Query psy5895
Match_columns 152
No_of_seqs 94 out of 96
Neff 5.0
Searched_HMMs 46136
Date Fri Aug 16 21:01:17 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5895.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5895hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0112|consensus 99.9 5.4E-25 1.2E-29 206.6 3.5 143 1-148 820-974 (975)
2 PF07744 SPOC: SPOC domain; I 99.7 2.3E-16 5.1E-21 115.0 6.7 102 1-113 17-119 (119)
3 PF03808 Glyco_tran_WecB: Glyc 57.9 9.7 0.00021 29.7 2.6 83 2-102 52-136 (172)
4 PHA01745 hypothetical protein 49.7 19 0.00041 31.5 3.2 70 36-124 51-124 (306)
5 PF09358 UBA_e1_C: Ubiquitin-a 45.2 53 0.0011 24.7 4.8 63 78-145 44-112 (125)
6 COG1931 Uncharacterized protei 34.6 14 0.0003 29.1 0.1 49 81-131 78-129 (140)
7 PTZ00198 60S ribosomal protein 33.2 2.2E+02 0.0048 21.9 6.5 64 79-148 36-107 (122)
8 PF00578 AhpC-TSA: AhpC/TSA fa 32.5 1.7E+02 0.0036 20.1 5.8 49 94-145 17-67 (124)
9 PF00770 Peptidase_C5: Adenovi 32.5 71 0.0015 26.2 3.9 44 81-126 12-65 (183)
10 PF14950 DUF4502: Domain of un 30.1 27 0.00058 31.3 1.2 12 105-116 345-356 (358)
11 KOG0112|consensus 30.1 14 0.0003 36.9 -0.6 53 81-140 660-712 (975)
12 cd06533 Glyco_transf_WecG_TagA 29.9 51 0.0011 25.6 2.7 77 2-95 50-128 (171)
13 PF14542 Acetyltransf_CG: GCN5 29.3 41 0.00089 23.0 1.8 34 76-128 41-74 (78)
14 smart00796 AHS1 Allophanate hy 29.2 3.1E+02 0.0067 22.1 7.5 66 50-124 3-68 (201)
15 PRK10424 ilvG operon leader pe 28.4 40 0.00086 20.0 1.3 13 106-118 14-26 (32)
16 PF07905 PucR: Purine cataboli 27.7 48 0.001 24.3 2.0 19 78-96 60-78 (123)
17 PF08643 DUF1776: Fungal famil 26.6 44 0.00094 29.1 1.9 47 54-100 27-102 (299)
18 PF05122 SpdB: Mobile element 25.7 34 0.00074 22.6 0.8 25 110-134 24-48 (53)
19 PF01776 Ribosomal_L22e: Ribos 23.3 1.6E+02 0.0035 22.2 4.2 58 80-142 24-89 (112)
20 PRK11538 ribosome-associated p 22.9 1.3E+02 0.0027 22.1 3.5 39 73-114 46-92 (105)
21 KOG3054|consensus 22.7 61 0.0013 28.2 2.0 26 64-90 188-213 (299)
22 TIGR02625 YiiL_rotase L-rhamno 22.3 28 0.00061 25.5 -0.1 19 31-49 1-19 (102)
23 PF12780 AAA_8: P-loop contain 21.9 76 0.0016 26.8 2.4 22 45-66 22-43 (268)
24 PF05827 ATP-synt_S1: Vacuolar 21.7 3.3E+02 0.0071 22.6 6.2 65 80-144 96-175 (282)
25 PF00532 Peripla_BP_1: Peripla 21.6 1.5E+02 0.0034 24.3 4.2 50 43-102 16-68 (279)
26 cd01422 MGS Methylglyoxal synt 21.1 95 0.0021 22.7 2.6 21 80-100 60-80 (115)
27 PF09756 DDRGK: DDRGK domain; 20.6 62 0.0013 26.4 1.6 14 78-91 100-113 (188)
28 TIGR00090 iojap_ybeB iojap-lik 20.4 1.8E+02 0.0039 20.8 3.8 39 73-114 41-87 (99)
29 COG1609 PurR Transcriptional r 20.3 1.3E+02 0.0028 25.6 3.5 53 37-98 67-122 (333)
No 1
>KOG0112|consensus
Probab=99.90 E-value=5.4e-25 Score=206.57 Aligned_cols=143 Identities=21% Similarity=0.310 Sum_probs=122.3
Q ss_pred CceeeCCHHHHHhhcCCCcCCCCCCCCCceeeeeecCCCCCcchhhhhhcc--cCCCeEEEEEeccCCCcc--------h
Q psy5895 1 MHYVFGNHLLARDALPLAAEGGLTPPTPTLRIAQRMRLEQTQIDGVVRKMQ--TDGEHCMLLALPCGRTEV--------D 70 (152)
Q Consensus 1 mH~l~Gn~~v~~~~L~~~~~g~~~~~~~~LrItQRlRLd~~~Ld~V~rri~--~~~~~cilLAlp~~~~~~--------d 70 (152)
||++.||.+++..+|....++ .+..+|+|+||+||||+++++|.+|+. ..+++++++++++..+.. |
T Consensus 820 ~~~~~gdk~v~~~ll~e~~t~---~k~a~~~ieq~~q~d~pk~~dv~k~~~~~~~~~~~g~s~~~~~s~s~k~~~pp~pd 896 (975)
T KOG0112|consen 820 QHLLLGDKGVIISLLKEERTS---DKRAHLSIEQRLQLDQPKLDDVEKRDDEAGKDGDAGNSGNGGSSDSEKADLPPPPD 896 (975)
T ss_pred hhhhccccchhhhhhhccccc---CcccCccHHHHhhccCCcccchhhhhhhcCCcccccccCCCCcccccCCCCCCCCC
Confidence 799999999998888754332 357999999999999999999999954 579999999999876532 3
Q ss_pred hhhhHHHHHHHHHHHhhhcccceEEecCCCCCCC--CceEEEEeCCChhHHHHHHHHhHHHHhhccCCCcEEEEEEeccC
Q psy5895 71 VVQQSAYLQSGFITYLQQKQAAGIVNIAAPGTQQ--AAYIVHVFPSCEFANNSLAQIDAQLLKKVSELTYLVIIIATTAN 148 (152)
Q Consensus 71 ~~~q~~~l~~~lV~YLkqKqAAGIisl~~~~~~~--~~~vlhiFPPCeFs~~~L~~~Ap~L~~~~~~~~hLviVi~~~~~ 148 (152)
..+-+++..+|||+||+||+|||+|++.+++.++ ..+|+|+||||||++++|...|..+-+. .++|+|+|+|++.+
T Consensus 897 ~~s~~~rp~q~l~~~~e~k~~~~~~s~d~e~~~d~~a~~~~~a~pp~e~~~e~~~~~a~s~~e~--~er~~vpv~~r~~s 974 (975)
T KOG0112|consen 897 PASLSERPLQNLVSYLEQKKAAGVISLDDEDHKDAEATGVLRAFPPCEFSKEQLSLTAYSLDEQ--GERKLVPVRVRGDS 974 (975)
T ss_pred CcccccchhHHHHHhhhhhhccCccccccccccchhcccccccCCCchhhhhcccchhhhcccc--cccccceEEeeccC
Confidence 3344556778999999999999999999988765 5799999999999999999999988885 57999999998765
No 2
>PF07744 SPOC: SPOC domain; InterPro: IPR012921 Spen (split end) proteins regulate the expression of key transcriptional effectors in diverse signalling pathways. They are large proteins characterised by N-terminal RNA-binding motifs and a highly conserved C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. The function of the SPOC domain is unknown, but the SPOC domain of the SHARP Spen protein has been implicated in the interaction of SHARP with the SMRT/NcoR corepressor, where SHARP plays an essential role in the repressor complex []. The SPOC domain is folded into a single compact domain consisting of a beta-barrel with seven strands framed by six alpha helices. A number of deep grooves and clefts in the surface, plus two nonpolar loops, render the SPOC domain well suited to protein-protein interactions; most of the conserved residues occur on the protein surface rather than in the core. Other proteins containing a SPOC domain include drosophila Split ends, which promotes sclerite development in the head and restricts it in the thorax, and mouse MINT (homologue of SHARP), which is involved in skeletal and neuronal development via its repression of Msx2.; PDB: 1OW1_A.
Probab=99.65 E-value=2.3e-16 Score=115.03 Aligned_cols=102 Identities=26% Similarity=0.430 Sum_probs=68.5
Q ss_pred CceeeCCHHHHHhhcCCCcCCCCCCCCCceeeeeecCCCCCcchhhhhhcccCC-CeEEEEEeccCCCcchhhhhHHHHH
Q psy5895 1 MHYVFGNHLLARDALPLAAEGGLTPPTPTLRIAQRMRLEQTQIDGVVRKMQTDG-EHCMLLALPCGRTEVDVVQQSAYLQ 79 (152)
Q Consensus 1 mH~l~Gn~~v~~~~L~~~~~g~~~~~~~~LrItQRlRLd~~~Ld~V~rri~~~~-~~cilLAlp~~~~~~d~~~q~~~l~ 79 (152)
+|+++|+.++.+..|... ..++.+|.+|+|||..++++..++|+..+ .+|+++++ ..++.+...+.+.++
T Consensus 17 a~~v~G~~~~~~~~l~~~-------~~~p~~i~i~gRl~~~~~~~yl~~i~~s~~~~v~v~~~--~~~~~~~~~~~~~~~ 87 (119)
T PF07744_consen 17 AHFVSGNCDLLDNVLPWQ-------QLPPKKIDIRGRLDPEKVWDYLRQIRKSRSKDVCVVAL--SSPESDSNSDRRPFQ 87 (119)
T ss_dssp EEEEEE-HHHHHHHS--------------EEE-EEEE-SHHHHHHHHHHTSSTTT-EEEEEEE---SSHHHHHHHHHHHH
T ss_pred EEEEEcchhHhhhhcccc-------cCCCcEEEEEeecCHHHHHHHHHhcccCCCceEEEEEE--cCCcccCHHHHHHHH
Confidence 589999988997888643 25889999999999999999999998765 48888888 111223334444454
Q ss_pred HHHHHHhhhcccceEEecCCCCCCCCceEEEEeC
Q psy5895 80 SGFITYLQQKQAAGIVNIAAPGTQQAAYIVHVFP 113 (152)
Q Consensus 80 ~~lV~YLkqKqAAGIisl~~~~~~~~~~vlhiFP 113 (152)
+|++||++|+.||||++++.+.+ ....+|+||
T Consensus 88 -~l~~Yl~~k~r~GVv~~~~~~~~-~~~dlYl~P 119 (119)
T PF07744_consen 88 -KLVDYLKSKQRAGVVSVGNSPSG-QVKDLYLFP 119 (119)
T ss_dssp -HTHHHHHHHTEEEEEEE--TT---S-EEEEEE-
T ss_pred -HHHHHHhhCCEEEEEecCCCCCC-ceeEEEEcC
Confidence 69999999999999999975543 379999999
No 3
>PF03808 Glyco_tran_WecB: Glycosyl transferase WecB/TagA/CpsF family; InterPro: IPR004629 The WecG member of this superfamily, believed to be UDP-N-acetyl-D-mannosaminuronic acid transferase, plays a role in Enterobacterial common antigen (eca) synthesis in Escherichia coli. Another family member, the Bacillus subtilis TagA protein, is involved in the biosynthesis of the cell wall polymer poly(glycerol phosphate). The third family member, CpsF, CMP-N-acetylneuraminic acid synthetase has a role in the capsular polysaccharide biosynthesis pathway.; GO: 0009058 biosynthetic process
Probab=57.89 E-value=9.7 Score=29.67 Aligned_cols=83 Identities=19% Similarity=0.332 Sum_probs=58.1
Q ss_pred ceeeCCHHHHHhhcCCCcCCCCCCCCCceeeeeecC--CCCCcchhhhhhcccCCCeEEEEEeccCCCcchhhhhHHHHH
Q psy5895 2 HYVFGNHLLARDALPLAAEGGLTPPTPTLRIAQRMR--LEQTQIDGVVRKMQTDGEHCMLLALPCGRTEVDVVQQSAYLQ 79 (152)
Q Consensus 2 H~l~Gn~~v~~~~L~~~~~g~~~~~~~~LrItQRlR--Ld~~~Ld~V~rri~~~~~~cilLAlp~~~~~~d~~~q~~~l~ 79 (152)
.++.|+++++......-.. +-|-++|+-+-- .|....+++..+|+..+--++++++.+.+ |
T Consensus 52 fllG~~~~~~~~~~~~l~~-----~yP~l~ivg~~~g~f~~~~~~~i~~~I~~~~pdiv~vglG~Pk------------Q 114 (172)
T PF03808_consen 52 FLLGGSEEVLEKAAANLRR-----RYPGLRIVGYHHGYFDEEEEEAIINRINASGPDIVFVGLGAPK------------Q 114 (172)
T ss_pred EEEeCCHHHHHHHHHHHHH-----HCCCeEEEEecCCCCChhhHHHHHHHHHHcCCCEEEEECCCCH------------H
Confidence 4677777777644322111 146789986654 47889999999999888889999998653 3
Q ss_pred HHHHHHhhhcccceEEecCCCCC
Q psy5895 80 SGFITYLQQKQAAGIVNIAAPGT 102 (152)
Q Consensus 80 ~~lV~YLkqKqAAGIisl~~~~~ 102 (152)
.-|+...+++--++ |.++.+++
T Consensus 115 E~~~~~~~~~l~~~-v~i~vG~~ 136 (172)
T PF03808_consen 115 ERWIARHRQRLPAG-VIIGVGGA 136 (172)
T ss_pred HHHHHHHHHHCCCC-EEEEECch
Confidence 56888888888888 44554443
No 4
>PHA01745 hypothetical protein
Probab=49.65 E-value=19 Score=31.54 Aligned_cols=70 Identities=14% Similarity=0.233 Sum_probs=47.5
Q ss_pred cCCCCCcchhhhhhcccCCCeEEEEEeccCCCcchhhhhHHHHHHHHHHHhhhcccce-EEe-cCCCCCCCCceEEEEeC
Q psy5895 36 MRLEQTQIDGVVRKMQTDGEHCMLLALPCGRTEVDVVQQSAYLQSGFITYLQQKQAAG-IVN-IAAPGTQQAAYIVHVFP 113 (152)
Q Consensus 36 lRLd~~~Ld~V~rri~~~~~~cilLAlp~~~~~~d~~~q~~~l~~~lV~YLkqKqAAG-Iis-l~~~~~~~~~~vlhiFP 113 (152)
+.+|..++.++.|++ ..++|+-|=.|...++.| .+||=.|.+-..+-+ |.+ +| |+|++|
T Consensus 51 i~i~vd~V~ekYk~i--dA~~y~SLDiP~~~dp~d--------~kNf~~feyLy~~ve~~~~vIP---------ViH~Y~ 111 (306)
T PHA01745 51 LKISVDDVLDKYKTY--NAYAFFSLDIPSIFEPLS--------RKNFEYFEYLYTKLEYIERIIP---------VIHLYP 111 (306)
T ss_pred CCCCHHHHHHHHHhc--chhheeecCCCCcCCChh--------hhhHHHHHHHHHHhhcccceee---------EEeecC
Confidence 678888888888888 445899999998766555 255655555555444 112 34 999998
Q ss_pred CChh--HHHHHHH
Q psy5895 114 SCEF--ANNSLAQ 124 (152)
Q Consensus 114 PCeF--s~~~L~~ 124 (152)
+=+. +-+|+++
T Consensus 112 ~e~l~~~ldfysq 124 (306)
T PHA01745 112 VREVDEAIDFYSQ 124 (306)
T ss_pred HHHHHHHHHHHHh
Confidence 8776 5566665
No 5
>PF09358 UBA_e1_C: Ubiquitin-activating enzyme e1 C-terminal domain; InterPro: IPR018965 This presumed domain found at the C terminus of Ubiquitin-activating enzyme e1 proteins is functionally uncharacterised. ; PDB: 3CMM_A.
Probab=45.17 E-value=53 Score=24.74 Aligned_cols=63 Identities=14% Similarity=0.195 Sum_probs=41.4
Q ss_pred HHHHHHHHhhhcccceEEecCCCCCCCCceEEEEeCCChhHHHHHHHHhHHHHhhccC------CCcEEEEEEe
Q psy5895 78 LQSGFITYLQQKQAAGIVNIAAPGTQQAAYIVHVFPSCEFANNSLAQIDAQLLKKVSE------LTYLVIIIAT 145 (152)
Q Consensus 78 l~~~lV~YLkqKqAAGIisl~~~~~~~~~~vlhiFPPCeFs~~~L~~~Ap~L~~~~~~------~~hLviVi~~ 145 (152)
-++.||+||++|-=.=|.+|..+ ..+||.+=|.+=.++.|+..-..|..++.+ ..||.+.|.-
T Consensus 44 Tl~~li~~~~~~~~lev~ml~~g-----~~~LY~~f~~~~~~~rl~~~i~elv~~v~k~~~~~~~~~l~l~v~~ 112 (125)
T PF09358_consen 44 TLQELIDYFKEKYGLEVTMLSQG-----VSLLYSSFPPPKHKERLKMPISELVEEVTKKPIPPGQKYLVLEVSC 112 (125)
T ss_dssp BHHHHHHHHHHTTS-EEEEEEET-----TEEEEETT-HHHHHHHTTSBHHHHHHHHTSS---TT--EEEEEEEE
T ss_pred CHHHHHHHHHHHhCceEEEEEeC-----CEEEEecCChhhhHHHhCCcHHHHHHHhcCCCCCCCceEEEEEEEE
Confidence 34589999999976666666643 569998327777777888877788886632 4566665543
No 6
>COG1931 Uncharacterized protein conserved in archaea [Function unknown]
Probab=34.64 E-value=14 Score=29.09 Aligned_cols=49 Identities=18% Similarity=0.168 Sum_probs=35.0
Q ss_pred HHHHHhhhcccc--eEEecCCCC-CCCCceEEEEeCCChhHHHHHHHHhHHHHh
Q psy5895 81 GFITYLQQKQAA--GIVNIAAPG-TQQAAYIVHVFPSCEFANNSLAQIDAQLLK 131 (152)
Q Consensus 81 ~lV~YLkqKqAA--GIisl~~~~-~~~~~~vlhiFPPCeFs~~~L~~~Ap~L~~ 131 (152)
+-|.+.-+|||| |+||+..++ +.=....+.|++.-.= ++++=+||....
T Consensus 78 ~~v~f~lnKQAA~vG~vnF~~e~espLG~I~v~I~~~~p~--k~idwLAP~T~~ 129 (140)
T COG1931 78 NEVTFYLNKQAAYVGRVNFVEEDESPLGPITVTIRTDEPE--KLIDWLAPRTKD 129 (140)
T ss_pred CeEEEEEehhhhhcCccccccCCCCCCCCEEEEEEcCCHH--HHHHhhCCCCcC
Confidence 567777889997 999998763 2224567778876654 888888887544
No 7
>PTZ00198 60S ribosomal protein L22; Provisional
Probab=33.21 E-value=2.2e+02 Score=21.90 Aligned_cols=64 Identities=23% Similarity=0.342 Sum_probs=41.4
Q ss_pred HHHHHHHhhhc--------ccceEEecCCCCCCCCceEEEEeCCChhHHHHHHHHhHHHHhhccCCCcEEEEEEeccC
Q psy5895 79 QSGFITYLQQK--------QAAGIVNIAAPGTQQAAYIVHVFPSCEFANNSLAQIDAQLLKKVSELTYLVIIIATTAN 148 (152)
Q Consensus 79 ~~~lV~YLkqK--------qAAGIisl~~~~~~~~~~vlhiFPPCeFs~~~L~~~Ap~L~~~~~~~~hLviVi~~~~~ 148 (152)
..+|-.||+++ +.++.|.+...+ .-|++-.--+||-+||+=+....+..-.=-|.|= |+++.++
T Consensus 36 ~a~fekfL~erIKV~GK~gnLg~~V~v~~~k-----~ki~V~s~~~FSKRYLKYLTKKyLKK~~LRDwlR-VVA~~K~ 107 (122)
T PTZ00198 36 LSGFEQFLQDRIKVDGKTGNLGNKVRVSREK-----NKITVTTTIPFSKRYLKYLTKKYLKKKQLRDFLR-VVATGKG 107 (122)
T ss_pred HHHHHHHHHHhEEECCCcCccCCcEEEEEEC-----CEEEEEecccccHHHHHHHHHHHHhhhhhhheEE-EEecCCC
Confidence 35899999986 333444444332 3577777778999999998888887554224444 4454443
No 8
>PF00578 AhpC-TSA: AhpC/TSA family; InterPro: IPR000866 Peroxiredoxins (Prxs) are a ubiquitous family of antioxidant enzymes that also control cytokine-induced peroxide levels which mediate signal transduction in mammalian cells. Prxs can be regulated by changes to phosphorylation, redox and possibly oligomerisation states. Prxs are divided into three classes: typical 2-Cys Prxs; atypical 2-Cys Prxs; and 1-Cys Prxs. All Prxs share the same basic catalytic mechanism, in which an active-site cysteine (the peroxidatic cysteine) is oxidised to a sulphenic acid by the peroxide substrate. The recycling of the sulphenic acid back to a thiol is what distinguishes the three enzyme classes. Using crystal structures, a detailed catalytic cycle has been derived for typical 2-Cys Prxs, including a model for the redox-regulated oligomeric state proposed to control enzyme activity []. Alkyl hydroperoxide reductase (AhpC) is responsible for directly reducing organic hyperoxides in its reduced dithiol form. Thiol specific antioxidant (TSA) is a physiologically important antioxidant which constitutes an enzymatic defence against sulphur-containing radicals. This family contains AhpC and TSA, as well as related proteins.; GO: 0016209 antioxidant activity, 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 1QMV_A 1PRX_B 3HJP_C 3HA9_A 2V41_G 2V32_C 2V2G_C 3LWA_A 3IA1_B 1ZYE_G ....
Probab=32.51 E-value=1.7e+02 Score=20.11 Aligned_cols=49 Identities=24% Similarity=0.480 Sum_probs=31.4
Q ss_pred EEecCCCCCCCCceEEEEeCC--ChhHHHHHHHHhHHHHhhccCCCcEEEEEEe
Q psy5895 94 IVNIAAPGTQQAAYIVHVFPS--CEFANNSLAQIDAQLLKKVSELTYLVIIIAT 145 (152)
Q Consensus 94 Iisl~~~~~~~~~~vlhiFPP--CeFs~~~L~~~Ap~L~~~~~~~~hLviVi~~ 145 (152)
-+++..- ++...||+.|+. |++....+.++. .+..++.+...=+|.|.+
T Consensus 17 ~~~l~~l--~gk~~vl~f~~~~~c~~c~~~l~~l~-~~~~~~~~~~~~vi~is~ 67 (124)
T PF00578_consen 17 TVSLSDL--KGKPVVLFFWPTAWCPFCQAELPELN-ELYKKYKDKGVQVIGIST 67 (124)
T ss_dssp EEEGGGG--TTSEEEEEEESTTTSHHHHHHHHHHH-HHHHHHHTTTEEEEEEES
T ss_pred EEEHHHH--CCCcEEEEEeCccCccccccchhHHH-HHhhhhccceEEeeeccc
Confidence 4455432 345789999999 999999998754 555666543344444444
No 9
>PF00770 Peptidase_C5: Adenovirus endoprotease; InterPro: IPR000855 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 aminopeptidases belong to the peptidase family C5 (adenain family, clan CE). Several adenovirus proteins are synthesised as precursors, requiring processing by a protease before the virion is assembled [, ]. Until recently, the adenovirus endopeptidase was classified as a serine protease, having been reported to be inhibited by serine protease inhibitors [, ]. However, it has since been shown to be inhibited by cysteine protease inhibitors, and the catalytic residues are believed to be His-54 and Cys-104 [, ].; GO: 0004197 cysteine-type endopeptidase activity, 0006508 proteolysis; PDB: 1NLN_A 1AVP_A.
Probab=32.51 E-value=71 Score=26.17 Aligned_cols=44 Identities=30% Similarity=0.446 Sum_probs=27.6
Q ss_pred HHHHHhhhcccceEEecCCCCCCC----------CceEEEEeCCChhHHHHHHHHh
Q psy5895 81 GFITYLQQKQAAGIVNIAAPGTQQ----------AAYIVHVFPSCEFANNSLAQID 126 (152)
Q Consensus 81 ~lV~YLkqKqAAGIisl~~~~~~~----------~~~vlhiFPPCeFs~~~L~~~A 126 (152)
+|++ +.|-|.-|||-...++.+ .+.-.|+|=|=-||.+-|.++.
T Consensus 12 GFl~--~~k~acAIVNT~~retGGvHWlA~Aw~P~s~t~YmFDPfGfsd~~L~qiY 65 (183)
T PF00770_consen 12 GFLS--KHKPACAIVNTGGRETGGVHWLAFAWDPRSRTFYMFDPFGFSDQKLKQIY 65 (183)
T ss_dssp ------TTS-EEEEEESS-TTT--S-EEEEEEETTTTEEEEE-TT---HHHHHHHH
T ss_pred CccC--CCCcceEEEecCCcccCceeEEEEEecCCcceEEEeCCCCCCHHHHHHHH
Confidence 5777 899999999998766654 4678999999999999998875
No 10
>PF14950 DUF4502: Domain of unknown function (DUF4502)
Probab=30.15 E-value=27 Score=31.29 Aligned_cols=12 Identities=25% Similarity=0.777 Sum_probs=9.8
Q ss_pred CceEEEEeCCCh
Q psy5895 105 AAYIVHVFPSCE 116 (152)
Q Consensus 105 ~~~vlhiFPPCe 116 (152)
+.-|||||||+.
T Consensus 345 P~DIIhIyPPWQ 356 (358)
T PF14950_consen 345 PGDIIHIYPPWQ 356 (358)
T ss_pred CCCEEEeCCCcc
Confidence 456999999984
No 11
>KOG0112|consensus
Probab=30.06 E-value=14 Score=36.86 Aligned_cols=53 Identities=11% Similarity=-0.019 Sum_probs=41.3
Q ss_pred HHHHHhhhcccceEEecCCCCCCCCceEEEEeCCChhHHHHHHHHhHHHHhhccCCCcEE
Q psy5895 81 GFITYLQQKQAAGIVNIAAPGTQQAAYIVHVFPSCEFANNSLAQIDAQLLKKVSELTYLV 140 (152)
Q Consensus 81 ~lV~YLkqKqAAGIisl~~~~~~~~~~vlhiFPPCeFs~~~L~~~Ap~L~~~~~~~~hLv 140 (152)
.+..|.+.++++|+++++ ....|.||-|+|+.-.+++.-+.......++..++
T Consensus 660 gl~~~~r~~e~d~~~~~~-------~~~~~sfa~s~~~tP~ts~~~~r~k~~n~~~k~k~ 712 (975)
T KOG0112|consen 660 GLRKLDRIPEKDSQNIQN-------HQKPHSFANSTPRTPSTSTSRARFKSKNKRSKKKL 712 (975)
T ss_pred cccccccccccccccccc-------CCccccccCCCcCCcchhhhhhhhccccccChhhh
Confidence 899999999999976666 45899999999999888887666655544444443
No 12
>cd06533 Glyco_transf_WecG_TagA The glycosyltransferase WecG/TagA superfamily contains Escherichia coli WecG, Bacillus subtilis TagA and related proteins. E. coli WecG is believed to be a UDP-N-acetyl-D-mannosaminuronic acid transferase, and is involved in enterobacterial common antigen (eca) synthesis. B. subtilis TagA plays a key role in the Wall Teichoic Acid (WTA) biosynthetic pathway, catalyzing the transfer of N-acetylmannosamine to the C4 hydroxyl of a membrane-anchored N-acetylglucosaminyl diphospholipid to make ManNAc-beta-(1,4)-GlcNAc-pp-undecaprenyl. This is the first committed step in this pathway. Also included in this group is Xanthomonas campestris pv. campestris GumM, a glycosyltransferase participating in the biosynthesis of the exopolysaccharide xanthan.
Probab=29.92 E-value=51 Score=25.58 Aligned_cols=77 Identities=10% Similarity=0.172 Sum_probs=49.5
Q ss_pred ceeeCCHHHHHhhcCCCcCCCCCCCCCceeeeee--cCCCCCcchhhhhhcccCCCeEEEEEeccCCCcchhhhhHHHHH
Q psy5895 2 HYVFGNHLLARDALPLAAEGGLTPPTPTLRIAQR--MRLEQTQIDGVVRKMQTDGEHCMLLALPCGRTEVDVVQQSAYLQ 79 (152)
Q Consensus 2 H~l~Gn~~v~~~~L~~~~~g~~~~~~~~LrItQR--lRLd~~~Ld~V~rri~~~~~~cilLAlp~~~~~~d~~~q~~~l~ 79 (152)
.++.|.++++...-..-.. .-|-++|+.. .-.+....+++.++|+..+--++++|+...+ |
T Consensus 50 ~llG~~~~~~~~~~~~l~~-----~yp~l~i~g~~~g~~~~~~~~~i~~~I~~~~pdiv~vglG~Pk------------Q 112 (171)
T cd06533 50 FLLGAKPEVLEKAAERLRA-----RYPGLKIVGYHHGYFGPEEEEEIIERINASGADILFVGLGAPK------------Q 112 (171)
T ss_pred EEECCCHHHHHHHHHHHHH-----HCCCcEEEEecCCCCChhhHHHHHHHHHHcCCCEEEEECCCCH------------H
Confidence 4667777777654211111 1466888863 3333445556889998888889999998653 3
Q ss_pred HHHHHHhhhcccceEE
Q psy5895 80 SGFITYLQQKQAAGIV 95 (152)
Q Consensus 80 ~~lV~YLkqKqAAGIi 95 (152)
.-|+...+++--+||+
T Consensus 113 E~~~~~~~~~l~~~v~ 128 (171)
T cd06533 113 ELWIARHKDRLPVPVA 128 (171)
T ss_pred HHHHHHHHHHCCCCEE
Confidence 4577777888766654
No 13
>PF14542 Acetyltransf_CG: GCN5-related N-acetyl-transferase; PDB: 2H5M_A 2Q44_A 1XMT_A 2Q4Y_A 2IL4_A 2EVN_A 1R57_A.
Probab=29.28 E-value=41 Score=22.98 Aligned_cols=34 Identities=15% Similarity=0.458 Sum_probs=24.5
Q ss_pred HHHHHHHHHHhhhcccceEEecCCCCCCCCceEEEEeCCChhHHHHHHHHhHH
Q psy5895 76 AYLQSGFITYLQQKQAAGIVNIAAPGTQQAAYIVHVFPSCEFANNSLAQIDAQ 128 (152)
Q Consensus 76 ~~l~~~lV~YLkqKqAAGIisl~~~~~~~~~~vlhiFPPCeFs~~~L~~~Ap~ 128 (152)
..|-+..++|.++.. +-|-|-|.|+..|+++ -|.
T Consensus 41 ~~L~~~~l~~a~~~~------------------~kv~p~C~y~~~~~~~-hpe 74 (78)
T PF14542_consen 41 KKLVEAALDYARENG------------------LKVVPTCSYVAKYFRR-HPE 74 (78)
T ss_dssp HHHHHHHHHHHHHTT-------------------EEEETSHHHHHHHHH--GG
T ss_pred HHHHHHHHHHHHHCC------------------CEEEEECHHHHHHHHh-Ccc
Confidence 457778888887652 2356999999999987 443
No 14
>smart00796 AHS1 Allophanate hydrolase subunit 1. This domain represents subunit 1 of allophanate hydrolase (AHS1).
Probab=29.16 E-value=3.1e+02 Score=22.14 Aligned_cols=66 Identities=12% Similarity=0.175 Sum_probs=40.2
Q ss_pred cccCCCeEEEEEeccCCCcchhhhhHHHHHHHHHHHhhhcccceEEecCCCCCCCCceEEEEeCCChhHHHHHHH
Q psy5895 50 MQTDGEHCMLLALPCGRTEVDVVQQSAYLQSGFITYLQQKQAAGIVNIAAPGTQQAAYIVHVFPSCEFANNSLAQ 124 (152)
Q Consensus 50 i~~~~~~cilLAlp~~~~~~d~~~q~~~l~~~lV~YLkqKqAAGIisl~~~~~~~~~~vlhiFPPCeFs~~~L~~ 124 (152)
+...++.++++-.....+ . ..+.-...|..+|+++...||+.+-..- .+..| .|=|......-|.+
T Consensus 3 i~~~Gd~allv~~~~~~~---~--~~~~~v~~l~~~l~~~~~~gi~e~vp~~---~sllv-~fdp~~~~~~~l~~ 68 (201)
T smart00796 3 IRPAGDRALLVEFGDEID---L--ALNRRVLALARALRAAPLPGVVELVPGY---RSLLV-HFDPLVIDPAALLA 68 (201)
T ss_pred EEEcCCcEEEEEECCcCC---H--HHHHHHHHHHHHHHhcCCCCeEEccccc---eEEEE-EEcCCCCCHHHHHH
Confidence 445678899988764322 1 1122234799999999999999976321 23344 46665444444443
No 15
>PRK10424 ilvG operon leader peptide; Provisional
Probab=28.38 E-value=40 Score=20.04 Aligned_cols=13 Identities=31% Similarity=0.697 Sum_probs=10.5
Q ss_pred ceEEEEeCCChhH
Q psy5895 106 AYIVHVFPSCEFA 118 (152)
Q Consensus 106 ~~vlhiFPPCeFs 118 (152)
+-|+-|-|||--+
T Consensus 14 svvviiippcgaa 26 (32)
T PRK10424 14 SVVVIIIPPCGAA 26 (32)
T ss_pred EEEEEEecCchhh
Confidence 5689999999754
No 16
>PF07905 PucR: Purine catabolism regulatory protein-like family; InterPro: IPR012914 This domain is found in the purine catabolism regulatory protein expressed by Bacillus subtilis (PucR, O32138 from SWISSPROT). PucR is thought to be a transcriptional regulator of genes involved in the purine degradation pathway, and may contain a LysR-like DNA-binding domain. It is similar to LysR-type regulators in that it represses its own expression []. The other members of this family are also putative regulatory proteins.
Probab=27.67 E-value=48 Score=24.31 Aligned_cols=19 Identities=37% Similarity=0.326 Sum_probs=16.7
Q ss_pred HHHHHHHHhhhcccceEEe
Q psy5895 78 LQSGFITYLQQKQAAGIVN 96 (152)
Q Consensus 78 l~~~lV~YLkqKqAAGIis 96 (152)
.+..||..|.++.+||++-
T Consensus 60 ~~~~~i~~L~~~~~agL~i 78 (123)
T PF07905_consen 60 ELREFIRELAEKGAAGLGI 78 (123)
T ss_pred HHHHHHHHHHHCCCeEEEE
Confidence 3568999999999999986
No 17
>PF08643 DUF1776: Fungal family of unknown function (DUF1776); InterPro: IPR013952 This is a fungal protein of unknown function. One of the proteins P32792 from SWISSPROT has been localised to the mitochondria [].
Probab=26.64 E-value=44 Score=29.11 Aligned_cols=47 Identities=15% Similarity=0.143 Sum_probs=31.5
Q ss_pred CCeEEEEEeccCCCcchhhhh-----------------HHHHHHHHHHHhhhc------------ccceEEecCCC
Q psy5895 54 GEHCMLLALPCGRTEVDVVQQ-----------------SAYLQSGFITYLQQK------------QAAGIVNIAAP 100 (152)
Q Consensus 54 ~~~cilLAlp~~~~~~d~~~q-----------------~~~l~~~lV~YLkqK------------qAAGIisl~~~ 100 (152)
.||.+.+.+...++...+.++ ...-.+.|.+||++. +-.|||-+|.-
T Consensus 27 RGFIV~v~~~~~ed~~~ve~e~~~dI~~L~ld~~~~~~~~~~l~~f~~~L~~p~~p~~~~~~h~l~L~svi~~Psl 102 (299)
T PF08643_consen 27 RGFIVYVTVSSAEDEKYVESEDRPDIRPLWLDDSDPSSIHASLSRFASLLSRPHVPFPGAPPHHLQLKSVIFIPSL 102 (299)
T ss_pred CCeEEEEEeCCHHHHHHHHhccCCCCCCcccCCCCCcchHHHHHHHHHHhcCCCCCCCCCCCceeEEEEEEEecCC
Confidence 589999888765543221111 112346899999988 88899999853
No 18
>PF05122 SpdB: Mobile element transfer protein; InterPro: IPR007806 This family is found in proteins involved in transferring a group of integrating conjugative DNA elements, such as pSAM2 from Streptomyces ambofaciens during mating []. Their precise role is not known.
Probab=25.70 E-value=34 Score=22.64 Aligned_cols=25 Identities=20% Similarity=0.376 Sum_probs=20.5
Q ss_pred EEeCCChhHHHHHHHHhHHHHhhcc
Q psy5895 110 HVFPSCEFANNSLAQIDAQLLKKVS 134 (152)
Q Consensus 110 hiFPPCeFs~~~L~~~Ap~L~~~~~ 134 (152)
--=|-|.||..|-++.|..|..+..
T Consensus 24 Cta~~Cg~SadY~sr~AAelAArtH 48 (53)
T PF05122_consen 24 CTAPRCGFSADYDSRSAAELAARTH 48 (53)
T ss_pred ecCCCCCcccccccHHHHHHHhhcc
Confidence 3458999999999999988877543
No 19
>PF01776 Ribosomal_L22e: Ribosomal L22e protein family; InterPro: IPR002671 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L22e forms part of the 60S ribosomal subunit []. This family is found in eukaryotes. Rattus norvegicus (Rat) L22 is related to ribosomal proteins from other eukaryotes and is identical in amino acid sequence to human EAP, the EBER 1 (Epstein-Barr virus (strain GD1) (HHV-4) (Human herpesvirus 4) encoded RNA) associated protein [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1D_M 4A1B_M 4A19_M 4A18_M 3IZR_W 3IZS_W.
Probab=23.30 E-value=1.6e+02 Score=22.22 Aligned_cols=58 Identities=21% Similarity=0.332 Sum_probs=37.9
Q ss_pred HHHHHHhhhc--------ccceEEecCCCCCCCCceEEEEeCCChhHHHHHHHHhHHHHhhccCCCcEEEE
Q psy5895 80 SGFITYLQQK--------QAAGIVNIAAPGTQQAAYIVHVFPSCEFANNSLAQIDAQLLKKVSELTYLVII 142 (152)
Q Consensus 80 ~~lV~YLkqK--------qAAGIisl~~~~~~~~~~vlhiFPPCeFs~~~L~~~Ap~L~~~~~~~~hLviV 142 (152)
.+|.+||+++ +..+-|.+... ..-+.+-.-.+||-.||+-+....++.-.=-++|=||
T Consensus 24 ~~fe~fL~erIKV~gk~gnlg~~V~i~~~-----~~ki~V~s~v~fsKrYLKYLTKKyLKK~~LRdwlrVv 89 (112)
T PF01776_consen 24 ADFEKFLQERIKVNGKTGNLGNKVTISRD-----KNKITVTSEVPFSKRYLKYLTKKYLKKNNLRDWLRVV 89 (112)
T ss_dssp HHHHHHHHHHHHHHSCSSSSTTTEEEEE------SSEEEEEESSS-SHHHHHHHHHHHHTTSSSTTTEEEC
T ss_pred HHHHHHHHHheEeCCcccccCCeEEEEec-----CCEEEEEecccccHHHHHHHHHHHHhhcchhheEEEE
Confidence 5789999883 33444555432 3356666788999999999888888754323566554
No 20
>PRK11538 ribosome-associated protein; Provisional
Probab=22.89 E-value=1.3e+02 Score=22.10 Aligned_cols=39 Identities=18% Similarity=0.348 Sum_probs=24.7
Q ss_pred hhHHHHHHHHHHHhhhcccceEEecCCCCCCC--------CceEEEEeCC
Q psy5895 73 QQSAYLQSGFITYLQQKQAAGIVNIAAPGTQQ--------AAYIVHVFPS 114 (152)
Q Consensus 73 ~q~~~l~~~lV~YLkqKqAAGIisl~~~~~~~--------~~~vlhiFPP 114 (152)
.|.+.+-.+++..+++ +|+......|.++ ...|||+|=|
T Consensus 46 rh~~aia~~v~~~~k~---~~~~~~~~eG~~~~~WillD~g~ivVHif~~ 92 (105)
T PRK11538 46 RHVMSIADHVVQESRA---AGLLPLGVEGENAADWIVVDLGDVIVHVMQE 92 (105)
T ss_pred HHHHHHHHHHHHHHHH---cCCCCCcccCCCCCCEEEEeCCCEEEEcCCH
Confidence 4555666677777764 4665555555443 3689999955
No 21
>KOG3054|consensus
Probab=22.72 E-value=61 Score=28.16 Aligned_cols=26 Identities=31% Similarity=0.503 Sum_probs=18.8
Q ss_pred cCCCcchhhhhHHHHHHHHHHHhhhcc
Q psy5895 64 CGRTEVDVVQQSAYLQSGFITYLQQKQ 90 (152)
Q Consensus 64 ~~~~~~d~~~q~~~l~~~lV~YLkqKq 90 (152)
.|++..+..+|+ +|++-||.|.|+-.
T Consensus 188 EGtee~~~eeqd-nll~eFv~YIk~nK 213 (299)
T KOG3054|consen 188 EGTEEVQGEEQD-NLLSEFVEYIKKNK 213 (299)
T ss_pred ccccccccchHH-HHHHHHHHHHHhcC
Confidence 355555555676 68889999998765
No 22
>TIGR02625 YiiL_rotase L-rhamnose 1-epimerase. Members of this protein family are rhamnose mutarotase from Escherichia coli, previously designated YiiL as an uncharacterized protein, and close homologs also associated with rhamnose dissimilation operons in other bacterial genomes. Mutarotase is a term for an epimerase that changes optical activity. This enzyme was shown experimentally to interconvert alpha and beta stereoisomers of the pyranose form of L-rhamnose. The crystal structure of this small (104 amino acid) protein shows a locally asymmetric dimer with active site residues of His, Tyr, and Trp.
Probab=22.31 E-value=28 Score=25.54 Aligned_cols=19 Identities=16% Similarity=0.137 Sum_probs=15.6
Q ss_pred eeeeecCCCCCcchhhhhh
Q psy5895 31 RIAQRMRLEQTQIDGVVRK 49 (152)
Q Consensus 31 rItQRlRLd~~~Ld~V~rr 49 (152)
|++++|||++..+++-.+|
T Consensus 1 R~af~~~l~p~~~~eY~~~ 19 (102)
T TIGR02625 1 RKAFVMYVNPDAHEEYQKR 19 (102)
T ss_pred CeeEEEEeCHHHHHHHHHH
Confidence 7899999999998875443
No 23
>PF12780 AAA_8: P-loop containing dynein motor region D4; InterPro: IPR024317 The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four (D1 - D4) correspond to the ATP binding sites with P-loop signatures described previously, and two (D5, D6) are modules in which the P loop has been lost in evolution. This particular entry represents the D4 ATP-binding domain of the motor [].; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.
Probab=21.92 E-value=76 Score=26.81 Aligned_cols=22 Identities=14% Similarity=0.271 Sum_probs=17.2
Q ss_pred hhhhhcccCCCeEEEEEeccCC
Q psy5895 45 GVVRKMQTDGEHCMLLALPCGR 66 (152)
Q Consensus 45 ~V~rri~~~~~~cilLAlp~~~ 66 (152)
-+.|.+..+.||++|++++|..
T Consensus 22 ri~RvL~~~~Gh~LLvG~~GsG 43 (268)
T PF12780_consen 22 RISRVLSQPRGHALLVGVGGSG 43 (268)
T ss_dssp HHHHHHCSTTEEEEEECTTTSC
T ss_pred HHHHHHcCCCCCeEEecCCCcc
Confidence 3566777889999999998643
No 24
>PF05827 ATP-synt_S1: Vacuolar ATP synthase subunit S1 (ATP6S1); InterPro: IPR024722 This family consists of metazoan vacuolar ATP synthase subunit S1 proteins [] and fungal proteins belonging to the BIG family. In Candida albicans BIG is required for normal beta-1,6-glucan synthesis, hyphal morphogenesis, adhesion and virulence [].
Probab=21.66 E-value=3.3e+02 Score=22.55 Aligned_cols=65 Identities=23% Similarity=0.366 Sum_probs=34.9
Q ss_pred HHHHHHhhhcccc--eEEecCCCCCC----CCceEEE-EeCCChhH----HHHHHHHh---HHHHhhccCCC-cEEEEEE
Q psy5895 80 SGFITYLQQKQAA--GIVNIAAPGTQ----QAAYIVH-VFPSCEFA----NNSLAQID---AQLLKKVSELT-YLVIIIA 144 (152)
Q Consensus 80 ~~lV~YLkqKqAA--GIisl~~~~~~----~~~~vlh-iFPPCeFs----~~~L~~~A---p~L~~~~~~~~-hLviVi~ 144 (152)
..|.+|+++|..+ .+|.+...... ...-|+- -|||++=+ .+.|.+.- ..++..+.+.. |-+|..+
T Consensus 96 ~~L~~~l~~~c~~~~~~v~~~~~~~~~~~~~~~~vi~V~l~~l~~~~~~R~~~L~~nD~~l~~vl~~l~s~~~ytvIyts 175 (282)
T PF05827_consen 96 SQLAEYLKEKCGASVVIVDVSDLSEDSFEEYKPRVIRVDLPPLPSSSESRKEALSDNDEFLRKVLSKLPSPDPYTVIYTS 175 (282)
T ss_pred HHHHHHHHHHhCcCceEEecCccccccccccCCcEEEEECCCCCCccccchhhhhhhhHHHHHHHHhcCCCCcEEEEEEc
Confidence 4799999999998 44444432211 0234444 49998654 33444322 23444454433 5555444
No 25
>PF00532 Peripla_BP_1: Periplasmic binding proteins and sugar binding domain of LacI family; InterPro: IPR001761 This family includes the periplasmic binding proteins, and the LacI family transcriptional regulators. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The LacI family of proteins consist of transcriptional regulators related to the lac repressor. In this case, generally the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain (lacI) [, ].; PDB: 1BAP_A 7ABP_A 6ABP_A 1ABF_A 5ABP_A 2WRZ_B 9ABP_A 1APB_A 1ABE_A 8ABP_A ....
Probab=21.59 E-value=1.5e+02 Score=24.27 Aligned_cols=50 Identities=18% Similarity=0.339 Sum_probs=32.4
Q ss_pred chhhhhhccc---CCCeEEEEEeccCCCcchhhhhHHHHHHHHHHHhhhcccceEEecCCCCC
Q psy5895 43 IDGVVRKMQT---DGEHCMLLALPCGRTEVDVVQQSAYLQSGFITYLQQKQAAGIVNIAAPGT 102 (152)
Q Consensus 43 Ld~V~rri~~---~~~~cilLAlp~~~~~~d~~~q~~~l~~~lV~YLkqKqAAGIisl~~~~~ 102 (152)
..++.+-|.. ..||-++|.-- +.+ .... ..++.|.++++.|||-.+...+
T Consensus 16 f~~ii~gIe~~a~~~Gy~l~l~~t-~~~--------~~~e-~~i~~l~~~~vDGiI~~s~~~~ 68 (279)
T PF00532_consen 16 FAEIIRGIEQEAREHGYQLLLCNT-GDD--------EEKE-EYIELLLQRRVDGIILASSEND 68 (279)
T ss_dssp HHHHHHHHHHHHHHTTCEEEEEEE-TTT--------HHHH-HHHHHHHHTTSSEEEEESSSCT
T ss_pred HHHHHHHHHHHHHHcCCEEEEecC-CCc--------hHHH-HHHHHHHhcCCCEEEEecccCC
Confidence 3445555543 57998888533 222 1223 6888999999999998865443
No 26
>cd01422 MGS Methylglyoxal synthase catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The first part of the catalytic mechanism is believed to be similar to TIM (triosephosphate isomerase) in that both enzymes utilize DHAP to form an ene-diolate phosphate intermediate. In MGS, the second catalytic step is characterized by the elimination of phosphate and collapse of the enediolate to form methylglyoxal instead of reprotonation to form the isomer glyceraldehyde 3-phosphate, as in TIM. This is the first reaction in the methylglyoxal bypass of the Embden-Myerhoff glycolytic pathway and is believed to provide physiological benefits under non-ideal growth conditions in bacteria.
Probab=21.14 E-value=95 Score=22.69 Aligned_cols=21 Identities=5% Similarity=0.183 Sum_probs=19.0
Q ss_pred HHHHHHhhhcccceEEecCCC
Q psy5895 80 SGFITYLQQKQAAGIVNIAAP 100 (152)
Q Consensus 80 ~~lV~YLkqKqAAGIisl~~~ 100 (152)
.++++.+++.+...|||.+.+
T Consensus 60 ~~i~~~i~~g~i~~VInt~~~ 80 (115)
T cd01422 60 QQIGALIAEGEIDAVIFFRDP 80 (115)
T ss_pred hHHHHHHHcCceeEEEEcCCC
Confidence 469999999999999999986
No 27
>PF09756 DDRGK: DDRGK domain; InterPro: IPR019153 This is a family of proteins of approximately 300 residues. They contain a highly conserved DDRGK motif. The function is unknown. ; PDB: 1WI9_A.
Probab=20.61 E-value=62 Score=26.37 Aligned_cols=14 Identities=29% Similarity=0.698 Sum_probs=11.4
Q ss_pred HHHHHHHHhhhccc
Q psy5895 78 LQSGFITYLQQKQA 91 (152)
Q Consensus 78 l~~~lV~YLkqKqA 91 (152)
++..||+|+|++..
T Consensus 100 lL~~Fi~yIK~~Kv 113 (188)
T PF09756_consen 100 LLQEFINYIKEHKV 113 (188)
T ss_dssp HHHHHHHHHHH-SE
T ss_pred HHHHHHHHHHHcce
Confidence 77899999999874
No 28
>TIGR00090 iojap_ybeB iojap-like ribosome-associated protein. This model describes a widely distributed family of bacterial proteins related to iojap from plants. It includes YbeB from E. coli. The gene iojap is a pattern-striping gene in maize, reflecting a chloroplast development defect in some cells. More recent work in bacteria suggests that the bacterial iojap-related protein physically associates with ribosomes. The function remains unknown.
Probab=20.36 E-value=1.8e+02 Score=20.84 Aligned_cols=39 Identities=18% Similarity=0.404 Sum_probs=25.7
Q ss_pred hhHHHHHHHHHHHhhhcccceEEecCCCCCCC--------CceEEEEeCC
Q psy5895 73 QQSAYLQSGFITYLQQKQAAGIVNIAAPGTQQ--------AAYIVHVFPS 114 (152)
Q Consensus 73 ~q~~~l~~~lV~YLkqKqAAGIisl~~~~~~~--------~~~vlhiFPP 114 (152)
.|-+.+-..+...+|+ .|+-....+|.+. ..-|||+|=|
T Consensus 41 rh~~aia~~v~~~~k~---~~~~~~~~EG~~~~~WillD~g~ivVHif~~ 87 (99)
T TIGR00090 41 RHVKAIADNVEEELKE---AGLKPLGVEGLEEGDWVLVDLGDVVVHIFQP 87 (99)
T ss_pred HHHHHHHHHHHHHHHH---cCCCcccccCCCCCCEEEEECCCEEEEeCCh
Confidence 4556677788888864 3665555555443 4578999954
No 29
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=20.33 E-value=1.3e+02 Score=25.63 Aligned_cols=53 Identities=13% Similarity=0.273 Sum_probs=35.8
Q ss_pred CCCCCcchhhhhhccc---CCCeEEEEEeccCCCcchhhhhHHHHHHHHHHHhhhcccceEEecC
Q psy5895 37 RLEQTQIDGVVRKMQT---DGEHCMLLALPCGRTEVDVVQQSAYLQSGFITYLQQKQAAGIVNIA 98 (152)
Q Consensus 37 RLd~~~Ld~V~rri~~---~~~~cilLAlp~~~~~~d~~~q~~~l~~~lV~YLkqKqAAGIisl~ 98 (152)
.+.++..-++.+-|.. ..||-++|+.... + ..-.+..+..|.++++.|||-++
T Consensus 67 ~~~~~~~~~i~~gi~~~~~~~gy~~~l~~~~~-~--------~~~e~~~~~~l~~~~vdGiIi~~ 122 (333)
T COG1609 67 DITNPFFAEILKGIEEAAREAGYSLLLANTDD-D--------PEKEREYLETLLQKRVDGLILLG 122 (333)
T ss_pred CCCCchHHHHHHHHHHHHHHcCCEEEEECCCC-C--------HHHHHHHHHHHHHcCCCEEEEec
Confidence 4444555555555553 5677777766543 1 12245788999999999999998
Done!