Query psy336
Match_columns 121
No_of_seqs 136 out of 783
Neff 6.5
Searched_HMMs 46136
Date Fri Aug 16 23:00:54 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy336.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/336hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05833 FbpA: Fibronectin-bin 99.9 1.3E-27 2.9E-32 196.9 6.9 117 1-119 76-204 (455)
2 COG1293 Predicted RNA-binding 99.9 1.5E-23 3.2E-28 178.6 8.4 115 1-119 81-202 (564)
3 KOG2030|consensus 99.6 2.6E-15 5.6E-20 130.6 4.9 120 1-120 74-199 (911)
4 PF05833 FbpA: Fibronectin-bin 68.7 12 0.00025 31.1 5.1 48 1-49 12-60 (455)
5 PF06099 Phenol_hyd_sub: Pheno 54.9 34 0.00075 21.2 4.2 33 8-42 9-41 (59)
6 PRK14810 formamidopyrimidine-D 43.5 1.6E+02 0.0034 23.1 8.3 34 83-118 137-173 (272)
7 COG1293 Predicted RNA-binding 43.0 21 0.00046 31.1 2.6 47 1-49 17-65 (564)
8 PRK01103 formamidopyrimidine/5 40.3 1.8E+02 0.0039 22.7 7.9 30 87-118 142-174 (274)
9 PF01453 B_lectin: D-mannose b 37.3 55 0.0012 22.1 3.5 29 34-62 54-82 (114)
10 PF02743 Cache_1: Cache domain 32.8 37 0.0008 20.9 1.9 17 40-56 50-67 (81)
11 PF13629 T2SS-T3SS_pil_N: Pilu 30.8 1.3E+02 0.0029 18.5 6.1 41 16-57 26-66 (72)
12 PF05651 Diacid_rec: Putative 27.3 48 0.001 23.5 1.9 18 43-60 19-36 (135)
13 PRK13612 photosystem II reacti 24.6 1.6E+02 0.0034 20.6 4.0 38 16-56 27-65 (113)
14 cd00028 B_lectin Bulb-type man 24.6 1.2E+02 0.0026 20.1 3.5 21 37-57 59-79 (116)
15 PF09695 YtfJ_HI0045: Bacteria 24.6 69 0.0015 23.7 2.3 16 43-58 126-141 (160)
16 PF05860 Haemagg_act: haemaggl 24.5 76 0.0016 21.9 2.5 49 15-64 56-107 (121)
17 smart00108 B_lectin Bulb-type 24.5 1.1E+02 0.0023 20.3 3.1 20 38-57 91-110 (114)
18 PF13426 PAS_9: PAS domain; PD 22.9 85 0.0018 18.8 2.3 18 45-62 4-21 (104)
19 COG0203 RplQ Ribosomal protein 22.0 73 0.0016 22.4 1.9 25 15-39 91-115 (116)
20 PRK13610 photosystem II reacti 21.4 1.6E+02 0.0034 20.6 3.5 38 16-56 31-69 (113)
21 PRK10234 DNA-binding transcrip 20.6 94 0.002 21.8 2.3 18 45-62 56-73 (118)
No 1
>PF05833 FbpA: Fibronectin-binding protein A N-terminus (FbpA); InterPro: IPR008616 This family consists of the N-terminal region of the prokaryotic fibronectin-binding protein, the C-terminal region is IPR008532 from INTERPRO. Fibronectin binding is considered to be an important virulence factor in streptococcal infections. Fibronectin is a dimeric glycoprotein that is present in a soluble form in plasma and extracellular fluids; it is also present in a fibrillar form on cell surfaces. Both the soluble and cellular forms of fibronectin may be incorporated into the extracellular tissue matrix. While fibronectin has critical roles in eukaryotic cellular processes, such as adhesion, migration and differentiation, it is also a substrate for the attachment of bacteria. The binding of pathogenic Streptococcus pyogenes and Staphylococcus aureus to epithelial cells via fibronectin facilitates their internalisation and systemic spread within the host [].; PDB: 3DOA_A 2ZBK_F 2HKJ_A 1Z5B_A 1Z5C_B 1MX0_F 1Z5A_A 1MU5_A 1Z59_A.
Probab=99.94 E-value=1.3e-27 Score=196.90 Aligned_cols=117 Identities=34% Similarity=0.497 Sum_probs=81.5
Q ss_pred CccccCCCceeEEEecCCCeEEEEEEccC-----CceEEEEEEeccC-ceEEEEcCCCcEEEeeccccCC----cceeec
Q psy336 1 MRKHLKNKRLESLKLLGLDRIIDLQFGTG-----EAEYHIIVELYDR-GNIVLTDKDYIILNVLRPHSDG----EEVRFY 70 (121)
Q Consensus 1 LRk~l~g~ri~~i~Q~~~DRIv~~~f~~~-----~~~~~L~~El~g~-~Niil~d~~~~Il~~lr~~~~~----~~v~~g 70 (121)
|||||+|++|++|+|+|+||||.|+|+++ ...++|++||||+ ||+||||++++|++|++++..+ |.+.+|
T Consensus 76 Lrk~l~g~~i~~i~q~~~dRii~~~~~~~~~~~~~~~~~Li~El~g~~~NiiL~d~~~~Il~a~~~~~~~~~~~R~i~~G 155 (455)
T PF05833_consen 76 LRKHLRGARIVSIEQLGFDRIIEIEFESGDELGDDEKYRLIIELMGRHSNIILTDEDGKILDALRRVSFSQSRDREILPG 155 (455)
T ss_dssp HHHHHTT-EEEEEEESTTSSEEEEEEEEE-TTS-EEEEEEEEE--GGG-EEEEEETT-BEEEESS-B---------BSTT
T ss_pred HHHHhCCCEEEEEEEcCCcEEEEEEeeccCcCCCceeEEEEEEEcCCcccEEEEcCCCeEEeehhhcCcccccceeeccC
Confidence 79999999999999999999999999998 4699999999999 9999999999999999999844 466777
Q ss_pred ccccCCCCcccCCCCCCCH-HHHHHHHHhccCchhhHhhhhccC-CCCCcc
Q psy336 71 VREKYPVDLAKVRSGAPTQ-EMLYELFTKEKYGEQIKKILVPQL-GPQAKI 119 (121)
Q Consensus 71 ~~~~yp~~~~~~~~~~~~~-e~~~~~l~~~~~~~~l~~~L~~~l-glg~~~ 119 (121)
..|.+||++.+.+|.+.+. ++|.+.++. ++.+++++|...+ ||||.+
T Consensus 156 ~~Y~~Pp~~~~~~p~~~~~~~~~~~~l~~--~~~~l~~~L~~~~~G~~~~l 204 (455)
T PF05833_consen 156 EPYIPPPPQDKLDPLDLEEFEEFIELLKK--KEKTLVKALSKNFQGFGPEL 204 (455)
T ss_dssp SB---------B-CCC--H-HHHHHHHHC--CG-BHHHHHHHHCTT--HHH
T ss_pred ccccccccccCCCcccchhHHHHHHhhcc--CcccHHHHHHHHHHHhHHHH
Confidence 7777777767889988776 778888876 3578999998877 999875
No 2
>COG1293 Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription]
Probab=99.89 E-value=1.5e-23 Score=178.59 Aligned_cols=115 Identities=28% Similarity=0.439 Sum_probs=101.6
Q ss_pred CccccCCCceeEEEecCCCeEEEEEEccC-----CceEEEEEEeccC-ceEEEEcCCCcEEEeeccccCC-cceeecccc
Q psy336 1 MRKHLKNKRLESLKLLGLDRIIDLQFGTG-----EAEYHIIVELYDR-GNIVLTDKDYIILNVLRPHSDG-EEVRFYVRE 73 (121)
Q Consensus 1 LRk~l~g~ri~~i~Q~~~DRIv~~~f~~~-----~~~~~L~~El~g~-~Niil~d~~~~Il~~lr~~~~~-~~v~~g~~~ 73 (121)
|||||+|++|++|+|+||||||.|+|+ + ...+.|++|+||+ ||+||||++++|++++|+++.+ |++.+|..|
T Consensus 81 LRK~l~g~~i~~i~Q~~~DRIl~~~f~-~~~~~~~~~~eL~~ei~g~~gNiil~d~~~~Ii~~~r~v~~~~R~i~pG~~Y 159 (564)
T COG1293 81 LRKHLKGARIEKIEQLGFDRILELKFK-KDEIGDKIIVELFLEIMGKHGNLILVDEERKIIEALRHVTFSDRTIKPGEIY 159 (564)
T ss_pred HHHHhccCceEeEEecCCceEEEEEEe-ccCCCCceeeeeehhhccccceEEEEcCCCeeeeeeeeccccceeecCCCcc
Confidence 799999999999999999999999998 3 2478899999999 9999999999999999999955 788999888
Q ss_pred cCCCCcccCCCCCCCHHHHHHHHHhccCchhhHhhhhccCCCCCcc
Q psy336 74 KYPVDLAKVRSGAPTQEMLYELFTKEKYGEQIKKILVPQLGPQAKI 119 (121)
Q Consensus 74 ~yp~~~~~~~~~~~~~e~~~~~l~~~~~~~~l~~~L~~~lglg~~~ 119 (121)
.+||...+ +|.+.+.+++.++.... +..+++++++.+|+||.+
T Consensus 160 ~~Pp~~~~-~p~~~~~~~~~~~~~~~--~~~~~~~~~~~~g~~~~~ 202 (564)
T COG1293 160 ILPPAQLK-NPYEQSEEDFKELQLNS--GADIVRLLARFLGLGGLL 202 (564)
T ss_pred cCCcccCC-ChhhcChHHHHHHHhcc--chHHHHHHHHhcCCCHHH
Confidence 88988877 89998888877766653 678899999999999864
No 3
>KOG2030|consensus
Probab=99.56 E-value=2.6e-15 Score=130.59 Aligned_cols=120 Identities=35% Similarity=0.566 Sum_probs=95.9
Q ss_pred CccccCCCceeEEEecCCCeEEEEEEccCCceEEEEEEeccCceEEEEcCCCcEEEeeccccCC-cceeecccccCCCCc
Q psy336 1 MRKHLKNKRLESLKLLGLDRIIDLQFGTGEAEYHIIVELYDRGNIVLTDKDYIILNVLRPHSDG-EEVRFYVREKYPVDL 79 (121)
Q Consensus 1 LRk~l~g~ri~~i~Q~~~DRIv~~~f~~~~~~~~L~~El~g~~Niil~d~~~~Il~~lr~~~~~-~~v~~g~~~~yp~~~ 79 (121)
|||||+..|+++|.|+|+|||+.|+|+.++..+++++|||.+||+||+|++.+|+..+|.+..+ ......+.+.||...
T Consensus 74 LRKhik~kRledv~Q~g~DRivvlqfG~g~~~~~lvLE~~d~GNviLtdqe~~i~~llrv~~dd~~~~~~~~rer~~~s~ 153 (911)
T KOG2030|consen 74 LRKHIKEKRLEDVRQVGFDRIVVLQFGTGDDEGYLVLEFFDRGNVLLTDQELRILQLLRVRTDDSESSRSASRERFDFSA 153 (911)
T ss_pred HHHHHhHhhhchhhhcCcceEEEEEecCCCccceEEEEecCCCceEEecccceeeeEEeeeeccccchhhhhhhhcchhh
Confidence 7999999999999999999999999999999999999999999999999999999999888844 344455677787754
Q ss_pred ccCC----CCCCCHH-HHHHHHHhccCchhhHhhhhccCCCCCccc
Q psy336 80 AKVR----SGAPTQE-MLYELFTKEKYGEQIKKILVPQLGPQAKIL 120 (121)
Q Consensus 80 ~~~~----~~~~~~e-~~~~~l~~~~~~~~l~~~L~~~lglg~~~~ 120 (121)
...+ -..+..+ ++.+++...+.+.++.++|...++.|++.+
T Consensus 154 ~e~~~~k~~~~le~s~dlk~~~~~~q~g~~~~~il~~~~~~g~sk~ 199 (911)
T KOG2030|consen 154 KERNEMKSVKKLEKSGDLKALEPKDQNGITLESILHIETKEGPSKI 199 (911)
T ss_pred hhhhhccccchhhhcchHHHhhccCccccchhhhhhhhccCCCccc
Confidence 2111 1112333 677777766666688899998999998765
No 4
>PF05833 FbpA: Fibronectin-binding protein A N-terminus (FbpA); InterPro: IPR008616 This family consists of the N-terminal region of the prokaryotic fibronectin-binding protein, the C-terminal region is IPR008532 from INTERPRO. Fibronectin binding is considered to be an important virulence factor in streptococcal infections. Fibronectin is a dimeric glycoprotein that is present in a soluble form in plasma and extracellular fluids; it is also present in a fibrillar form on cell surfaces. Both the soluble and cellular forms of fibronectin may be incorporated into the extracellular tissue matrix. While fibronectin has critical roles in eukaryotic cellular processes, such as adhesion, migration and differentiation, it is also a substrate for the attachment of bacteria. The binding of pathogenic Streptococcus pyogenes and Staphylococcus aureus to epithelial cells via fibronectin facilitates their internalisation and systemic spread within the host [].; PDB: 3DOA_A 2ZBK_F 2HKJ_A 1Z5B_A 1Z5C_B 1MX0_F 1Z5A_A 1MU5_A 1Z59_A.
Probab=68.67 E-value=12 Score=31.09 Aligned_cols=48 Identities=19% Similarity=0.292 Sum_probs=32.3
Q ss_pred CccccCCCceeEEEecCCCeEEEEEEccCCceEEEEEEeccC-ceEEEEc
Q psy336 1 MRKHLKNKRLESLKLLGLDRIIDLQFGTGEAEYHIIVELYDR-GNIVLTD 49 (121)
Q Consensus 1 LRk~l~g~ri~~i~Q~~~DRIv~~~f~~~~~~~~L~~El~g~-~Niil~d 49 (121)
|++.|.|++|..|.|++. +.+.|.|...+..+.|+++.=+. .=+.+++
T Consensus 12 l~~~l~g~~i~~i~q~~~-~~~~l~~~~~~~~~~L~i~~~~~~~ri~lt~ 60 (455)
T PF05833_consen 12 LKKKLEGGRIDKIYQPDK-RELLLKFRKPGGNHWLLISAHPSGPRIHLTE 60 (455)
T ss_dssp HGG-GTT-EEEEEEEEET-TEEEEEEEETTEEEEEEEE--TTT-EEEEE-
T ss_pred HHHhhcCCEEEEEEcCCC-CEEEEEEEeCCCcEEEEEEEcCCCceeEecC
Confidence 466799999999999885 56678888666666799999555 4555664
No 5
>PF06099 Phenol_hyd_sub: Phenol hydroxylase subunit; InterPro: IPR010353 This family consists of several bacterial phenol hydroxylase subunit proteins, which are part of a multicomponent phenol hydroxylase. Some bacteria can utilise phenol or some of its methylated derivatives as their sole source of carbon and energy. The first step in this process is the conversion of phenol into catechol. Catechol is then further metabolised via the meta-cleavage pathway into TCA cycle intermediates [].
Probab=54.94 E-value=34 Score=21.22 Aligned_cols=33 Identities=21% Similarity=0.360 Sum_probs=26.4
Q ss_pred CceeEEEecCCCeEEEEEEccCCceEEEEEEeccC
Q psy336 8 KRLESLKLLGLDRIIDLQFGTGEAEYHIIVELYDR 42 (121)
Q Consensus 8 ~ri~~i~Q~~~DRIv~~~f~~~~~~~~L~~El~g~ 42 (121)
.|-+.|....-|..|+|+|+-++. .|.+||+=+
T Consensus 9 ~ryVRv~~~~~~gfVEFeFaIG~P--eL~VELvLP 41 (59)
T PF06099_consen 9 RRYVRVTGRRDDGFVEFEFAIGDP--ELFVELVLP 41 (59)
T ss_pred cCEEEEecccCCCeEEEEEecCCc--ceeEEecCC
Confidence 455677888899999999999863 689998754
No 6
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=43.54 E-value=1.6e+02 Score=23.09 Aligned_cols=34 Identities=24% Similarity=0.167 Sum_probs=25.8
Q ss_pred CCCCCCHHHHHHHHHhccCchhhHhhhhcc---CCCCCc
Q psy336 83 RSGAPTQEMLYELFTKEKYGEQIKKILVPQ---LGPQAK 118 (121)
Q Consensus 83 ~~~~~~~e~~~~~l~~~~~~~~l~~~L~~~---lglg~~ 118 (121)
+|..++.+.|.+.+++. ...++++|... .|+|+.
T Consensus 137 dpl~~~~~~~~~~~~~~--~~~ik~~Lldq~viaGiGNi 173 (272)
T PRK14810 137 EPLEISFEDFAALFRGR--KTRIKSALLNQTLLRGVGNI 173 (272)
T ss_pred CCCCCCHHHHHHHHhcC--CccHHHHhhcCceeccccHh
Confidence 45557889999998663 45799999766 798864
No 7
>COG1293 Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription]
Probab=42.99 E-value=21 Score=31.13 Aligned_cols=47 Identities=23% Similarity=0.374 Sum_probs=37.0
Q ss_pred CccccCCCceeEEEecC-CCeEEEEEEccCCceEEEEEEeccC-ceEEEEc
Q psy336 1 MRKHLKNKRLESLKLLG-LDRIIDLQFGTGEAEYHIIVELYDR-GNIVLTD 49 (121)
Q Consensus 1 LRk~l~g~ri~~i~Q~~-~DRIv~~~f~~~~~~~~L~~El~g~-~Niil~d 49 (121)
|+.+|.|+||..|.|++ .+.++.+++... ....|++|- |. +=|.+++
T Consensus 17 L~~~l~g~ri~kIyq~~~~~~~l~i~~~~~-~~~~li~~~-~~~~~i~lT~ 65 (564)
T COG1293 17 LKEQLEGGRIDKIYQPGEDELILLLRFGGK-GRKLLLSEH-PVRSRIHLTK 65 (564)
T ss_pred HHhhhhhhhhhhhcCCCCceEEEEEEcCCC-CceEEEEec-CCcceEEeCC
Confidence 56779999999999996 589999999876 345566665 65 7788887
No 8
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=40.31 E-value=1.8e+02 Score=22.74 Aligned_cols=30 Identities=23% Similarity=0.144 Sum_probs=23.2
Q ss_pred CCHHHHHHHHHhccCchhhHhhh---hccCCCCCc
Q psy336 87 PTQEMLYELFTKEKYGEQIKKIL---VPQLGPQAK 118 (121)
Q Consensus 87 ~~~e~~~~~l~~~~~~~~l~~~L---~~~lglg~~ 118 (121)
++.+.|.+.+++. ...++++| +...|+|.-
T Consensus 142 ~~~~~~~~~l~~~--~~~Ik~~LLDQ~~iaGiGNi 174 (274)
T PRK01103 142 FDGEYLAAKLRKK--KTAIKPALLDQTVVVGVGNI 174 (274)
T ss_pred CCHHHHHHHHhcC--CccHHHHhhcCCeEecccHh
Confidence 4677899988753 46899999 777899864
No 9
>PF01453 B_lectin: D-mannose binding lectin; InterPro: IPR001480 A bulb lectin super-family (Amaryllidaceae, Orchidaceae and Aliaceae) contains a ~115-residue-long domain whose overall three dimensional fold is very similar to that of [, ]: Dictyostelium discoideum comitin, an actin binding protein Curculigo latifolia curculin, a sweet tasting and taste-modifying protein This domain generally binds mannose, but in at least one protein, curculin, it is apparently devoid of mannose-binding activity. Each bulb-type lectin domain consists of three sequential beta-sheet subdomains (I, II, III) that are inter-related by pseudo three-fold symmetry. The three subdomains are flat four-stranded, antiparrallel beta-sheets. Together they form a 12-stranded beta-barrel in which the barrel axis coincides with the pseudo 3-fold axis.; GO: 0005529 sugar binding; PDB: 3M7H_A 3M7J_B 3MEZ_D 1DLP_A 1BWU_D 1KJ1_A 1B2P_A 1XD6_A 2DPF_C 2D04_B ....
Probab=37.34 E-value=55 Score=22.11 Aligned_cols=29 Identities=28% Similarity=0.172 Sum_probs=22.9
Q ss_pred EEEEEeccCceEEEEcCCCcEEEeecccc
Q psy336 34 HIIVELYDRGNIVLTDKDYIILNVLRPHS 62 (121)
Q Consensus 34 ~L~~El~g~~Niil~d~~~~Il~~lr~~~ 62 (121)
.-++.|-..||++|.|.++.+++.....+
T Consensus 54 ~~~~~L~~~GNlvl~d~~~~~lW~Sf~~p 82 (114)
T PF01453_consen 54 GCYLVLQDDGNLVLYDSSGNVLWQSFDYP 82 (114)
T ss_dssp SEEEEEETTSEEEEEETTSEEEEESTTSS
T ss_pred CeEEEEeCCCCEEEEeecceEEEeecCCC
Confidence 35667777799999999999999984443
No 10
>PF02743 Cache_1: Cache domain; InterPro: IPR004010 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins, including the animal dihydropyridine-sensitive voltage-gated Ca2+ channel; alpha-2delta subunit, and various bacterial chemotaxis receptors. The name Cache comes from CAlcium channels and CHEmotaxis receptors. This domain consists of an N-terminal part with three predicted strands and an alpha-helix, and a C-terminal part with a strand dyad followed by a relatively unstructured region. The N-terminal portion of the (unpermuted) Cache domain contains three predicted strands that could form a sheet analogous to that present in the core of the PAS domain structure. Cache domains are particularly widespread in bacteria, with Vibrio cholerae. The animal calcium channel alpha-2delta subunits might have acquired a part of their extracellular domains from a bacterial source []. The Cache domain appears to have arisen from the GAF-PAS fold despite their divergent functions [].; GO: 0016020 membrane; PDB: 3C8C_A 3LIB_D 3LIA_A 3LI8_A 3LI9_A.
Probab=32.77 E-value=37 Score=20.87 Aligned_cols=17 Identities=24% Similarity=0.487 Sum_probs=14.3
Q ss_pred ccC-ceEEEEcCCCcEEE
Q psy336 40 YDR-GNIVLTDKDYIILN 56 (121)
Q Consensus 40 ~g~-~Niil~d~~~~Il~ 56 (121)
+|. |.++++|++|.|+.
T Consensus 50 ~~~~g~~~ivd~~G~ii~ 67 (81)
T PF02743_consen 50 FGNNGYAFIVDKNGTIIA 67 (81)
T ss_dssp BTTTBEEEEEETTSBBCE
T ss_pred ECCCEEEEEEECCCCEEE
Confidence 466 89999999999874
No 11
>PF13629 T2SS-T3SS_pil_N: Pilus formation protein N terminal region
Probab=30.82 E-value=1.3e+02 Score=18.47 Aligned_cols=41 Identities=20% Similarity=0.189 Sum_probs=27.6
Q ss_pred cCCCeEEEEEEccCCceEEEEEEeccCceEEEEcCCCcEEEe
Q psy336 16 LGLDRIIDLQFGTGEAEYHIIVELYDRGNIVLTDKDYIILNV 57 (121)
Q Consensus 16 ~~~DRIv~~~f~~~~~~~~L~~El~g~~Niil~d~~~~Il~~ 57 (121)
++...|.....-+.. +..++-.=.|..|++++|++++.+..
T Consensus 26 v~dp~Iadv~~~~~~-~v~i~gk~~G~T~l~vw~~~~~~~~~ 66 (72)
T PF13629_consen 26 VGDPEIADVTVLSPN-EVYITGKKPGTTTLIVWDKDGRVIQT 66 (72)
T ss_pred ECCCCEEEEEEeCCC-EEEEEEeCceeEEEEEECCCCCEEEE
Confidence 567777777775432 34455555555799999999986544
No 12
>PF05651 Diacid_rec: Putative sugar diacid recognition; InterPro: IPR008599 This region is found in several proteins characterised as carbohydrate diacid regulators (e.g. P36047 from SWISSPROT). An HTH DNA-binding motif is found at the C terminus of these proteins suggesting that this region includes the sugar recognition region.
Probab=27.31 E-value=48 Score=23.50 Aligned_cols=18 Identities=33% Similarity=0.434 Sum_probs=15.2
Q ss_pred ceEEEEcCCCcEEEeecc
Q psy336 43 GNIVLTDKDYIILNVLRP 60 (121)
Q Consensus 43 ~Niil~d~~~~Il~~lr~ 60 (121)
.|+.++|++|.||.+--.
T Consensus 19 ~~inimd~~G~IIAStd~ 36 (135)
T PF05651_consen 19 YNINIMDENGIIIASTDP 36 (135)
T ss_pred CCEEEECCCcEEEecCCh
Confidence 499999999999988643
No 13
>PRK13612 photosystem II reaction center protein Psb28; Provisional
Probab=24.61 E-value=1.6e+02 Score=20.64 Aligned_cols=38 Identities=16% Similarity=0.159 Sum_probs=29.0
Q ss_pred cCCCeEEEEEEccCCceEEEEEEeccC-ceEEEEcCCCcEEE
Q psy336 16 LGLDRIIDLQFGTGEAEYHIIVELYDR-GNIVLTDKDYIILN 56 (121)
Q Consensus 16 ~~~DRIv~~~f~~~~~~~~L~~El~g~-~Niil~d~~~~Il~ 56 (121)
-|.-+.+.|.|..... |--+..|. ..+.|.|++|.|..
T Consensus 27 dg~~g~a~f~F~~p~a---l~~~~~~~itgm~LiDeEGei~t 65 (113)
T PRK13612 27 DGRTGQATFYFEQPQA---LAPETTGEITGMYMIDEEGEIVT 65 (113)
T ss_pred CCCeeEEEEEECCccc---cCccccCceeeEEEEccCccEEE
Confidence 5778889999988742 22256788 78999999999864
No 14
>cd00028 B_lectin Bulb-type mannose-specific lectin. The domain contains a three-fold internal repeat (beta-prism architecture). The consensus sequence motif QXDXNXVXY is involved in alpha-D-mannose recognition. Lectins are carbohydrate-binding proteins which specifically recognize diverse carbohydrates and mediate a wide variety of biological processes, such as cell-cell and host-pathogen interactions, serum glycoprotein turnover, and innate immune responses.
Probab=24.60 E-value=1.2e+02 Score=20.12 Aligned_cols=21 Identities=24% Similarity=0.343 Sum_probs=12.8
Q ss_pred EEeccCceEEEEcCCCcEEEe
Q psy336 37 VELYDRGNIVLTDKDYIILNV 57 (121)
Q Consensus 37 ~El~g~~Niil~d~~~~Il~~ 57 (121)
+.|-..||++|.|.++.+++.
T Consensus 59 l~l~~dGnLvl~~~~g~~vW~ 79 (116)
T cd00028 59 LTLQSDGNLVIYDGSGTVVWS 79 (116)
T ss_pred EEEecCCCeEEEcCCCcEEEE
Confidence 334344777777766666654
No 15
>PF09695 YtfJ_HI0045: Bacterial protein of unknown function (YtfJ_HI0045); InterPro: IPR006513 These are sequences from gammaproteobacteria that are related to the Escherichia coli protein, YtfJ.
Probab=24.55 E-value=69 Score=23.73 Aligned_cols=16 Identities=25% Similarity=0.212 Sum_probs=13.4
Q ss_pred ceEEEEcCCCcEEEee
Q psy336 43 GNIVLTDKDYIILNVL 58 (121)
Q Consensus 43 ~Niil~d~~~~Il~~l 58 (121)
|.||++|++|+|..+-
T Consensus 126 SaiiVlDK~G~V~F~k 141 (160)
T PF09695_consen 126 SAIIVLDKQGKVQFVK 141 (160)
T ss_pred ceEEEEcCCccEEEEE
Confidence 7899999999997653
No 16
>PF05860 Haemagg_act: haemagglutination activity domain; InterPro: IPR008638 This entry represents a conserved domain found near the N terminus of a number of large, repetitive bacterial proteins, including many proteins of over 2500 amino acids. A number of the members of this family have been designated adhesins, filamentous haemagglutinins, haem/haemopexin-binding protein, etc. Members generally have a signal sequence, then an intervening region, then the region described in this entry. Following this region, proteins typically have regions rich in repeats but may show no homology between the repeats of one member and the repeats of another. This domain is suggested to be a carbohydrate-dependent haemagglutination activity site []. In Bordetella pertussis, the infectious agent in childhood whooping cough, filamentous haemagglutinin (FHA) is a surface-exposed and secreted protein that acts as a major virulence attachment factor, functioning as both a primary adhesin and an immunomodulator to bind the bacterial to cells of the respiratory epithelium []. The FHA molecule has a globular head that consists of two domains: a shaft and a flexible tail. Its sequence contains two regions of tandem 19-residue repeats, where the repeat motif consists of short beta-helical strands separated by beta-turns [].; GO: 0005488 binding; PDB: 2ODL_A 3FY3_A 1RWR_A.
Probab=24.53 E-value=76 Score=21.92 Aligned_cols=49 Identities=18% Similarity=0.167 Sum_probs=29.4
Q ss_pred ecCCCeEEEEEEccCCceEEE--EEEeccC-ceEEEEcCCCcEEEeeccccCC
Q psy336 15 LLGLDRIIDLQFGTGEAEYHI--IVELYDR-GNIVLTDKDYIILNVLRPHSDG 64 (121)
Q Consensus 15 Q~~~DRIv~~~f~~~~~~~~L--~~El~g~-~Niil~d~~~~Il~~lr~~~~~ 64 (121)
|.+-.+++.-++...+. ..| .+|..|. ++++|.+++|.+......+.-.
T Consensus 56 ~~~~a~~iln~V~g~~~-S~I~G~l~v~g~~~~v~l~NpnGI~~~~~~~in~~ 107 (121)
T PF05860_consen 56 QPGAASNILNRVTGGNP-SQINGTLEVAGANANVFLANPNGIVFGGCAFINVG 107 (121)
T ss_dssp SSSTTSEEEEEE-SS---EEEESEEEEEESSEEEEEE-TT-EEECCEEEESEE
T ss_pred cCChheeeeeecCCCCc-cEEEeeeeEcccceeEEEECCCeEEEcCCeEEecC
Confidence 44555555555543322 223 5777777 9999999999998877666633
No 17
>smart00108 B_lectin Bulb-type mannose-specific lectin.
Probab=24.46 E-value=1.1e+02 Score=20.32 Aligned_cols=20 Identities=40% Similarity=0.444 Sum_probs=10.9
Q ss_pred EeccCceEEEEcCCCcEEEe
Q psy336 38 ELYDRGNIVLTDKDYIILNV 57 (121)
Q Consensus 38 El~g~~Niil~d~~~~Il~~ 57 (121)
.|-..||++|.|.++.+++.
T Consensus 91 ~L~ddGnlvl~~~~~~~~W~ 110 (114)
T smart00108 91 VLLDDGNLVIYDSDGNFLWQ 110 (114)
T ss_pred EEeCCCCEEEECCCCCEEeC
Confidence 34334666666655555554
No 18
>PF13426 PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_B 3P7N_B 1LL8_A 3MJQ_A 3BWL_A 4EET_B 4EEP_A ....
Probab=22.87 E-value=85 Score=18.84 Aligned_cols=18 Identities=33% Similarity=0.270 Sum_probs=13.8
Q ss_pred EEEEcCCCcEEEeecccc
Q psy336 45 IVLTDKDYIILNVLRPHS 62 (121)
Q Consensus 45 iil~d~~~~Il~~lr~~~ 62 (121)
++++|.+|+|+++.....
T Consensus 4 i~i~d~~g~i~~~N~~~~ 21 (104)
T PF13426_consen 4 IFILDPDGRILYVNPAFE 21 (104)
T ss_dssp EEEEETTSBEEEE-HHHH
T ss_pred EEEECCcCcEEehhHHHH
Confidence 678999999999975544
No 19
>COG0203 RplQ Ribosomal protein L17 [Translation, ribosomal structure and biogenesis]
Probab=21.99 E-value=73 Score=22.39 Aligned_cols=25 Identities=36% Similarity=0.514 Sum_probs=20.9
Q ss_pred ecCCCeEEEEEEccCCceEEEEEEe
Q psy336 15 LLGLDRIIDLQFGTGEAEYHIIVEL 39 (121)
Q Consensus 15 Q~~~DRIv~~~f~~~~~~~~L~~El 39 (121)
+=|+-||+.+.|..+|..---++||
T Consensus 91 ~GGYtRIlK~g~R~GD~A~maiiEl 115 (116)
T COG0203 91 NGGYTRILKLGFRRGDNAPMAIIEL 115 (116)
T ss_pred CCCeeEEEecCCCCCCCCceEEEEe
Confidence 3488999999999998777778887
No 20
>PRK13610 photosystem II reaction center protein Psb28; Provisional
Probab=21.39 E-value=1.6e+02 Score=20.60 Aligned_cols=38 Identities=16% Similarity=0.197 Sum_probs=28.3
Q ss_pred cCCCeEEEEEEccCCceEEEEEEeccC-ceEEEEcCCCcEEE
Q psy336 16 LGLDRIIDLQFGTGEAEYHIIVELYDR-GNIVLTDKDYIILN 56 (121)
Q Consensus 16 ~~~DRIv~~~f~~~~~~~~L~~El~g~-~Niil~d~~~~Il~ 56 (121)
-|.-+...|.|..... |--+..|. .++.|+|++|.|..
T Consensus 31 dG~tG~A~f~F~~p~~---l~~~~~~~ItGM~LiDeEGei~t 69 (113)
T PRK13610 31 DGKKGKAVYKFYKPKT---ITLTNYKSVQRMFLIDSEGVLST 69 (113)
T ss_pred CCCccEEEEEECCchh---cccccccceeeeEEEccCceEEE
Confidence 3677888888887632 22366788 78999999999864
No 21
>PRK10234 DNA-binding transcriptional activator GutM; Provisional
Probab=20.57 E-value=94 Score=21.76 Aligned_cols=18 Identities=11% Similarity=0.145 Sum_probs=14.2
Q ss_pred EEEEcCCCcEEEeecccc
Q psy336 45 IVLTDKDYIILNVLRPHS 62 (121)
Q Consensus 45 iil~d~~~~Il~~lr~~~ 62 (121)
++.+|++++|+++.....
T Consensus 56 llaiD~~~~I~d~~~M~G 73 (118)
T PRK10234 56 ALALDEQQRVVDTLFMKG 73 (118)
T ss_pred EEEECCCCcEEeeEEEcc
Confidence 467899999999986544
Done!