Query psy17078
Match_columns 68
No_of_seqs 120 out of 464
Neff 5.9
Searched_HMMs 46136
Date Fri Aug 16 21:17:49 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17078.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17078hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK11573 hypothetical protein; 99.2 1.4E-11 3.1E-16 90.6 3.6 60 2-66 156-215 (413)
2 TIGR03520 GldE gliding motilit 99.2 2.4E-11 5.3E-16 89.1 3.8 61 2-66 159-219 (408)
3 PRK15094 magnesium/cobalt effl 99.1 3.2E-11 6.9E-16 85.4 2.6 58 2-61 34-91 (292)
4 KOG2118|consensus 99.1 3E-11 6.5E-16 91.2 0.5 66 2-67 168-234 (498)
5 COG1253 TlyC Hemolysins and re 99.0 2.3E-10 5E-15 84.2 4.2 46 13-58 182-227 (429)
6 COG4536 CorB Putative Mg2+ and 98.9 3.9E-10 8.5E-15 83.7 1.4 57 2-60 167-223 (423)
7 COG4535 CorC Putative Mg2+ and 98.2 1.7E-07 3.7E-12 66.8 -0.3 50 12-61 42-91 (293)
8 TIGR00400 mgtE Mg2+ transporte 94.6 0.029 6.4E-07 41.8 2.6 41 18-60 112-152 (449)
9 cd07178 terB_like_YebE telluri 57.2 6.5 0.00014 23.6 1.2 27 5-33 3-29 (95)
10 PF00571 CBS: CBS domain CBS d 55.3 3 6.5E-05 21.5 -0.5 20 39-60 1-20 (57)
11 PF04504 DUF573: Protein of un 50.8 7.3 0.00016 23.7 0.7 19 21-39 9-27 (98)
12 TIGR01302 IMP_dehydrog inosine 50.6 13 0.00029 27.9 2.2 48 4-60 49-101 (450)
13 COG4109 Predicted transcriptio 44.7 7 0.00015 29.9 -0.1 34 25-58 171-209 (432)
14 PF08899 DUF1844: Domain of un 43.8 22 0.00048 20.9 2.0 16 17-32 52-67 (74)
15 PF04545 Sigma70_r4: Sigma-70, 33.5 36 0.00079 17.3 1.7 23 19-42 4-26 (50)
16 COG5208 HAP5 CCAAT-binding fac 30.2 27 0.00059 25.1 1.0 45 23-67 99-143 (286)
17 PRK10892 D-arabinose 5-phospha 28.9 21 0.00046 25.0 0.3 27 35-61 200-226 (326)
18 PF02318 FYVE_2: FYVE-type zin 28.1 39 0.00085 20.8 1.4 15 19-33 2-16 (118)
19 PRK05974 phosphoribosylformylg 26.0 1.4E+02 0.003 17.1 4.4 53 12-66 6-61 (80)
20 PF04391 DUF533: Protein of un 25.2 44 0.00096 22.7 1.3 20 15-34 91-110 (188)
21 PF00036 EF-hand_1: EF hand; 24.5 40 0.00086 15.9 0.7 21 5-25 2-22 (29)
22 cd04801 CBS_pair_M50_like This 24.0 38 0.00083 19.1 0.7 25 36-60 56-80 (114)
23 PF14513 DAG_kinase_N: Diacylg 23.4 38 0.00083 22.0 0.7 30 16-45 4-33 (138)
24 PRK07107 inosine 5-monophospha 22.7 36 0.00079 26.2 0.6 27 34-60 158-184 (502)
25 PTZ00314 inosine-5'-monophosph 21.9 36 0.00079 26.1 0.4 26 35-60 157-182 (495)
26 smart00054 EFh EF-hand, calciu 21.3 62 0.0013 12.9 1.0 10 15-24 12-21 (29)
No 1
>PRK11573 hypothetical protein; Provisional
Probab=99.19 E-value=1.4e-11 Score=90.62 Aligned_cols=60 Identities=13% Similarity=0.338 Sum_probs=50.4
Q ss_pred hhhhcccceecccCCCccCCHhHHHHHHhhhccCcceeccceeecccEEEeeCCCCCCHHHHHHh
Q psy17078 2 KKKFKTGIPMEATSNLVALKKDEVNIISGALEMTQKKVEEIMTKLDDCYMLDIETILNFTVISEI 66 (68)
Q Consensus 2 k~elk~Lv~lh~~~~~g~l~~~E~~mi~g~lel~~~~V~diMtPr~~V~~L~~d~~l~~~t~~~I 66 (68)
++||+.+++.+. +.++++|++||+|+|+|++++|+||||||.+|++++.+++++ +.+..+
T Consensus 156 ~eEl~~lv~~~~----~~l~~~e~~mi~~vl~l~~~~v~eiMtPr~~i~~l~~~~~~~-e~~~~~ 215 (413)
T PRK11573 156 KEELRTIVHESR----SQISRRNQDMLLSVLDLEKVTVDDIMVPRNEIVGIDINDDWK-SILRQL 215 (413)
T ss_pred HHHHHHHHHHHh----hhcCHHHHHHHHHHhccCCCChhhcCCccceEEEEECCCCHH-HHHHHH
Confidence 468888887543 259999999999999999999999999999999999999984 444443
No 2
>TIGR03520 GldE gliding motility-associated protein GldE. Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldC is a protein linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. GldE was discovered because of its adjacency to GldD in F. johnsonii. Overexpression of GldE partially supresses the effects of a GldB point mutant suggesting that GldB and GldE interact. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. Not all Bacteroidetes with members of this protein family appear to have all of the genes associated with gliding motility and in fact some do not appear to express the gliding phenotype.
Probab=99.16 E-value=2.4e-11 Score=89.15 Aligned_cols=61 Identities=21% Similarity=0.393 Sum_probs=50.6
Q ss_pred hhhhcccceecccCCCccCCHhHHHHHHhhhccCcceeccceeecccEEEeeCCCCCCHHHHHHh
Q psy17078 2 KKKFKTGIPMEATSNLVALKKDEVNIISGALEMTQKKVEEIMTKLDDCYMLDIETILNFTVISEI 66 (68)
Q Consensus 2 k~elk~Lv~lh~~~~~g~l~~~E~~mi~g~lel~~~~V~diMtPr~~V~~L~~d~~l~~~t~~~I 66 (68)
+.|++.+++.. .++| +.++|++||+|+|+|++++|+||||||.+|++++.+++++ +.++.+
T Consensus 159 ~eEl~~lv~~~--~~~g-~~~~E~~~i~~vl~l~~~~v~diMtpr~~v~~l~~~~~~~-e~~~~~ 219 (408)
T TIGR03520 159 VDQLSQALELT--DEED-TTKEEQKILQGIVSFGNTDTKQVMRPRLDIFALDIETSFS-EIIPKI 219 (408)
T ss_pred HHHHHHHHHhH--hhcC-CChHHHHHHHHHhccCCCEeeeeCCchHhEEEEECCCCHH-HHHHHH
Confidence 46788888754 3345 6899999999999999999999999999999999999984 454444
No 3
>PRK15094 magnesium/cobalt efflux protein CorC; Provisional
Probab=99.12 E-value=3.2e-11 Score=85.38 Aligned_cols=58 Identities=14% Similarity=0.265 Sum_probs=51.7
Q ss_pred hhhhcccceecccCCCccCCHhHHHHHHhhhccCcceeccceeecccEEEeeCCCCCCHH
Q psy17078 2 KKKFKTGIPMEATSNLVALKKDEVNIISGALEMTQKKVEEIMTKLDDCYMLDIETILNFT 61 (68)
Q Consensus 2 k~elk~Lv~lh~~~~~g~l~~~E~~mi~g~lel~~~~V~diMtPr~~V~~L~~d~~l~~~ 61 (68)
+.||+.|+.. +.++|.|+++|+.||+|+|+|++++|++|||||.++++++.++++.+.
T Consensus 34 ~eEl~~l~~~--~~~~g~l~~~e~~~i~~vl~l~~~~V~diMtpr~~i~~l~~~~sl~e~ 91 (292)
T PRK15094 34 RDELLALIRD--SEQNDLIDEDTRDMLEGVMDIADQRVRDIMIPRSQMITLKRNQTLDEC 91 (292)
T ss_pred HHHHHHHHHh--HhhcCCCCHHHHHHHHHHhccCCCEEeEEccchHHEEEEeCCCCHHHH
Confidence 4688888874 345688999999999999999999999999999999999999998753
No 4
>KOG2118|consensus
Probab=99.06 E-value=3e-11 Score=91.25 Aligned_cols=66 Identities=35% Similarity=0.499 Sum_probs=61.9
Q ss_pred hhhhcccceecccCCC-ccCCHhHHHHHHhhhccCcceeccceeecccEEEeeCCCCCCHHHHHHhh
Q psy17078 2 KKKFKTGIPMEATSNL-VALKKDEVNIISGALEMTQKKVEEIMTKLDDCYMLDIETILNFTVISEIV 67 (68)
Q Consensus 2 k~elk~Lv~lh~~~~~-g~l~~~E~~mi~g~lel~~~~V~diMtPr~~V~~L~~d~~l~~~t~~~I~ 67 (68)
.+++++||.+|..... |.+..+|..|+.|+++|.+++|+|||||++++|+++.+..++.+++.+|.
T Consensus 168 ~~~l~~lv~~~~~e~~~g~~~~~e~~ii~g~l~l~ek~~~evmtpi~~~f~l~~n~~l~~~~~~~i~ 234 (498)
T KOG2118|consen 168 RASLLALVQLVGNEAGKGDLTYDELTIITGALELTEKLVGEVMTPIEDVFALDANTKLDRETVGEIV 234 (498)
T ss_pred hHHHHHHHHHHhcccccCcccchhhhHhhhhHHHHHHHHHHhccchhhheeeccccccchHHHhhHh
Confidence 3689999999988666 89999999999999999999999999999999999999999999998875
No 5
>COG1253 TlyC Hemolysins and related proteins containing CBS domains [General function prediction only]
Probab=99.03 E-value=2.3e-10 Score=84.19 Aligned_cols=46 Identities=26% Similarity=0.436 Sum_probs=41.5
Q ss_pred ccCCCccCCHhHHHHHHhhhccCcceeccceeecccEEEeeCCCCC
Q psy17078 13 ATSNLVALKKDEVNIISGALEMTQKKVEEIMTKLDDCYMLDIETIL 58 (68)
Q Consensus 13 ~~~~~g~l~~~E~~mi~g~lel~~~~V~diMtPr~~V~~L~~d~~l 58 (68)
.+.+.|.++++|+.||+|+|+|++++|++|||||.+|++++.+.+.
T Consensus 182 ~~~~~g~~~~~E~~mi~~v~~l~~~~v~eiMtPR~~i~~l~~~~~~ 227 (429)
T COG1253 182 ESAEEGVLEEEEREMINNVLDLDDRTVREIMTPRTDIVALDLTDTV 227 (429)
T ss_pred hHHhcCCcCHHHHHHHHHHhccCCcEeeeEeeecccEEEEcCCCCH
Confidence 3456899999999999999999999999999999999999995553
No 6
>COG4536 CorB Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]
Probab=98.91 E-value=3.9e-10 Score=83.73 Aligned_cols=57 Identities=18% Similarity=0.307 Sum_probs=50.0
Q ss_pred hhhhcccceecccCCCccCCHhHHHHHHhhhccCcceeccceeecccEEEeeCCCCCCH
Q psy17078 2 KKKFKTGIPMEATSNLVALKKDEVNIISGALEMTQKKVEEIMTKLDDCYMLDIETILNF 60 (68)
Q Consensus 2 k~elk~Lv~lh~~~~~g~l~~~E~~mi~g~lel~~~~V~diMtPr~~V~~L~~d~~l~~ 60 (68)
+.||+..|+.+ +.+|...+++++||.|+|||.+.||.||||||.+|.++++|.+++.
T Consensus 167 ~EElR~~v~~~--~~e~~~~~~~rdmL~gvLDLe~~tV~DIMvpR~~i~~id~d~~~e~ 223 (423)
T COG4536 167 KEELRTAVNES--GSEGSVNKIDRDMLLGVLDLENLTVSDIMVPRNEIIGIDIDDPWEE 223 (423)
T ss_pred HHHHHHHHHHh--hcccccccccHHHHhcccccccceeeeeeccccceeeecCCCCHHH
Confidence 56888888855 4457777889999999999999999999999999999999998753
No 7
>COG4535 CorC Putative Mg2+ and Co2+ transporter CorC [Inorganic ion transport and metabolism]
Probab=98.25 E-value=1.7e-07 Score=66.83 Aligned_cols=50 Identities=14% Similarity=0.302 Sum_probs=44.6
Q ss_pred cccCCCccCCHhHHHHHHhhhccCcceeccceeecccEEEeeCCCCCCHH
Q psy17078 12 EATSNLVALKKDEVNIISGALEMTQKKVEEIMTKLDDCYMLDIETILNFT 61 (68)
Q Consensus 12 h~~~~~g~l~~~E~~mi~g~lel~~~~V~diMtPr~~V~~L~~d~~l~~~ 61 (68)
+.++.++-+.++.+.||.|++++++.+|+|||+||.++..|..+..+++=
T Consensus 42 Rdse~n~LiD~dt~~mlEGvm~iadl~vrDiMIPRSQM~~l~~~~~l~~~ 91 (293)
T COG4535 42 RDSEQNELIDADTLDMLEGVMDIADLRVRDIMIPRSQMITLKRNQTLDEC 91 (293)
T ss_pred HHhhhccccChhHHHHHHHHHHHHHhhHhhhcccHHHheeccccCCHHHH
Confidence 34556778999999999999999999999999999999999999887753
No 8
>TIGR00400 mgtE Mg2+ transporter (mgtE). This family of prokaryotic proteins models a class of Mg++ transporter first described in Bacillus firmus. May form a homodimer.
Probab=94.58 E-value=0.029 Score=41.78 Aligned_cols=41 Identities=17% Similarity=0.146 Sum_probs=35.7
Q ss_pred ccCCHhHHHHHHhhhccCcceeccceeecccEEEeeCCCCCCH
Q psy17078 18 VALKKDEVNIISGALEMTQKKVEEIMTKLDDCYMLDIETILNF 60 (68)
Q Consensus 18 g~l~~~E~~mi~g~lel~~~~V~diMtPr~~V~~L~~d~~l~~ 60 (68)
+.++++|++.+.+++++.+.+|+++|+ .++.+++.+.++.+
T Consensus 112 ~~l~~~er~~i~~ll~~~e~tvg~iMt--~~~~~v~~~~tv~e 152 (449)
T TIGR00400 112 ASSTEEERKAINLLLSYSDDSAGRIMT--IEYVELKEDYTVGK 152 (449)
T ss_pred HcCCHHHHHHHHHHhCCCcchHHHhCc--CceEEECCCCcHHH
Confidence 468999999999999999999999999 47888888876654
No 9
>cd07178 terB_like_YebE tellurium resistance terB-like protein, subgroup 3. This family includes several uncharacterized bacterial proteins including an Escherichia coli protein called YebE. Protein sequence homology analysis shows they are similar to tellurium resistance protein terB, but the function of this family is unknown.
Probab=57.15 E-value=6.5 Score=23.62 Aligned_cols=27 Identities=19% Similarity=0.143 Sum_probs=20.0
Q ss_pred hcccceecccCCCccCCHhHHHHHHhhhc
Q psy17078 5 FKTGIPMEATSNLVALKKDEVNIISGALE 33 (68)
Q Consensus 5 lk~Lv~lh~~~~~g~l~~~E~~mi~g~le 33 (68)
|++++..-. ..|.++++|+..|.+.++
T Consensus 3 lrami~aAk--ADG~id~~E~~~I~~~~~ 29 (95)
T cd07178 3 LRAMIAAAK--ADGHIDEAERARILGELG 29 (95)
T ss_pred HHHHHHHHH--hcCCCCHHHHHHHHHHHH
Confidence 455666444 358899999999998875
No 10
>PF00571 CBS: CBS domain CBS domain web page. Mutations in the CBS domain of Swiss:P35520 lead to homocystinuria.; InterPro: IPR000644 CBS (cystathionine-beta-synthase) domains are small intracellular modules, mostly found in two or four copies within a protein, that occur in a variety of proteins in bacteria, archaea, and eukaryotes [, ]. Tandem pairs of CBS domains can act as binding domains for adenosine derivatives and may regulate the activity of attached enzymatic or other domains []. In some cases, CBS domains may act as sensors of cellular energy status by being activated by AMP and inhibited by ATP []. In chloride ion channels, the CBS domains have been implicated in intracellular targeting and trafficking, as well as in protein-protein interactions, but results vary with different channels: in the CLC-5 channel, the CBS domain was shown to be required for trafficking [], while in the CLC-1 channel, the CBS domain was shown to be critical for channel function, but not necessary for trafficking []. Recent experiments revealing that CBS domains can bind adenosine-containing ligands such ATP, AMP, or S-adenosylmethionine have led to the hypothesis that CBS domains function as sensors of intracellular metabolites [, ]. Crystallographic studies of CBS domains have shown that pairs of CBS sequences form a globular domain where each CBS unit adopts a beta-alpha-beta-beta-alpha pattern []. Crystal structure of the CBS domains of the AMP-activated protein kinase in complexes with AMP and ATP shows that the phosphate groups of AMP/ATP lie in a surface pocket at the interface of two CBS domains, which is lined with basic residues, many of which are associated with disease-causing mutations []. In humans, mutations in conserved residues within CBS domains cause a variety of human hereditary diseases, including (with the gene mutated in parentheses): homocystinuria (cystathionine beta-synthase); Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase); retinitis pigmentosa (IMP dehydrogenase-1); congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members).; GO: 0005515 protein binding; PDB: 3JTF_A 3TE5_C 3TDH_C 3T4N_C 2QLV_C 3OI8_A 3LV9_A 2QH1_B 1PVM_B 3LQN_A ....
Probab=55.31 E-value=3 Score=21.45 Aligned_cols=20 Identities=25% Similarity=0.202 Sum_probs=15.8
Q ss_pred eccceeecccEEEeeCCCCCCH
Q psy17078 39 VEEIMTKLDDCYMLDIETILNF 60 (68)
Q Consensus 39 V~diMtPr~~V~~L~~d~~l~~ 60 (68)
|+++|+| ++..++.++++.+
T Consensus 1 v~~~m~~--~~~~v~~~~~l~~ 20 (57)
T PF00571_consen 1 VGDIMTP--PPITVSPDDSLEE 20 (57)
T ss_dssp HHHHSBS--SSEEEETTSBHHH
T ss_pred CeECCcC--CCEEEcCcCcHHH
Confidence 5788998 8888888877644
No 11
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=50.76 E-value=7.3 Score=23.67 Aligned_cols=19 Identities=26% Similarity=0.539 Sum_probs=15.6
Q ss_pred CHhHHHHHHhhhccCccee
Q psy17078 21 KKDEVNIISGALEMTQKKV 39 (68)
Q Consensus 21 ~~~E~~mi~g~lel~~~~V 39 (68)
++||..||+|++++..++=
T Consensus 9 ~eDEi~iL~gl~~~~~~~G 27 (98)
T PF04504_consen 9 EEDEIVILQGLIDFRAKTG 27 (98)
T ss_pred chHHHHHHHHHHHHHHhcC
Confidence 5799999999999965543
No 12
>TIGR01302 IMP_dehydrog inosine-5'-monophosphate dehydrogenase. This model describes a rather tightly conserved cluster of IMP dehydrogenase sequences, many of which are characterized. The model excludes two related families of proteins proposed also to be IMP dehydrogenases, but without characterized members. These are related families are the subject of separate models.
Probab=50.58 E-value=13 Score=27.85 Aligned_cols=48 Identities=6% Similarity=0.138 Sum_probs=32.6
Q ss_pred hhcccceecccCCCccCCH-----hHHHHHHhhhccCcceeccceeecccEEEeeCCCCCCH
Q psy17078 4 KFKTGIPMEATSNLVALKK-----DEVNIISGALEMTQKKVEEIMTKLDDCYMLDIETILNF 60 (68)
Q Consensus 4 elk~Lv~lh~~~~~g~l~~-----~E~~mi~g~lel~~~~V~diMtPr~~V~~L~~d~~l~~ 60 (68)
|+...+. ..+..|.|++ +|.+++++++++++..+. +++.++.+.++.+
T Consensus 49 ema~~ma--~~gg~GvI~~n~~~e~q~~~V~~Vk~~~~~~~~-------~~vtl~~~~tv~e 101 (450)
T TIGR01302 49 RMAIAMA--REGGIGVIHRNMSIEEQAEQVKRVKRAENGIIS-------DPVTISPETTVAD 101 (450)
T ss_pred HHHHHHH--hcCCCceeecCCCHHHHHHHHhhhccccCceec-------CceEeCCCCCHHH
Confidence 4444433 3345778884 899999999988876544 5677777766554
No 13
>COG4109 Predicted transcriptional regulator containing CBS domains [Transcription]
Probab=44.66 E-value=7 Score=29.86 Aligned_cols=34 Identities=32% Similarity=0.384 Sum_probs=25.0
Q ss_pred HHHHHhhhc-----cCcceeccceeecccEEEeeCCCCC
Q psy17078 25 VNIISGALE-----MTQKKVEEIMTKLDDCYMLDIETIL 58 (68)
Q Consensus 25 ~~mi~g~le-----l~~~~V~diMtPr~~V~~L~~d~~l 58 (68)
.+||..||. =.=++|+|||+|.++-..|..++..
T Consensus 171 AtmIN~Al~n~lIKkdI~~Vedi~~P~~~~~yL~~~d~v 209 (432)
T COG4109 171 ATMINKALSNQLIKKDIITVEDIMTPLEDTSYLRETDTV 209 (432)
T ss_pred HHHHHHHHHHhhhhhheeeHHHhccccccceeccccccH
Confidence 466666653 2336899999999999888776654
No 14
>PF08899 DUF1844: Domain of unknown function (DUF1844); InterPro: IPR014995 This group of proteins are functionally uncharacterised.
Probab=43.78 E-value=22 Score=20.92 Aligned_cols=16 Identities=25% Similarity=0.362 Sum_probs=14.5
Q ss_pred CccCCHhHHHHHHhhh
Q psy17078 17 LVALKKDEVNIISGAL 32 (68)
Q Consensus 17 ~g~l~~~E~~mi~g~l 32 (68)
.|.|+.+|.++|.++|
T Consensus 52 kGNL~~~E~~lL~~~L 67 (74)
T PF08899_consen 52 KGNLDEEEERLLESAL 67 (74)
T ss_pred ccCCCHHHHHHHHHHH
Confidence 6789999999999987
No 15
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=33.49 E-value=36 Score=17.35 Aligned_cols=23 Identities=26% Similarity=0.265 Sum_probs=14.8
Q ss_pred cCCHhHHHHHHhhhccCcceeccc
Q psy17078 19 ALKKDEVNIISGALEMTQKKVEEI 42 (68)
Q Consensus 19 ~l~~~E~~mi~g~lel~~~~V~di 42 (68)
.|++.|+.+|.-.+ +.+.|..+|
T Consensus 4 ~L~~~er~vi~~~y-~~~~t~~eI 26 (50)
T PF04545_consen 4 QLPPREREVIRLRY-FEGLTLEEI 26 (50)
T ss_dssp TS-HHHHHHHHHHH-TST-SHHHH
T ss_pred hCCHHHHHHHHHHh-cCCCCHHHH
Confidence 47888888888777 556555543
No 16
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=30.24 E-value=27 Score=25.08 Aligned_cols=45 Identities=22% Similarity=0.383 Sum_probs=37.3
Q ss_pred hHHHHHHhhhccCcceeccceeecccEEEeeCCCCCCHHHHHHhh
Q psy17078 23 DEVNIISGALEMTQKKVEEIMTKLDDCYMLDIETILNFTVISEIV 67 (68)
Q Consensus 23 ~E~~mi~g~lel~~~~V~diMtPr~~V~~L~~d~~l~~~t~~~I~ 67 (68)
+|++++..-..|.-..++.||---++|-||+++.|+=+.-+.+|+
T Consensus 99 ~~~q~~~k~h~LPlARIkkvMKtdedVkMisaEaPvlFak~~EiF 143 (286)
T COG5208 99 EERQILLKDHNLPLARIKKVMKTDEDVKMISAEAPVLFAKITEIF 143 (286)
T ss_pred HhHHHHHHhccCcHHHHHHHHhcccchhheecccchHHHHHHHHH
Confidence 344566666677777889999999999999999999998888875
No 17
>PRK10892 D-arabinose 5-phosphate isomerase; Provisional
Probab=28.86 E-value=21 Score=25.02 Aligned_cols=27 Identities=19% Similarity=0.112 Sum_probs=22.8
Q ss_pred CcceeccceeecccEEEeeCCCCCCHH
Q psy17078 35 TQKKVEEIMTKLDDCYMLDIETILNFT 61 (68)
Q Consensus 35 ~~~~V~diMtPr~~V~~L~~d~~l~~~ 61 (68)
...+|+|+|++..++..++.++++...
T Consensus 200 ~~~~V~dim~~~~~~~~v~~~~sl~~a 226 (326)
T PRK10892 200 LLLRVSDIMHTGDEIPHVSKTASLRDA 226 (326)
T ss_pred ccCcHHHHhCCCCCCeEECCCCCHHHH
Confidence 677899999987788999999888754
No 18
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=28.15 E-value=39 Score=20.79 Aligned_cols=15 Identities=33% Similarity=0.454 Sum_probs=11.7
Q ss_pred cCCHhHHHHHHhhhc
Q psy17078 19 ALKKDEVNIISGALE 33 (68)
Q Consensus 19 ~l~~~E~~mi~g~le 33 (68)
.|+++|+++|.++|.
T Consensus 2 ~Lt~eE~~~I~~Vl~ 16 (118)
T PF02318_consen 2 HLTEEEREIILQVLQ 16 (118)
T ss_dssp TS-CHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHH
Confidence 488899999998874
No 19
>PRK05974 phosphoribosylformylglycinamidine synthase subunit PurS; Reviewed
Probab=25.98 E-value=1.4e+02 Score=17.10 Aligned_cols=53 Identities=15% Similarity=0.115 Sum_probs=35.3
Q ss_pred cccCCCccCCHhHHHHHHhhhccCcceeccceeecccEEEeeCCC---CCCHHHHHHh
Q psy17078 12 EATSNLVALKKDEVNIISGALEMTQKKVEEIMTKLDDCYMLDIET---ILNFTVISEI 66 (68)
Q Consensus 12 h~~~~~g~l~~~E~~mi~g~lel~~~~V~diMtPr~~V~~L~~d~---~l~~~t~~~I 66 (68)
..+-..|.+++.-..+.+.+-+|+-..|.+ +-..++|.+..+. ....+.+..|
T Consensus 6 ~V~~k~gv~Dp~G~ai~~~l~~lg~~~v~~--Vr~~k~~~l~~~~~~~~~a~~~v~~i 61 (80)
T PRK05974 6 TVTLKEGVLDPQGQAIKGALGSLGYDGVED--VRQGKYFELELEGESEEKAEADLKEM 61 (80)
T ss_pred EEEECCCCcChHHHHHHHHHHHcCCCCcce--EEEEEEEEEEEcCCchhhhHHHHHHH
Confidence 344557888888888888888776666777 5566777777544 3445555544
No 20
>PF04391 DUF533: Protein of unknown function (DUF533); InterPro: IPR007486 Some family members may be secreted or integral membrane proteins.
Probab=25.23 E-value=44 Score=22.69 Aligned_cols=20 Identities=25% Similarity=0.263 Sum_probs=15.7
Q ss_pred CCCccCCHhHHHHHHhhhcc
Q psy17078 15 SNLVALKKDEVNIISGALEM 34 (68)
Q Consensus 15 ~~~g~l~~~E~~mi~g~lel 34 (68)
...|.|+++|+..|.+.++=
T Consensus 91 kADG~ID~~Er~~I~~~l~~ 110 (188)
T PF04391_consen 91 KADGHIDEEERQRIEGALQE 110 (188)
T ss_pred HcCCCCCHHHHHHHHHHHHH
Confidence 44688999999999887653
No 21
>PF00036 EF-hand_1: EF hand; InterPro: IPR018248 Many calcium-binding proteins belong to the same evolutionary family and share a type of calcium-binding domain known as the EF-hand. This type of domain consists of a twelve residue loop flanked on both sides by a twelve residue alpha-helical domain. In an EF-hand loop the calcium ion is coordinated in a pentagonal bipyramidal configuration. The six residues involved in the binding are in positions 1, 3, 5, 7, 9 and 12; these residues are denoted by X, Y, Z, -Y, -X and -Z. The invariant Glu or Asp at position 12 provides two oxygens for liganding Ca (bidentate ligand).; PDB: 1BJF_A 1XFW_R 1XFV_O 2K0J_A 2F3Z_A 3BYA_A 1XFU_Q 2R28_B 1ZOT_B 3G43_D ....
Probab=24.53 E-value=40 Score=15.87 Aligned_cols=21 Identities=10% Similarity=-0.010 Sum_probs=12.7
Q ss_pred hcccceecccCCCccCCHhHH
Q psy17078 5 FKTGIPMEATSNLVALKKDEV 25 (68)
Q Consensus 5 lk~Lv~lh~~~~~g~l~~~E~ 25 (68)
++.....--.+..|.|+.+|-
T Consensus 2 ~~~~F~~~D~d~dG~I~~~Ef 22 (29)
T PF00036_consen 2 LKEAFREFDKDGDGKIDFEEF 22 (29)
T ss_dssp HHHHHHHHSTTSSSEEEHHHH
T ss_pred HHHHHHHHCCCCCCcCCHHHH
Confidence 334444444466888988883
No 22
>cd04801 CBS_pair_M50_like This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with the metalloprotease peptidase M50. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown.
Probab=24.01 E-value=38 Score=19.09 Aligned_cols=25 Identities=24% Similarity=0.108 Sum_probs=19.7
Q ss_pred cceeccceeecccEEEeeCCCCCCH
Q psy17078 36 QKKVEEIMTKLDDCYMLDIETILNF 60 (68)
Q Consensus 36 ~~~V~diMtPr~~V~~L~~d~~l~~ 60 (68)
+.++.++|.|...++.++.++++..
T Consensus 56 ~~~v~~~~~~~~~~~~v~~~~~l~~ 80 (114)
T cd04801 56 QTTVIQVMTPAAKLVTVLSEESLAE 80 (114)
T ss_pred ccchhhhhcccccceEECCCCcHHH
Confidence 5689999998777778888777654
No 23
>PF14513 DAG_kinase_N: Diacylglycerol kinase N-terminus; PDB: 1TUZ_A.
Probab=23.39 E-value=38 Score=21.98 Aligned_cols=30 Identities=20% Similarity=0.381 Sum_probs=19.9
Q ss_pred CCccCCHhHHHHHHhhhccCcceeccceee
Q psy17078 16 NLVALKKDEVNIISGALEMTQKKVEEIMTK 45 (68)
Q Consensus 16 ~~g~l~~~E~~mi~g~lel~~~~V~diMtP 45 (68)
+-+.|++.|-.-|+.-.+.+.++++||+.-
T Consensus 4 ~~~~lsp~eF~qLq~y~eys~kklkdvl~e 33 (138)
T PF14513_consen 4 EWVSLSPEEFAQLQKYSEYSTKKLKDVLKE 33 (138)
T ss_dssp --S-S-HHHHHHHHHHHHH----HHHHHHH
T ss_pred ceeccCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 346789999999999999999999999853
No 24
>PRK07107 inosine 5-monophosphate dehydrogenase; Validated
Probab=22.70 E-value=36 Score=26.23 Aligned_cols=27 Identities=22% Similarity=0.228 Sum_probs=22.1
Q ss_pred cCcceeccceeecccEEEeeCCCCCCH
Q psy17078 34 MTQKKVEEIMTKLDDCYMLDIETILNF 60 (68)
Q Consensus 34 l~~~~V~diMtPr~~V~~L~~d~~l~~ 60 (68)
..+.+|+++|+|..++..++.++++.+
T Consensus 158 ~~~~~V~dIMt~~~~~itv~~d~~l~e 184 (502)
T PRK07107 158 SLDTKVKDFMTPFEKLVTANEGTTLKE 184 (502)
T ss_pred CCCCCHHHHhCCCCCeEEECCCCcHHH
Confidence 456789999999888888888887755
No 25
>PTZ00314 inosine-5'-monophosphate dehydrogenase; Provisional
Probab=21.90 E-value=36 Score=26.09 Aligned_cols=26 Identities=19% Similarity=0.151 Sum_probs=21.6
Q ss_pred CcceeccceeecccEEEeeCCCCCCH
Q psy17078 35 TQKKVEEIMTKLDDCYMLDIETILNF 60 (68)
Q Consensus 35 ~~~~V~diMtPr~~V~~L~~d~~l~~ 60 (68)
.+.+|.++|+|+.++..++.++++.+
T Consensus 157 ~~~~V~diMt~~~~lvtv~~~~sl~e 182 (495)
T PTZ00314 157 KSTPVSEVMTPREKLVVGNTPISLEE 182 (495)
T ss_pred CCCCHHHhhCCcCCceEeCCCCCHHH
Confidence 35689999999999999988888754
No 26
>smart00054 EFh EF-hand, calcium binding motif. EF-hands are calcium-binding motifs that occur at least in pairs. Links between disease states and genes encoding EF-hands, particularly the S100 subclass, are emerging. Each motif consists of a 12 residue loop flanked on either side by a 12 residue alpha-helix. EF-hands undergo a conformational change unpon binding calcium ions.
Probab=21.27 E-value=62 Score=12.87 Aligned_cols=10 Identities=10% Similarity=-0.014 Sum_probs=5.9
Q ss_pred CCCccCCHhH
Q psy17078 15 SNLVALKKDE 24 (68)
Q Consensus 15 ~~~g~l~~~E 24 (68)
+..|.++.+|
T Consensus 12 ~~~g~i~~~e 21 (29)
T smart00054 12 DGDGKIDFEE 21 (29)
T ss_pred CCCCcEeHHH
Confidence 4456666666
Done!