Query 038672
Match_columns 148
No_of_seqs 107 out of 122
Neff 3.3
Searched_HMMs 46136
Date Fri Mar 29 13:28:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038672.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038672hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF07911 DUF1677: Protein of u 100.0 9.5E-56 2E-60 324.3 8.4 91 30-128 1-91 (91)
2 COG0675 Transposase and inacti 45.2 8.6 0.00019 30.5 0.5 24 32-69 308-331 (364)
3 PF08093 Toxin_23: Magi 5 toxi 44.4 9.3 0.0002 23.6 0.4 10 37-46 14-23 (30)
4 PF07637 PSD5: Protein of unkn 34.9 1.4E+02 0.003 20.0 6.3 40 86-133 18-57 (64)
5 PF13913 zf-C2HC_2: zinc-finge 34.0 30 0.00064 19.6 1.4 12 90-101 14-25 (25)
6 PF07874 DUF1660: Prophage pro 34.0 18 0.0004 25.5 0.6 38 59-98 21-64 (64)
7 PF04810 zf-Sec23_Sec24: Sec23 32.3 18 0.00039 22.4 0.3 11 58-68 22-32 (40)
8 TIGR03114 cas_csf1 CRISPR-asso 31.5 19 0.00041 30.5 0.5 15 58-72 30-44 (202)
9 PF04959 ARS2: Arsenite-resist 30.8 10 0.00022 31.8 -1.2 19 54-72 71-89 (214)
10 COG1998 RPS31 Ribosomal protei 30.6 19 0.00042 24.6 0.3 25 34-67 20-44 (51)
11 cd03132 GATase1_catalase Type 29.8 29 0.00064 25.1 1.2 26 45-70 80-106 (142)
12 PF05605 zf-Di19: Drought indu 28.2 1E+02 0.0022 19.7 3.4 40 33-73 2-44 (54)
13 PRK00432 30S ribosomal protein 27.5 24 0.00052 23.2 0.3 23 35-67 22-44 (50)
14 TIGR01562 FdhE formate dehydro 27.4 61 0.0013 28.5 2.9 92 33-130 184-293 (305)
15 COG5028 Vesicle coat complex C 26.7 11 0.00023 37.7 -2.0 28 34-68 200-229 (861)
16 TIGR01383 not_thiJ DJ-1 family 25.5 44 0.00095 24.9 1.5 27 45-71 81-108 (179)
17 smart00547 ZnF_RBZ Zinc finger 24.4 29 0.00063 19.0 0.3 11 59-69 1-11 (26)
18 COG2191 Formylmethanofuran deh 24.0 25 0.00054 29.8 -0.1 31 33-70 172-203 (206)
19 PRK12722 transcriptional activ 23.9 22 0.00048 29.4 -0.4 33 29-68 130-162 (187)
20 PRK09855 PTS system N-acetylga 23.5 87 0.0019 27.0 3.1 14 89-105 53-66 (263)
21 PLN02489 homocysteine S-methyl 23.2 59 0.0013 28.3 2.0 19 38-60 316-334 (335)
22 PRK11574 oxidative-stress-resi 22.8 53 0.0012 25.2 1.5 24 47-70 86-110 (196)
23 cd03139 GATase1_PfpI_2 Type 1 21.2 63 0.0014 24.0 1.6 26 45-70 79-105 (183)
24 COG1405 SUA7 Transcription ini 21.0 20 0.00043 31.1 -1.3 32 35-74 3-34 (285)
25 PRK12860 transcriptional activ 20.8 36 0.00077 28.3 0.2 32 29-67 130-161 (189)
26 PF00641 zf-RanBP: Zn-finger i 20.8 38 0.00083 19.4 0.3 10 58-67 2-11 (30)
27 PRK07534 methionine synthase I 20.1 73 0.0016 27.9 2.0 19 38-60 278-296 (336)
No 1
>PF07911 DUF1677: Protein of unknown function (DUF1677); InterPro: IPR012876 The sequences found in this family are all derived from hypothetical plant proteins of unknown function. The region features a number of highly conserved cysteine residues.
Probab=100.00 E-value=9.5e-56 Score=324.29 Aligned_cols=91 Identities=68% Similarity=1.246 Sum_probs=86.7
Q ss_pred hhhceeeCccCCCccccHHHHHHHHhhcCCccccchhhHHHHHHHHHhhcccccCCCCCHHHHHHHHHHHHhhhccCCCC
Q 038672 30 EVEFARCECCGLTEECTAAYVSRVKERYGGRWICGLCTEAVKDEITCRSKKRENHMMISTDEALNRHMKFCEQFRSSSPP 109 (148)
Q Consensus 30 EVE~akCeCCGltEECT~~YI~~VR~ry~GrWvCGLCsEAVkeE~~~R~~~~~~~~~i~~eEAl~~Hm~fC~~fn~~~~~ 109 (148)
|||+|+||||||+|||||+||++||++|+||||||||+||||||+. |.++ .+++||||++||+||++||+++|+
T Consensus 1 EvE~akCeCCG~~EECT~~YI~~VR~ry~GrWvCGLC~EAVkeE~~-r~~~-----~~~~eeAl~~Hm~fC~~f~~~~~~ 74 (91)
T PF07911_consen 1 EVESAKCECCGLTEECTPEYIARVRERYGGRWVCGLCSEAVKEEVG-RSKP-----GISVEEALDRHMSFCRKFNSSTRP 74 (91)
T ss_pred CCceeeecCCCCchhccHHHHHHHHHHhCCeehhhcCHHHHHHHHh-ccCC-----CCCHHHHHHHHHHHHHHcCCCCCC
Confidence 7999999999999999999999999999999999999999999998 7555 799999999999999999998755
Q ss_pred CCCCchhHHHHHHHHHHHh
Q 038672 110 ARPAADDLISAMKHILRRS 128 (148)
Q Consensus 110 ~nP~a~~la~aMR~iLRRs 128 (148)
||+ ++||+|||||||||
T Consensus 75 -np~-~~l~~amr~ilrRs 91 (91)
T PF07911_consen 75 -NPA-LSLASAMRQILRRS 91 (91)
T ss_pred -Chh-HHHHHHHHHHHhcC
Confidence 999 99999999999986
No 2
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=45.20 E-value=8.6 Score=30.50 Aligned_cols=24 Identities=29% Similarity=0.699 Sum_probs=19.4
Q ss_pred hceeeCccCCCccccHHHHHHHHhhcCCccccchhhHH
Q 038672 32 EFARCECCGLTEECTAAYVSRVKERYGGRWICGLCTEA 69 (148)
Q Consensus 32 E~akCeCCGltEECT~~YI~~VR~ry~GrWvCGLCsEA 69 (148)
-+..|-|||. ...+.|.|.-|+.-
T Consensus 308 tS~~C~~cg~--------------~~~r~~~C~~cg~~ 331 (364)
T COG0675 308 TSKTCPCCGH--------------LSGRLFKCPRCGFV 331 (364)
T ss_pred CcccccccCC--------------ccceeEECCCCCCe
Confidence 4688999999 44677999999863
No 3
>PF08093 Toxin_23: Magi 5 toxic peptide family; InterPro: IPR012628 This family consists of toxic peptides (Magi 5) found in the venom of the Hexathelidae spider. Magi 5 is the first spider toxin with binding affinity to site 4 of a mammalian sodium channel and the toxin has an insecticidal effect on larvae, causing paralysis when injected into the larvae.; GO: 0019871 sodium channel inhibitor activity, 0009405 pathogenesis, 0005576 extracellular region; PDB: 1HP3_A 1G9P_A 2GX1_A.
Probab=44.41 E-value=9.3 Score=23.58 Aligned_cols=10 Identities=50% Similarity=1.441 Sum_probs=7.1
Q ss_pred CccCCCcccc
Q 038672 37 ECCGLTEECT 46 (148)
Q Consensus 37 eCCGltEECT 46 (148)
|||||+--||
T Consensus 14 ~CCg~tp~C~ 23 (30)
T PF08093_consen 14 DCCGWTPVCK 23 (30)
T ss_dssp CCCTT--EEE
T ss_pred ccccCccccc
Confidence 7999998887
No 4
>PF07637 PSD5: Protein of unknown function (DUF1595); InterPro: IPR013043 A region of similarity shared by several Rhodopirellula baltica cytochrome-like proteins that are predicted to be secreted. These proteins also contain IPR011478 from INTERPRO, IPR013036 from INTERPRO, IPR013039 from INTERPRO and IPR013042 from INTERPRO.
Probab=34.92 E-value=1.4e+02 Score=19.95 Aligned_cols=40 Identities=25% Similarity=0.451 Sum_probs=31.9
Q ss_pred CCCHHHHHHHHHHHHhhhccCCCCCCCCchhHHHHHHHHHHHhcCCCC
Q 038672 86 MISTDEALNRHMKFCEQFRSSSPPARPAADDLISAMKHILRRSLDSPR 133 (148)
Q Consensus 86 ~i~~eEAl~~Hm~fC~~fn~~~~~~nP~a~~la~aMR~iLRRsldSpr 133 (148)
+++-+| ++..+.+-..-...+ .+..+||+..|.--|-||.
T Consensus 18 p~~~~e-~~~~~~~~~~~~~~g-------~~~~~a~~~~l~aiL~SP~ 57 (64)
T PF07637_consen 18 PLTDEE-VDRYLALYDSARAQG-------EDFEEALKEALQAILCSPS 57 (64)
T ss_pred CCCHHH-HHHHHHHHHHHHHcC-------CCHHHHHHHHHHHHHcCcc
Confidence 467677 999999987655422 5788999999999999986
No 5
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=33.99 E-value=30 Score=19.56 Aligned_cols=12 Identities=33% Similarity=0.830 Sum_probs=10.4
Q ss_pred HHHHHHHHHHHh
Q 038672 90 DEALNRHMKFCE 101 (148)
Q Consensus 90 eEAl~~Hm~fC~ 101 (148)
.++|..|+..|+
T Consensus 14 ~~~l~~H~~~C~ 25 (25)
T PF13913_consen 14 PDRLEKHEKICK 25 (25)
T ss_pred HHHHHHHHHhcC
Confidence 689999999984
No 6
>PF07874 DUF1660: Prophage protein (DUF1660); InterPro: IPR012455 This entry is represented by Bacteriophage bIL285, Orf33. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=33.95 E-value=18 Score=25.55 Aligned_cols=38 Identities=26% Similarity=0.510 Sum_probs=22.4
Q ss_pred CccccchhhHHHHHHHHH------hhcccccCCCCCHHHHHHHHHH
Q 038672 59 GRWICGLCTEAVKDEITC------RSKKRENHMMISTDEALNRHMK 98 (148)
Q Consensus 59 GrWvCGLCsEAVkeE~~~------R~~~~~~~~~i~~eEAl~~Hm~ 98 (148)
.+|-|-=| +.++....+ |++- +....+-+|.+|+.||.
T Consensus 21 ~~~~C~RC-~~~k~~~~~~~~~~NrsDl-Desenv~~ekwldkhmd 64 (64)
T PF07874_consen 21 MEWKCERC-KIVKATANRFAADFNRSDL-DESENVFPEKWLDKHMD 64 (64)
T ss_pred hhHHHHHH-HHHHhhHhhhhhhhccccc-cccccccHHHHhhhhcC
Confidence 45777788 777654421 2221 11123567999999983
No 7
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=32.26 E-value=18 Score=22.41 Aligned_cols=11 Identities=45% Similarity=1.443 Sum_probs=7.7
Q ss_pred CCccccchhhH
Q 038672 58 GGRWICGLCTE 68 (148)
Q Consensus 58 ~GrWvCGLCsE 68 (148)
+.+|+|-||..
T Consensus 22 ~~~w~C~~C~~ 32 (40)
T PF04810_consen 22 GKTWICNFCGT 32 (40)
T ss_dssp TTEEEETTT--
T ss_pred CCEEECcCCCC
Confidence 35899999964
No 8
>TIGR03114 cas_csf1 CRISPR-associated protein, Csf1 family. Members of this family show up near CRISPR repeats in Acidithiobacillus ferrooxidans ATCC 23270, Azoarcus sp. EbN1, and Rhodoferax ferrireducens DSM 15236. In the latter two species, the CRISPR/cas locus is found on a plasmid. This family is one of several characteristic of a type of CRISPR-associated (cas) gene cluster we designate Aferr after A. ferrooxidans, where it is both chromosomal and the only type of cas gene cluster found. The gene is designated csf1 (CRISPR/cas Subtype as in A. ferrooxidans protein 1), as it lies closest to the repeats.
Probab=31.53 E-value=19 Score=30.48 Aligned_cols=15 Identities=40% Similarity=1.010 Sum_probs=11.7
Q ss_pred CCccccchhhHHHHH
Q 038672 58 GGRWICGLCTEAVKD 72 (148)
Q Consensus 58 ~GrWvCGLCsEAVke 72 (148)
.|.||||-|.--...
T Consensus 30 ~g~~vCG~C~al~sk 44 (202)
T TIGR03114 30 GGGMVCGHCTALMSK 44 (202)
T ss_pred CCCeeecccHHHhhH
Confidence 689999999865443
No 9
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=30.79 E-value=10 Score=31.81 Aligned_cols=19 Identities=37% Similarity=0.805 Sum_probs=12.5
Q ss_pred HhhcCCccccchhhHHHHH
Q 038672 54 KERYGGRWICGLCTEAVKD 72 (148)
Q Consensus 54 R~ry~GrWvCGLCsEAVke 72 (148)
.+....||.|+||+.--|.
T Consensus 71 ~e~~~~K~~C~lc~KlFkg 89 (214)
T PF04959_consen 71 KEEDEDKWRCPLCGKLFKG 89 (214)
T ss_dssp -SSSSEEEEE-SSS-EESS
T ss_pred HHHcCCEECCCCCCcccCC
Confidence 5578899999999855443
No 10
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=30.64 E-value=19 Score=24.56 Aligned_cols=25 Identities=32% Similarity=0.765 Sum_probs=16.8
Q ss_pred eeeCccCCCccccHHHHHHHHhhcCCccccchhh
Q 038672 34 ARCECCGLTEECTAAYVSRVKERYGGRWICGLCT 67 (148)
Q Consensus 34 akCeCCGltEECT~~YI~~VR~ry~GrWvCGLCs 67 (148)
-.|.-||=. -+=+.+.-||.||-|+
T Consensus 20 ~~CPrCG~g---------vfmA~H~dR~~CGkCg 44 (51)
T COG1998 20 RFCPRCGPG---------VFMADHKDRWACGKCG 44 (51)
T ss_pred ccCCCCCCc---------chhhhcCceeEecccc
Confidence 457778821 1234677799999996
No 11
>cd03132 GATase1_catalase Type 1 glutamine amidotransferase (GATase1)-like domain found in at the C-terminal of several large catalases. Type 1 glutamine amidotransferase (GATase1)-like domain found in at the C-terminal of several large catalases. Catalase catalyzes the dismutation of hydrogen peroxide (H2O2) to water and oxygen. This group includes the large catalases: Neurospora crassa Catalase-1 and Catalase-3 and, Escherichia coli HP-II. This GATase1-like domain has an essential role in HP-II catalase activity. However, it lacks enzymatic activity and the catalytic triad typical of GATase1 domains. Catalase-1 and -3 are homotetrameric, HP-II is homohexameric. It has been proposed that this domain may facilitate the folding and oligomerization process. The interface between this GATase1-like domain of HP-II and the core of the subunit forms part of a channel which provides access to the deeply buried catalase active sites of HPII. Catalase-1 is associated with non-growing cells; C
Probab=29.75 E-value=29 Score=25.14 Aligned_cols=26 Identities=15% Similarity=0.112 Sum_probs=20.9
Q ss_pred ccHHHHHHHHhhc-CCccccchhhHHH
Q 038672 45 CTAAYVSRVKERY-GGRWICGLCTEAV 70 (148)
Q Consensus 45 CT~~YI~~VR~ry-~GrWvCGLCsEAV 70 (148)
-.+.+++-+|+.| .|+||++.|+-+.
T Consensus 80 ~~~~l~~~l~~~~~~~~~I~aic~G~~ 106 (142)
T cd03132 80 PSGRALHFVTEAFKHGKPIGAVGEGSD 106 (142)
T ss_pred cChHHHHHHHHHHhcCCeEEEcCchHH
Confidence 4577888888866 5999999998763
No 12
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=28.17 E-value=1e+02 Score=19.68 Aligned_cols=40 Identities=20% Similarity=0.497 Sum_probs=26.9
Q ss_pred ceeeCccCCCccccHHHHHHHHhhcCC---ccccchhhHHHHHH
Q 038672 33 FARCECCGLTEECTAAYVSRVKERYGG---RWICGLCTEAVKDE 73 (148)
Q Consensus 33 ~akCeCCGltEECT~~YI~~VR~ry~G---rWvCGLCsEAVkeE 73 (148)
+..|.-||- +==-...+.-|.+...+ .-+|-+|+..+++.
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~~~ 44 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVTDN 44 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhhhH
Confidence 456778887 32235677788876553 58999999755443
No 13
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=27.47 E-value=24 Score=23.19 Aligned_cols=23 Identities=35% Similarity=0.837 Sum_probs=15.5
Q ss_pred eeCccCCCccccHHHHHHHHhhcCCccccchhh
Q 038672 35 RCECCGLTEECTAAYVSRVKERYGGRWICGLCT 67 (148)
Q Consensus 35 kCeCCGltEECT~~YI~~VR~ry~GrWvCGLCs 67 (148)
-|.-||= . +-....++|.||-|+
T Consensus 22 fCP~Cg~------~----~m~~~~~r~~C~~Cg 44 (50)
T PRK00432 22 FCPRCGS------G----FMAEHLDRWHCGKCG 44 (50)
T ss_pred cCcCCCc------c----hheccCCcEECCCcC
Confidence 5777772 1 233455999999985
No 14
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=27.42 E-value=61 Score=28.49 Aligned_cols=92 Identities=22% Similarity=0.331 Sum_probs=45.9
Q ss_pred ceeeCccCCCccccHHHHHHHHhh---cCCcc-ccchhhHHHHHHHHHhhcccccCCC---CCHHH---HHHHHHHHHhh
Q 038672 33 FARCECCGLTEECTAAYVSRVKER---YGGRW-ICGLCTEAVKDEITCRSKKRENHMM---ISTDE---ALNRHMKFCEQ 102 (148)
Q Consensus 33 ~akCeCCGltEECT~~YI~~VR~r---y~GrW-vCGLCsEAVkeE~~~R~~~~~~~~~---i~~eE---Al~~Hm~fC~~ 102 (148)
...|-+||- ++.++.||.. =+.|| .|+||.-.=...-. +-..+|.... ++++. -=......|..
T Consensus 184 ~~~CPvCGs-----~P~~s~~~~~~~~~G~RyL~CslC~teW~~~R~-~C~~Cg~~~~l~y~~~e~~~~~~~~r~e~C~~ 257 (305)
T TIGR01562 184 RTLCPACGS-----PPVASMVRQGGKETGLRYLSCSLCATEWHYVRV-KCSHCEESKHLAYLSLEHDAEKAVLKAETCDS 257 (305)
T ss_pred CCcCCCCCC-----hhhhhhhcccCCCCCceEEEcCCCCCcccccCc-cCCCCCCCCceeeEeecCCCCCcceEEeeccc
Confidence 349999995 4566667652 23344 57887654333211 1111222111 23321 00122234433
Q ss_pred hc---c-----CCCCCCCCchhHHHHHHHHHHHhcC
Q 038672 103 FR---S-----SSPPARPAADDLISAMKHILRRSLD 130 (148)
Q Consensus 103 fn---~-----~~~~~nP~a~~la~aMR~iLRRsld 130 (148)
-+ + ..+..+|.++++++-+-+|+=.--+
T Consensus 258 C~~YlK~~~~~~d~~~~~~adDlaSL~LD~~a~e~G 293 (305)
T TIGR01562 258 CQGYLKILYQEKDPHADAVADDLASLALDMRMAEDG 293 (305)
T ss_pred cccchhhhccccCCccCchHHHHhhhHhhHHHHhcC
Confidence 22 1 1234578888898888888775433
No 15
>COG5028 Vesicle coat complex COPII, subunit SEC24/subunit SFB2/subunit SFB3 [Intracellular trafficking and secretion]
Probab=26.70 E-value=11 Score=37.67 Aligned_cols=28 Identities=32% Similarity=0.920 Sum_probs=23.2
Q ss_pred eeeCccCCCccccHHHHH-HHHhhcCC-ccccchhhH
Q 038672 34 ARCECCGLTEECTAAYVS-RVKERYGG-RWICGLCTE 68 (148)
Q Consensus 34 akCeCCGltEECT~~YI~-~VR~ry~G-rWvCGLCsE 68 (148)
++|.+| ..||. -|---++| ||.|-+|.-
T Consensus 200 vRCrrC-------rsYiNPfv~fi~~g~kw~CNiC~~ 229 (861)
T COG5028 200 VRCRRC-------RSYINPFVQFIEQGRKWRCNICRS 229 (861)
T ss_pred hhhhhh-------HhhcCceEEEecCCcEEEEeeccc
Confidence 999999 46887 66667889 999999963
No 16
>TIGR01383 not_thiJ DJ-1 family protein. This model represents the DJ-1 clade of the so-called ThiJ/PfpI family of proteins. PfpI, represented by a distinct model, is a putative intracellular cysteine protease. DJ-1 is described as an oncogene that acts cooperatively with H-Ras. Many members of the DJ-1 clade are annotated (apparently incorrectly) as ThiJ, a protein of thiamine biosynthesis. However, published reports of ThiJ activity and identification of a ThiJ/ThiD bifunctional protein describe an unrelated locus mapping near ThiM, rather than the DJ-1 homolog of E. coli. The ThiJ designation for this family may be spurious; the cited paper PubMed:8885414 refers to a locus near thiD and thiM in E. coli, unlike the gene represented here. Current public annotation reflects ThiJ/ThiD bifunctional activity, apparently a property of ThiD and not of this locus.
Probab=25.46 E-value=44 Score=24.87 Aligned_cols=27 Identities=11% Similarity=0.354 Sum_probs=21.6
Q ss_pred ccHHHHHHHHhhc-CCccccchhhHHHH
Q 038672 45 CTAAYVSRVKERY-GGRWICGLCTEAVK 71 (148)
Q Consensus 45 CT~~YI~~VR~ry-~GrWvCGLCsEAVk 71 (148)
-.+..++-+|+-| .|+||+++|.-+.-
T Consensus 81 ~~~~l~~~l~~~~~~~~~i~~ic~G~~~ 108 (179)
T TIGR01383 81 NSKLLLNILKKQESKGKLVAAICAAPAV 108 (179)
T ss_pred hCHHHHHHHHHHHHCCCEEEEEChhHHH
Confidence 3567888888776 79999999988753
No 17
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=24.36 E-value=29 Score=18.99 Aligned_cols=11 Identities=45% Similarity=1.072 Sum_probs=8.4
Q ss_pred CccccchhhHH
Q 038672 59 GRWICGLCTEA 69 (148)
Q Consensus 59 GrWvCGLCsEA 69 (148)
|.|+|.-|.-.
T Consensus 1 g~W~C~~C~~~ 11 (26)
T smart00547 1 GDWECPACTFL 11 (26)
T ss_pred CcccCCCCCCc
Confidence 68999988643
No 18
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=24.01 E-value=25 Score=29.81 Aligned_cols=31 Identities=26% Similarity=0.545 Sum_probs=25.1
Q ss_pred ceeeCccCCCccccHHHHHHHHhhcC-CccccchhhHHH
Q 038672 33 FARCECCGLTEECTAAYVSRVKERYG-GRWICGLCTEAV 70 (148)
Q Consensus 33 ~akCeCCGltEECT~~YI~~VR~ry~-GrWvCGLCsEAV 70 (148)
+++|+-|| +|+-.-|+++. |+-||.-|.+..
T Consensus 172 ~v~C~kCG-------E~~~e~~~~~~ng~~vC~~C~~~~ 203 (206)
T COG2191 172 SVRCSKCG-------ELFMEPRAVVLNGKPVCKPCAEKK 203 (206)
T ss_pred eeeccccC-------cccccchhhhcCCceecccccccc
Confidence 48999999 56666677776 999999998754
No 19
>PRK12722 transcriptional activator FlhC; Provisional
Probab=23.94 E-value=22 Score=29.41 Aligned_cols=33 Identities=30% Similarity=0.985 Sum_probs=24.9
Q ss_pred chhhceeeCccCCCccccHHHHHHHHhhcCCccccchhhH
Q 038672 29 SEVEFARCECCGLTEECTAAYVSRVKERYGGRWICGLCTE 68 (148)
Q Consensus 29 ~EVE~akCeCCGltEECT~~YI~~VR~ry~GrWvCGLCsE 68 (148)
.++.-+.|-|||= .||...-+. ....+||||.-
T Consensus 130 ~~L~l~~C~~Cgg------~fv~~~~e~-~~~f~CplC~~ 162 (187)
T PRK12722 130 GMLQLSSCNCCGG------HFVTHAHDP-VGSFVCGLCQP 162 (187)
T ss_pred CcEeeccCCCCCC------Ceecccccc-CCCCcCCCCCC
Confidence 3566788999985 477666444 66899999987
No 20
>PRK09855 PTS system N-acetylgalactosamine-specific transporter subunit IID; Provisional
Probab=23.54 E-value=87 Score=26.97 Aligned_cols=14 Identities=14% Similarity=0.475 Sum_probs=11.9
Q ss_pred HHHHHHHHHHHHhhhcc
Q 038672 89 TDEALNRHMKFCEQFRS 105 (148)
Q Consensus 89 ~eEAl~~Hm~fC~~fn~ 105 (148)
..||+++|+.| ||.
T Consensus 53 ~~~Al~rHl~f---fNT 66 (263)
T PRK09855 53 LSAAMKDNLEF---INT 66 (263)
T ss_pred HHHHHHHHHHH---HCC
Confidence 35899999999 885
No 21
>PLN02489 homocysteine S-methyltransferase
Probab=23.15 E-value=59 Score=28.30 Aligned_cols=19 Identities=21% Similarity=0.557 Sum_probs=15.6
Q ss_pred ccCCCccccHHHHHHHHhhcCCc
Q 038672 38 CCGLTEECTAAYVSRVKERYGGR 60 (148)
Q Consensus 38 CCGltEECT~~YI~~VR~ry~Gr 60 (148)
|||- ||+||+.+++...++
T Consensus 316 CCgt----~P~hI~al~~~l~~~ 334 (335)
T PLN02489 316 CCRT----TPNTIRAISKALSER 334 (335)
T ss_pred CCCC----CHHHHHHHHHHHhcC
Confidence 8987 599999999877655
No 22
>PRK11574 oxidative-stress-resistance chaperone; Provisional
Probab=22.76 E-value=53 Score=25.17 Aligned_cols=24 Identities=21% Similarity=0.476 Sum_probs=20.1
Q ss_pred HHHHHHHHhhc-CCccccchhhHHH
Q 038672 47 AAYVSRVKERY-GGRWICGLCTEAV 70 (148)
Q Consensus 47 ~~YI~~VR~ry-~GrWvCGLCsEAV 70 (148)
+.++..+|..+ .|+||+++|.-+.
T Consensus 86 ~~l~~~L~~~~~~g~~v~aic~G~~ 110 (196)
T PRK11574 86 PLLVETVRQFHRSGRIVAAICAAPA 110 (196)
T ss_pred HHHHHHHHHHHHCCCEEEEECHhHH
Confidence 56888888776 6999999999984
No 23
>cd03139 GATase1_PfpI_2 Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus. Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus. PfpI is an ATP-independent intracellular proteases which may hydrolyze small peptides to provide a nutritional source. Only Cys of the catalytic triad typical of GATase1 domains is conserved in this group. This Cys residue is found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow.
Probab=21.23 E-value=63 Score=24.02 Aligned_cols=26 Identities=15% Similarity=0.437 Sum_probs=21.2
Q ss_pred ccHHHHHHHHhhc-CCccccchhhHHH
Q 038672 45 CTAAYVSRVKERY-GGRWICGLCTEAV 70 (148)
Q Consensus 45 CT~~YI~~VR~ry-~GrWvCGLCsEAV 70 (148)
-.+.++.-+|+.| .|+||+++|.-+.
T Consensus 79 ~~~~~~~~l~~~~~~~k~i~aic~g~~ 105 (183)
T cd03139 79 NDPALLDFIRRQAARAKYVTSVCTGAL 105 (183)
T ss_pred cCHHHHHHHHHhcccCCEEEEEchHHH
Confidence 4577888888765 7899999999874
No 24
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=20.98 E-value=20 Score=31.10 Aligned_cols=32 Identities=25% Similarity=0.624 Sum_probs=23.3
Q ss_pred eeCccCCCccccHHHHHHHHhhcCCccccchhhHHHHHHH
Q 038672 35 RCECCGLTEECTAAYVSRVKERYGGRWICGLCTEAVKDEI 74 (148)
Q Consensus 35 kCeCCGltEECT~~YI~~VR~ry~GrWvCGLCsEAVkeE~ 74 (148)
.|.-||-+ ..|++-=.|.|||+-|+.-+.|.+
T Consensus 3 ~CpeCg~~--------~~~~d~~~ge~VC~~CG~Vi~~~~ 34 (285)
T COG1405 3 SCPECGST--------NIITDYERGEIVCADCGLVLEDSL 34 (285)
T ss_pred CCCCCCCc--------cceeeccCCeEEeccCCEEecccc
Confidence 57778876 233333379999999999888854
No 25
>PRK12860 transcriptional activator FlhC; Provisional
Probab=20.85 E-value=36 Score=28.30 Aligned_cols=32 Identities=31% Similarity=0.831 Sum_probs=22.7
Q ss_pred chhhceeeCccCCCccccHHHHHHHHhhcCCccccchhh
Q 038672 29 SEVEFARCECCGLTEECTAAYVSRVKERYGGRWICGLCT 67 (148)
Q Consensus 29 ~EVE~akCeCCGltEECT~~YI~~VR~ry~GrWvCGLCs 67 (148)
.++.-+.|-|||= .||...- .=....+||||.
T Consensus 130 ~~L~l~~C~~Cgg------~fv~~~~-e~~~~f~CplC~ 161 (189)
T PRK12860 130 GMLQLARCCRCGG------KFVTHAH-DLRHNFVCGLCQ 161 (189)
T ss_pred CCeeeccCCCCCC------Ceecccc-ccCCCCcCCCCC
Confidence 3567789999985 4664433 234589999998
No 26
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=20.80 E-value=38 Score=19.35 Aligned_cols=10 Identities=50% Similarity=1.311 Sum_probs=8.0
Q ss_pred CCccccchhh
Q 038672 58 GGRWICGLCT 67 (148)
Q Consensus 58 ~GrWvCGLCs 67 (148)
.|.|.|.-|.
T Consensus 2 ~g~W~C~~C~ 11 (30)
T PF00641_consen 2 EGDWKCPSCT 11 (30)
T ss_dssp SSSEEETTTT
T ss_pred CcCccCCCCc
Confidence 3789998886
No 27
>PRK07534 methionine synthase I; Validated
Probab=20.13 E-value=73 Score=27.86 Aligned_cols=19 Identities=21% Similarity=0.651 Sum_probs=15.3
Q ss_pred ccCCCccccHHHHHHHHhhcCCc
Q 038672 38 CCGLTEECTAAYVSRVKERYGGR 60 (148)
Q Consensus 38 CCGltEECT~~YI~~VR~ry~Gr 60 (148)
|||- ||+||+.+++...++
T Consensus 278 CCGT----tP~hI~~la~~l~~~ 296 (336)
T PRK07534 278 CCGT----MPEHLAAMRAALDAR 296 (336)
T ss_pred ecCC----CHHHHHHHHHHHccC
Confidence 8997 599999999876653
Done!