKQKE 59 (62)
T ss_dssp SSS--S--CHHHHHHHHHHHHH-HHHHHHHHHCCTTTS-HHHHHHHHHCHHHHHHHHH
T ss_pred cchhhcccccCCHHHHHHHHHhCHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhh
Confidence 3445667777789999999999999999999999999999999999999999998765
No 3
>smart00751 BSD domain in transcription factors and synapse-associated proteins.
Probab=99.49 E-value=1.8e-14 Score=93.27 Aligned_cols=49 Identities=31% Similarity=0.533 Sum_probs=44.4
Q ss_pred eecCchhHHHHHHhhcchhhhhhchhcCcccchhhhhhhhhhhhHHhhh
Q psy11017 51 FDYTTQYPVAMVTLAQDKKLEHMRFELVPATLNETTFWRNYFYRVSLIT 99 (142)
Q Consensus 51 FDfd~~~~~A~aLLkeDpnL~kmR~~LVPk~i~Ee~FWrnYFyrV~lIk 99 (142)
|+.+.....+.++|+++|+|+++|.+|||+.|+|++||++||+++..++
T Consensus 3 f~~~~~~~~i~~il~~~p~l~~~~~~lVP~~~se~~FW~ryF~~~~~~~ 51 (51)
T smart00751 3 FSLDAKKEEIESLLKENPLLKKLYNELVPKVLSEEEFWARYFYLLYKIK 51 (51)
T ss_pred CcccCCHHHHHHHHHHCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHhhC
Confidence 4556677888999999999999999999999999999999999998763
No 4
>KOG4310|consensus
Probab=99.08 E-value=1.6e-11 Score=105.57 Aligned_cols=79 Identities=20% Similarity=0.341 Sum_probs=69.4
Q ss_pred CCCCCCCCCCCccccccchhHHHhhhhhhhhhhhccccccCCCCCcceeecCchhHHHHHHhhcchhhhhh-chhcCccc
Q psy11017 3 SRNPPPGVDYEFDYTTQYPVAMVTLEQDKKLEHKKNFTRNPPPGVDYEFDYTTQYPVAMVTLAQDKKLEHM-RFELVPAT 81 (142)
Q Consensus 3 ~r~pP~gVdF~fd~~~~~pvai~~L~~D~~l~DkRnFlr~PP~g~~f~FDfd~~~~~A~aLLkeDpnL~km-R~~LVPk~ 81 (142)
+|+||+|+.|+|||+.|+++|+++|.+|+++.++| |-.+|+-.. +-.||++|++++.|++++..++.+ |-.-.|.+
T Consensus 171 LRDppaaan~efdfdQ~~amA~llLk~D~~LakmR-FaLVPK~VK--EeqFWqNYFYRigLIkQS~laq~~~~qqpa~~~ 247 (373)
T KOG4310|consen 171 LRDPPAAANFEFDFDQMQAMALLLLKEDELLAKMR-FALVPKLVK--EEQFWQNYFYRIGLIKQSALAQALAAQQPAAGK 247 (373)
T ss_pred ccCCchhccccccHHHHHHHHHHHHccchHHhhhH-HHhhHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCc
Confidence 79999999999999999999999999999999999 999999988 666799999999999999888765 44445554
Q ss_pred chh
Q psy11017 82 LNE 84 (142)
Q Consensus 82 i~E 84 (142)
+-|
T Consensus 248 ~~e 250 (373)
T KOG4310|consen 248 EEE 250 (373)
T ss_pred hhh
Confidence 443
No 5
>KOG2690|consensus
Probab=98.78 E-value=4.3e-09 Score=91.36 Aligned_cols=79 Identities=20% Similarity=0.440 Sum_probs=65.0
Q ss_pred hhHHHhhhhhhhhhhhccccccCCCCCcc-----eeecCchhHHHHHHhhcchhhhhhchhcCcccchhhhhhhhhhhhH
Q psy11017 21 PVAMVTLEQDKKLEHKKNFTRNPPPGVDY-----EFDYTTQYPVAMVTLAQDKKLEHMRFELVPATLNETTFWRNYFYRV 95 (142)
Q Consensus 21 pvai~~L~~D~~l~DkRnFlr~PP~g~~f-----~FDfd~~~~~A~aLLkeDpnL~kmR~~LVPk~i~Ee~FWrnYFyrV 95 (142)
..++..|+ +|..+|.+-|-....| .|+-+....-+..||..+|.|++|--+|||..++-+.||++|||+|
T Consensus 144 e~~L~~lq-----sd~~ty~~EP~~~~~fe~W~s~f~lDeK~eEI~~LL~gnpdir~ly~~lVP~~VshetFW~RYFy~v 218 (331)
T KOG2690|consen 144 EAQLLELQ-----SDENTYCDEPDDLEDFELWLSPFSLDEKTEEISELLEGNPDIRKLYEDLVPSEVSHETFWHRYFYKV 218 (331)
T ss_pred HHHHHHhh-----cCccccccCCCCHHHHHHHhhccCcccchHHHHHHHhcCccHHHHHHHhCcccccHHHHHHHHHHHH
Confidence 34555665 5667787777666544 3666777788999999999999999999999999999999999999
Q ss_pred Hhhhhhhhc
Q psy11017 96 SLITQYFDT 104 (142)
Q Consensus 96 ~lIkq~~~l 104 (142)
..+.|...+
T Consensus 219 ~kleq~e~~ 227 (331)
T KOG2690|consen 219 EKLEQEEAK 227 (331)
T ss_pred HHHhHHHHH
Confidence 999887663
No 6
>KOG2074|consensus
Probab=95.16 E-value=0.014 Score=54.11 Aligned_cols=37 Identities=19% Similarity=0.395 Sum_probs=34.2
Q ss_pred hhHHHHHHhhcchhhhhhchhcCcccchhhhhhhhhh
Q psy11017 56 QYPVAMVTLAQDKKLEHMRFELVPATLNETTFWRNYF 92 (142)
Q Consensus 56 ~~~~A~aLLkeDpnL~kmR~~LVPk~i~Ee~FWrnYF 92 (142)
.-.++..+-++-|.+++.--+.||+.++|+.||.+||
T Consensus 192 t~eiI~~IF~~yPaVkk~y~e~VP~nmtE~eFWtrFF 228 (548)
T KOG2074|consen 192 TSEIIEQIFETYPAVKKKYAENVPHNMTEKEFWTRFF 228 (548)
T ss_pred CHHHHHHHHHhChHHHHHHHhhCCccccchhHHHHHH
Confidence 5678899999999999999999999999999999965
No 7
>PF03909 BSD: BSD domain ; InterPro: IPR005607 The BSD domain is an about 60-residue long domain named after the BTF2-like transcription factors, Synapse-associated proteins and DOS2-like proteins in which it is found. Additionally, it is also found in several hypothetical proteins. The BSD domain occurs in one or two copies in a variety of species ranging from primal protozoan to human. It can be found associated with other domains such as the BTB domain (see PDOC50097 from PROSITEDOC) or the U-box in multidomain proteins. The function of the BSD domain is yet unknown []. Secondary structure prediction indicates the presence of three predicted alpha helices, which probably form a three-helical bundle in small domains. The third predicted helix contains neighbouring phenylalanine and tryptophan residues - less common amino acids that are invariant in all the BSD domains identified and that are the most striking sequence features of the domain []. Some proteins known to contain one or two BSD domains are listed below: Mammalian TFIIH basal transcription factor complex p62 subunit (GTF2H1). Yeast RNA polymerase II transcription factor B 73 kDa subunit (TFB1), the homologue of BTF2. Yeast DOS2 protein. It is involved in single-copy DNA replication and ubiquitination. Drosophila synapse-associated protein SAP47. Mammalian SYAP1. Various Arabidopsis thaliana (Mouse-ear cress) hypothetical proteins.; PDB: 1X3A_A 1PFJ_A 2RNR_B 2DII_A.
Probab=86.80 E-value=0.25 Score=32.70 Aligned_cols=57 Identities=25% Similarity=0.274 Sum_probs=38.6
Q ss_pred CCCCCCCccccccchhHHHhhhhhhhhhhhccccccCCCCCcceeecCchhHHHHHHhhc
Q psy11017 7 PPGVDYEFDYTTQYPVAMVTLEQDKKLEHKKNFTRNPPPGVDYEFDYTTQYPVAMVTLAQ 66 (142)
Q Consensus 7 P~gVdF~fd~~~~~pvai~~L~~D~~l~DkRnFlr~PP~g~~f~FDfd~~~~~A~aLLke 66 (142)
|...+++|+.+.....+..+|.+|+.+...+ .-.+|.... +-+||..|+.....++.
T Consensus 1 ~~~~~~~f~~~~~~e~i~~lL~~~p~l~~~~-~~lVP~~~~--e~~FW~rYf~~~~~~~~ 57 (62)
T PF03909_consen 1 PENWDFEFDIDEQTEEIKKLLEEDPNLRKLY-NELVPSKMS--EEEFWKRYFYRLHKIKQ 57 (62)
T ss_dssp -SSS--S--CHHHHHHHHHHHHH-HHHHHHH-HHCCTTTS---HHHHHHHHHCHHHHHHH
T ss_pred CcchhhcccccCCHHHHHHHHHhCHHHHHHH-HHhCCCCCC--HHHHHHHHHHHHHHHHH
Confidence 4566778888777888888999999998888 666766666 67789988887766543
No 8
>KOG2074|consensus
Probab=86.62 E-value=0.31 Score=45.48 Aligned_cols=36 Identities=22% Similarity=0.349 Sum_probs=31.4
Q ss_pred hHHHHHHhhcchhhhhhchhcCcc-cchhhhhhhhhh
Q psy11017 57 YPVAMVTLAQDKKLEHMRFELVPA-TLNETTFWRNYF 92 (142)
Q Consensus 57 ~~~A~aLLkeDpnL~kmR~~LVPk-~i~Ee~FWrnYF 92 (142)
...-.+||++||.|.|+.-++|=+ +|++++||.++.
T Consensus 116 lelk~~lLqen~~L~kl~ke~V~s~~ls~eeFWStrl 152 (548)
T KOG2074|consen 116 LELKQSLLQENPVLFKLYKELVVSKVLSPEEFWSTRL 152 (548)
T ss_pred HHHHHHHhhcCHHHHHHHHHHHHhcCCCHHHHHHHHh
Confidence 345678999999999999999865 899999999964
No 9
>smart00751 BSD domain in transcription factors and synapse-associated proteins.
Probab=58.75 E-value=5 Score=25.55 Aligned_cols=47 Identities=13% Similarity=0.072 Sum_probs=33.4
Q ss_pred ccccccchhHHHhhhhhhhhhhhccccccCCCCCcceeecCchhHHHHHH
Q psy11017 14 FDYTTQYPVAMVTLEQDKKLEHKKNFTRNPPPGVDYEFDYTTQYPVAMVT 63 (142)
Q Consensus 14 fd~~~~~pvai~~L~~D~~l~DkRnFlr~PP~g~~f~FDfd~~~~~A~aL 63 (142)
|..+.+...+-.+|.+|+.+.+.+ .-.+|.... +-+||..|+.....
T Consensus 3 f~~~~~~~~i~~il~~~p~l~~~~-~~lVP~~~s--e~~FW~ryF~~~~~ 49 (51)
T smart00751 3 FSLDAKKEEIESLLKENPLLKKLY-NELVPKVLS--EEEFWARYFYLLYK 49 (51)
T ss_pred CcccCCHHHHHHHHHHCHHHHHHH-HHHCCCCCC--HHHHHHHHHHHHHh
Confidence 344555555567899999999888 457776666 66779988876543
No 10
>PRK15215 fimbriae biosynthesis regulatory protein; Provisional
Probab=57.31 E-value=4.9 Score=30.23 Aligned_cols=17 Identities=47% Similarity=0.839 Sum_probs=14.6
Q ss_pred hchhcCcccchhhhhhh
Q psy11017 73 MRFELVPATLNETTFWR 89 (142)
Q Consensus 73 mR~~LVPk~i~Ee~FWr 89 (142)
-...|.|+.++|++||-
T Consensus 22 k~~~L~pG~v~eehF~L 38 (100)
T PRK15215 22 RRGALIPAKVNEEHFWL 38 (100)
T ss_pred ccCcccCCccCHHHHHH
Confidence 34689999999999994
No 11
>PF03333 PapB: Adhesin biosynthesis transcription regulatory protein; InterPro: IPR004356 P pili, or fimbriae, are ~68A in diameter and 1 micron in length, the bulk of which is a fibre composed of the main structural protein PapA []. At its tip, the pilus is terminated by a fibrillum consisting of repeating units of the PapE protein. This, in turn, is topped by the adhesins, PapF and PapG, both of which are needed for receptor binding. The tip fibrillum is anchored to the main PapA fibre by the PapK pilus-adaptor protein. PapH, an outer membrane protein, then anchors the entire rod in the bacterial envelope []. A cytoplasmic chaperone (PapD) assists in assembling the monomers of the macromolecule in the membrane. All of the functional pap genes are arranged in a cluster (operon) on the Escherichia coli genome. It is believed that selective pressure exerted by the host's urinal and intestinal tract isoreceptors forced the spread of this operon to other strains via lateral transfer []. PapB, encoded within the cluster, acts as a transcriptional regulator of the functional pap genes and is located in the bacterial cytoplasm []. Its mechanism involves differential binding to separate sites in the cluster, suggesting that this protein is both an activator and repressor of pilus-adhesion transcription. The protein shares similarity with other E. coli fimbrial- adhesion transcription regulators, such as AfaA, DaaA and FanB. ; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 3M8J_A.
Probab=32.94 E-value=22 Score=26.11 Aligned_cols=20 Identities=30% Similarity=0.604 Sum_probs=11.5
Q ss_pred hhhhchhcCcccchhhhhhh
Q psy11017 70 LEHMRFELVPATLNETTFWR 89 (142)
Q Consensus 70 L~kmR~~LVPk~i~Ee~FWr 89 (142)
+++-.-.|+|+.++|+.||-
T Consensus 11 ~~~~~~~L~pG~vs~e~F~l 30 (91)
T PF03333_consen 11 LRKKNGYLIPGKVSEEHFWL 30 (91)
T ss_dssp HHHHHC---TT-S-HHHHHH
T ss_pred HHHhcCccCCCCcCHHHHHH
Confidence 44555689999999999994
No 12
>KOG0073|consensus
Probab=30.30 E-value=26 Score=28.95 Aligned_cols=20 Identities=25% Similarity=0.551 Sum_probs=13.8
Q ss_pred CcccchhhhhhhhhhhhHHh
Q psy11017 78 VPATLNETTFWRNYFYRVSL 97 (142)
Q Consensus 78 VPk~i~Ee~FWrnYFyrV~l 97 (142)
|-+..+=..||+|||=..+-
T Consensus 67 vGGq~~lr~~W~nYfestdg 86 (185)
T KOG0073|consen 67 VGGQKTLRSYWKNYFESTDG 86 (185)
T ss_pred cCCcchhHHHHHHhhhccCe
Confidence 34455667899999975543
No 13
>KOG1654|consensus
Probab=27.79 E-value=36 Score=26.28 Aligned_cols=34 Identities=26% Similarity=0.458 Sum_probs=28.0
Q ss_pred hcchhhhhhchhcCcccchhhhhhhhhhhhHHhhhhhhhcCc
Q psy11017 65 AQDKKLEHMRFELVPATLNETTFWRNYFYRVSLITQYFDTSL 106 (142)
Q Consensus 65 keDpnL~kmR~~LVPk~i~Ee~FWrnYFyrV~lIkq~~~l~~ 106 (142)
++-|.|.|-+| |||..++=.+| |.+||.-.+|++
T Consensus 39 ~~lp~lDK~Ky-LVP~dltvgqf-------i~iIRkRiqL~~ 72 (116)
T KOG1654|consen 39 SQLPDLDKKKY-LVPDDLTVGQF-------IKIIRKRIQLSP 72 (116)
T ss_pred ccCccccccee-eccccccHHHH-------HHHHHHHhccCh
Confidence 34577888776 99999999999 789999999873
No 14
>PF09094 DUF1925: Domain of unknown function (DUF1925); InterPro: IPR015178 Alpha-amylase is classified as family 13 of the glycosyl hydrolases and is present in archaea, bacteria, plants and animals. Alpha-amylase is an essential enzyme in alpha-glucan metabolism, acting to catalyse the hydrolysis of alpha-1,4-glucosidic bonds of glycogen, starch and related polysaccharides. Although all alpha-amylases possess the same catalytic function, they can vary with respect to sequence. In general, they are composed of three domains: a TIM barrel containing the active site residues and chloride ion-binding site (domain A), a long loop region inserted between the third beta strand and the alpha-helix of domain A that contains calcium-binding site(s) (domain B), and a C-terminal beta-sheet domain that appears to show some variability in sequence and length between amylases (domain C) []. Amylases have at least one conserved calcium-binding site, as calcium is essential for the stability of the enzyme. The chloride-binding functions to activate the enzyme, which acts by a two-step mechanism involving a catalytic nucleophile base (usually an Asp) and a catalytic proton donor (usually a Glu) that are responsible for the formation of the beta-linked glycosyl-enzyme intermediate. This entry represents a domain found in prokaryotic alpha-amylase (3.2.1.1 from EC) and 4-alpha-glucanotransferase (2.4.1.25 from EC). It is adjacent to the C-terminal domain (see IPR015179 from INTERPRO). The exact function of this domain is, as yet, unknown. More information about this protein can be found at Protein of the Month: alpha-Amylase [].; PDB: 1K1X_B 1K1W_A 1K1Y_A.
Probab=24.46 E-value=36 Score=24.60 Aligned_cols=11 Identities=36% Similarity=1.056 Sum_probs=7.5
Q ss_pred hhhhhhhhHHh
Q psy11017 87 FWRNYFYRVSL 97 (142)
Q Consensus 87 FWrnYFyrV~l 97 (142)
||||+|.|-..
T Consensus 2 ~wrNFlvkYpE 12 (80)
T PF09094_consen 2 FWRNFLVKYPE 12 (80)
T ss_dssp -GGGHHHH-HH
T ss_pred cchhhhhcCcc
Confidence 89999988643
No 15
>PF00594 Gla: Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain; InterPro: IPR000294 The GLA (gamma-carboxyglutamic acid-rich) domain contains glutamate residues that have been post-translationally modified by vitamin K-dependent carboxylation to form gamma-carboxyglutamate (Gla) [, , ]. All glutamic acid (Glu) residues present in the GLA domain are potential carboxylation sites; in coagulation proteins, all Gu residues are modified to Gla, while in osteocalcin and matrix Gla proteins only some Glu residues are modified to Gla. The GLA domain is responsible for the high-affinity binding of calcium ions. It starts at the N-terminal extremity of the mature form of proteins and ends with a conserved aromatic residue; a conserved Gla-x(3)-Gla-x-Cys motif [] is found in the middle of the domain which seems to be important for substrate recognition by the carboxylase. The 3D structure of the GLA domain has been solved [, ]. Calcium ions induce conformational changes in the GLA domain that and are necessary for the proper folding of the GLA domain. A common structural feature of functional GLA domains is the clustering of N-terminal hydrophobic residues into a hydrophobic patch that mediates interaction with the cell surface membrane []. Proteins known to contain a GLA domain include []: Coagulation factor X [] Coagulation factor VII [] Coagulation factor IX [] Coagulation factor XIV (vitamin K-dependent protein C) [] Vitamin K-dependent protein S [] Vitamin K-dependent protein Z [] Prothrombin Transthyretin Osteocalcin (also known as bone-Gla protein, BGP) Matrix Gla protein (MGP) [] Inter-alpha-trypsin inhibitor heavy chain H2 Growth arrest-specific protein 6 (Gas-6) [] ; GO: 0005509 calcium ion binding, 0005576 extracellular region; PDB: 1Q3M_A 1VZM_C 2PF1_A 1NL2_A 1NL1_A 2SPT_A 2PF2_A 2ZP0_L 1W0Y_L 2AEI_L ....
Probab=23.62 E-value=39 Score=21.21 Aligned_cols=10 Identities=40% Similarity=1.361 Sum_probs=7.6
Q ss_pred hhhhhhhhhh
Q psy11017 83 NETTFWRNYF 92 (142)
Q Consensus 83 ~Ee~FWrnYF 92 (142)
.-..||+.||
T Consensus 32 ~t~~fw~~Y~ 41 (42)
T PF00594_consen 32 GTNAFWKKYF 41 (42)
T ss_dssp HHHHHHHHHH
T ss_pred hHHHHHHHhc
Confidence 3467999997
No 16
>PRK05590 hypothetical protein; Provisional
Probab=21.69 E-value=43 Score=27.20 Aligned_cols=27 Identities=26% Similarity=0.455 Sum_probs=15.9
Q ss_pred hhhchhcCcccchhhhhhhhhhhhHHhh
Q psy11017 71 EHMRFELVPATLNETTFWRNYFYRVSLI 98 (142)
Q Consensus 71 ~kmR~~LVPk~i~Ee~FWrnYFyrV~lI 98 (142)
++|-+.-+-.. .|..||..||--=.-|
T Consensus 8 ~~~~~~~~~~~-~~~~fw~~y~~~ek~i 34 (166)
T PRK05590 8 TDMVVDYVKTK-GEAAFWKEYGSVEKNI 34 (166)
T ss_pred HHHHHHhhcch-HHHHHHHHHHHHHHHH
Confidence 34444444333 4599999999543333
No 17
>KOG2660|consensus
Probab=21.27 E-value=53 Score=29.37 Aligned_cols=31 Identities=26% Similarity=0.547 Sum_probs=23.6
Q ss_pred hhcchhhhhhchhcCcccchhhhhhhhhhhh
Q psy11017 64 LAQDKKLEHMRFELVPATLNETTFWRNYFYR 94 (142)
Q Consensus 64 LkeDpnL~kmR~~LVPk~i~Ee~FWrnYFyr 94 (142)
|+-|..|+.+.|+|||+.-..|.==++=||+
T Consensus 69 i~~DrtlqdiVyKLVPgl~erE~k~~rdFy~ 99 (331)
T KOG2660|consen 69 IRSDRTLQDIVYKLVPGLQEREMKRRRDFYK 99 (331)
T ss_pred CCcchHHHHHHHHHcchHHHHHHHHHHHHHH
Confidence 6778899999999999977666554555554
No 18
>PF02517 Abi: CAAX protease self-immunity; InterPro: IPR003675 Members of this family are probably proteases (after a isoprenyl group is attached to the Cys residue in the C-terminal CAAX motif of a protein to attach it to the membrane, the AAX tripeptide is removed by one of the CAAX prenyl proteases). The family contains the Q03530 from SWISSPROT CAAX prenyl protease []. The proteins contain a highly conserved Glu-Glu motif at the amino end of the alignment. The alignment also contains two histidine residues that may be involved in zinc binding []. While these proteins are involved in membrane anchoring of proteins in eukaryotes, little is known about their function in prokaryotes. In some known bacteriocin loci, Abi genes have been found downstream of bacteriocin structural genes where they are probably involved in self-immunity. Investigation of the bacteriocin-like loci in the Gram positive bacteria locus from Lactobacillus sakei 23K confirmed that the bacteriocin-like genes (sak23Kalphabeta) exhibited antimicrobial activity when expressed in a heterologous host and that the associated Abi gene (sak23Ki) conferred immunity against the cognate bacteriocin. Interestingly, the immunity genes from three similar systems conferred a high degree of cross-immunity against each other's bacteriocins, suggesting the recognition of a common receptor. Site-directed mutagenesis demonstrated that the conserved motifs constituting the putative proteolytic active site of the Abi proteins are essential for the immunity function of Sak23Ki - thus a new concept in self-immunity []. This family also includes lysostaphin resistance protein A [].; GO: 0016020 membrane
Probab=20.42 E-value=59 Score=21.52 Aligned_cols=19 Identities=16% Similarity=0.424 Sum_probs=14.5
Q ss_pred cchhhhhhhhhhhhHHhhh
Q psy11017 81 TLNETTFWRNYFYRVSLIT 99 (142)
Q Consensus 81 ~i~Ee~FWrnYFyrV~lIk 99 (142)
-+.||.+||.|.++.-.-+
T Consensus 15 ~~~EEl~fRg~l~~~l~~~ 33 (91)
T PF02517_consen 15 PIAEELFFRGFLFNRLRRR 33 (91)
T ss_pred HHHHHHHHHHHHHHHHHHh
Confidence 3689999999998864443
Done!