Query 031396
Match_columns 160
No_of_seqs 40 out of 42
Neff 2.6
Searched_HMMs 46136
Date Fri Mar 29 13:30:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031396.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031396hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN02231 alanine transaminase 45.8 13 0.00029 34.1 1.9 36 1-37 1-36 (534)
2 PRK02228 V-type ATP synthase s 33.6 52 0.0011 24.1 3.0 41 62-111 54-94 (100)
3 PF09478 CBM49: Carbohydrate b 26.7 32 0.0007 23.9 0.9 14 78-91 59-73 (80)
4 PF07621 DUF1582: Protein of u 25.7 39 0.00085 21.1 1.0 17 126-142 1-17 (29)
5 PF14475 Mso1_Sec1_bdg: Sec1-b 25.4 54 0.0012 21.7 1.7 25 52-83 11-41 (41)
6 TIGR01644 phage_P2_V phage bas 22.0 67 0.0014 25.4 2.0 20 79-98 32-55 (191)
7 PF07999 RHSP: Retrotransposon 20.5 44 0.00096 30.8 0.8 17 118-134 59-75 (439)
8 PF09535 Gmx_para_CXXCG: Prote 19.2 70 0.0015 28.0 1.7 20 72-91 74-93 (237)
9 cd08049 TAF8 TATA Binding Prot 17.7 65 0.0014 21.3 0.9 15 79-93 3-17 (54)
10 KOG2317 Putative translation i 15.7 47 0.001 26.7 -0.2 13 86-98 8-20 (138)
No 1
>PLN02231 alanine transaminase
Probab=45.79 E-value=13 Score=34.09 Aligned_cols=36 Identities=19% Similarity=0.378 Sum_probs=23.9
Q ss_pred CcchhcccchhHHHhhccccccCCCCCCCCCcceeee
Q 031396 1 MARFLLSKTSTAIATAGASSRHHHLQLSIPSSRLVPR 37 (160)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ss~~~~~ 37 (160)
|-||+.+..+.++++...- +|.|++.+.|--+-.++
T Consensus 1 ~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~ 36 (534)
T PLN02231 1 MRRFLINQAKGLVDHSRRQ-HHKSPSFLSPQPRPLAS 36 (534)
T ss_pred CchHHHhHHHHHHHHhhhh-hhcCCCCCCCCCCchhH
Confidence 7899999999988875544 55556555554443333
No 2
>PRK02228 V-type ATP synthase subunit F; Provisional
Probab=33.64 E-value=52 Score=24.07 Aligned_cols=41 Identities=15% Similarity=0.259 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHHHHhhcCCCcccCCCCCccccCCCCCCCcchHHHHHHhc
Q 031396 62 LISKLEDAIHRIIVRRSAPDWLPFLPGSSYWVPPPKSQFYGVAQLVEKLA 111 (160)
Q Consensus 62 ~irRLEdaIh~i~vr~AaPDWLPF~PGsSyWVPP~~~~~~gva~Lv~kla 111 (160)
+.+++.+.|++.+-++..|-|+|+ ||. .+ ...+.++|.+..
T Consensus 54 ~~~~i~e~i~~~~~~~~~P~ii~I-P~~-------~~-~~~i~~~v~raI 94 (100)
T PRK02228 54 DLEKLPRRLRRTLEESVEPTVVTL-GGG-------GG-SGGLREKIKRAI 94 (100)
T ss_pred HhHhhHHHHHHHHhcCCCCEEEEE-CCC-------cc-chHHHHHHHHHh
Confidence 778889999999999999999999 771 21 246777877754
No 3
>PF09478 CBM49: Carbohydrate binding domain CBM49; InterPro: IPR019028 A carbohydrate-binding module (CBM) is defined as a contiguous amino acid sequence within a carbohydrate-active enzyme with a discreet fold having carbohydrate-binding activity. A few exceptions are CBMs in cellulosomal scaffolding proteins and rare instances of independent putative CBMs. The requirement of CBMs existing as modules within larger enzymes sets this class of carbohydrate-binding protein apart from other non-catalytic sugar binding proteins such as lectins and sugar transport proteins. CBMs were previously classified as cellulose-binding domains (CBDs) based on the initial discovery of several modules that bound cellulose [, ]. However, additional modules in carbohydrate-active enzymes are continually being found that bind carbohydrates other than cellulose yet otherwise meet the CBM criteria, hence the need to reclassify these polypeptides using more inclusive terminology. Previous classification of cellulose-binding domains were based on amino acid similarity. Groupings of CBDs were called "Types" and numbered with roman numerals (e.g. Type I or Type II CBDs). In keeping with the glycoside hydrolase classification, these groupings are now called families and numbered with Arabic numerals. Families 1 to 13 are the same as Types I to XIII. For a detailed review on the structure and binding modes of CBMs see []. This domain is found at the C-terminal of cellulases and in vitro binding studies have shown it to binds to crystalline cellulose []. ; GO: 0030246 carbohydrate binding, 0005576 extracellular region
Probab=26.74 E-value=32 Score=23.85 Aligned_cols=14 Identities=29% Similarity=0.752 Sum_probs=12.1
Q ss_pred cCCCcc-cCCCCCcc
Q 031396 78 SAPDWL-PFLPGSSY 91 (160)
Q Consensus 78 AaPDWL-PF~PGsSy 91 (160)
..|+|+ ++.||.+|
T Consensus 59 ~lPs~~~~i~pg~s~ 73 (80)
T PF09478_consen 59 TLPSYQPTIKPGQSF 73 (80)
T ss_pred ECCccccccCCCCEE
Confidence 469998 99999987
No 4
>PF07621 DUF1582: Protein of unknown function (DUF1582); InterPro: IPR011476 This is a family of hypothetical proteins found in Rhodopirellula baltica.
Probab=25.66 E-value=39 Score=21.05 Aligned_cols=17 Identities=18% Similarity=0.444 Sum_probs=14.3
Q ss_pred cCCCCccccccCCCCcc
Q 031396 126 RGWPSSDYYIKGKPLHK 142 (160)
Q Consensus 126 RGWPss~YFi~G~~p~~ 142 (160)
|+|||+.+-.+-.+++.
T Consensus 1 R~lpsp~~l~~~ri~~~ 17 (29)
T PF07621_consen 1 RALPSPEFLLEARISTL 17 (29)
T ss_pred CCcCCCCcChhhhcCCC
Confidence 79999999888877764
No 5
>PF14475 Mso1_Sec1_bdg: Sec1-binding region of Mso1
Probab=25.43 E-value=54 Score=21.74 Aligned_cols=25 Identities=36% Similarity=0.900 Sum_probs=14.9
Q ss_pred eecCCCCCchHHHHHHHHHHHHHHh------hcCCCcc
Q 031396 52 ETSGSSSTDPLISKLEDAIHRIIVR------RSAPDWL 83 (160)
Q Consensus 52 Eid~~ss~d~~irRLEdaIh~i~vr------~AaPDWL 83 (160)
|-|+++..|- .||+++|+ +.-|+||
T Consensus 11 E~DGdteddT-------~v~r~l~~yY~~k~~~~P~WL 41 (41)
T PF14475_consen 11 ESDGDTEDDT-------HVHRVLRKYYTEKGRPFPGWL 41 (41)
T ss_pred ccCCCCcchh-------HHHHHHHHHHHHcCCCCCCcC
Confidence 4355555554 35666654 6778997
No 6
>TIGR01644 phage_P2_V phage baseplate assembly protein V. This model describes a family of phage (and bacteriocin) proteins related to the phage P2 V gene product, which forms the small spike at the tip of the tail. Homologs in general are annotated as baseplate assembly protein V. At least one member is encoded within a region of Pectobacterium carotovorum (Erwinia carotovora) described as a bacteriocin, a phage tail-derived module able to kill bacteria closely related to the host strain.
Probab=21.95 E-value=67 Score=25.37 Aligned_cols=20 Identities=25% Similarity=0.675 Sum_probs=12.6
Q ss_pred CCCcccCCCCC----ccccCCCCC
Q 031396 79 APDWLPFLPGS----SYWVPPPKS 98 (160)
Q Consensus 79 aPDWLPF~PGs----SyWVPP~~~ 98 (160)
.=+|||+.-.. .+|-||..+
T Consensus 32 ~t~wl~~~~~~ag~~~~~~~P~vG 55 (191)
T TIGR01644 32 LTGWLPWDVERAGNYRHWSAPSPG 55 (191)
T ss_pred cccchhhhhHhhCCCceEcCCCCC
Confidence 34699987432 367777654
No 7
>PF07999 RHSP: Retrotransposon hot spot protein; InterPro: IPR006518 These sequences are full-length and part-length members of the RHS (retrotransposon hot spot) family in Trypanosoma brucei and Trypanosoma cruzi. Members of this family are frequently interrupted by non-LTR retrotransposons inserted at exactly the same relative position.
Probab=20.48 E-value=44 Score=30.79 Aligned_cols=17 Identities=18% Similarity=0.569 Sum_probs=14.7
Q ss_pred cccccccccCCCCcccc
Q 031396 118 QSLSTSTVRGWPSSDYY 134 (160)
Q Consensus 118 Eals~st~RGWPss~YF 134 (160)
|.+++||-.|||..-|=
T Consensus 59 ~l~VLtS~~GWPy~~f~ 75 (439)
T PF07999_consen 59 ELMVLTSEKGWPYTWFD 75 (439)
T ss_pred EEEEEEcCCCCCCcccc
Confidence 68899999999998653
No 8
>PF09535 Gmx_para_CXXCG: Protein of unknown function (Gmx_para_CXXCG); InterPro: IPR011750 This entry consists of at least 10 paralogous proteins from Myxococcus xanthus that lack detectable sequence similarity to any other protein family. An imperfectly conserved CXXCG motif, a probable binding site, appears twice in the multiple sequence alignment.
Probab=19.18 E-value=70 Score=28.05 Aligned_cols=20 Identities=40% Similarity=0.697 Sum_probs=17.7
Q ss_pred HHHHhhcCCCcccCCCCCcc
Q 031396 72 RIIVRRSAPDWLPFLPGSSY 91 (160)
Q Consensus 72 ~i~vr~AaPDWLPF~PGsSy 91 (160)
+-+||--+|.|++..||+.|
T Consensus 74 relVRP~~Ppga~l~PGt~f 93 (237)
T PF09535_consen 74 RELVRPLAPPGAPLEPGTQF 93 (237)
T ss_pred HHHhcccCCCCCcCCCCCcc
Confidence 45688899999999999997
No 9
>cd08049 TAF8 TATA Binding Protein (TBP) Associated Factor 8. The TATA Binding Protein (TBP) Associated Factor 8 (TAF8) is one of several TAFs that bind TBP, and is involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and the assembly of the preinitiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs' functions, such as serving as activator-binding sites, involvement in the core-promo
Probab=17.66 E-value=65 Score=21.35 Aligned_cols=15 Identities=33% Similarity=0.882 Sum_probs=11.2
Q ss_pred CCCcccCCCCCcccc
Q 031396 79 APDWLPFLPGSSYWV 93 (160)
Q Consensus 79 aPDWLPF~PGsSyWV 93 (160)
-|+|||=-|+.==|+
T Consensus 3 IP~~LP~FP~~HTY~ 17 (54)
T cd08049 3 IPSWLPPFPDPHTYK 17 (54)
T ss_pred CCcCCCCCCCchhhc
Confidence 389999888865444
No 10
>KOG2317 consensus Putative translation initiation inhibitor UK114/IBM1 [Translation, ribosomal structure and biogenesis]
Probab=15.75 E-value=47 Score=26.66 Aligned_cols=13 Identities=31% Similarity=0.670 Sum_probs=10.6
Q ss_pred CCCCccccCCCCC
Q 031396 86 LPGSSYWVPPPKS 98 (160)
Q Consensus 86 ~PGsSyWVPP~~~ 98 (160)
++|.|||.|+-.+
T Consensus 8 v~v~S~~Ap~~ig 20 (138)
T KOG2317|consen 8 VQVISYWAPANIG 20 (138)
T ss_pred EEEeeccCCCCcC
Confidence 6899999997643
Done!