Query 035434
Match_columns 48
No_of_seqs 15 out of 17
Neff 1.8
Searched_HMMs 46136
Date Fri Mar 29 02:57:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035434.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035434hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF15365 PNRC: Proline-rich nu 98.5 5.3E-08 1.2E-12 55.6 1.3 40 8-47 15-57 (58)
2 COG3807 Uncharacterized protei 91.7 0.072 1.6E-06 36.8 0.7 19 5-23 24-43 (171)
3 PRK11187 replication initiatio 49.4 10 0.00023 26.1 1.3 15 33-47 21-35 (182)
4 PF08100 Dimerisation: Dimeris 44.5 14 0.00029 20.2 1.1 15 33-47 35-49 (51)
5 PF14983 DUF4513: Domain of un 42.0 12 0.00025 25.2 0.7 31 10-40 29-77 (132)
6 PF03925 SeqA: SeqA protein; 41.7 14 0.00031 25.4 1.1 15 33-47 21-35 (190)
7 PF01186 Lysyl_oxidase: Lysyl 40.9 5.8 0.00013 27.6 -0.9 23 25-47 25-53 (205)
8 TIGR01745 asd_gamma aspartate- 39.5 14 0.00031 27.0 0.9 15 33-47 350-364 (366)
9 PF15148 Apolipo_F: Apolipopro 36.7 8.9 0.00019 27.0 -0.5 23 9-31 14-42 (200)
10 COG3382 Solo B3/4 domain (OB-f 36.7 19 0.0004 25.5 1.0 22 16-46 72-93 (229)
11 PF05720 Dicty_CAD: Cell-cell 32.7 19 0.00042 22.1 0.5 15 2-16 5-19 (82)
12 cd07031 RNAP_II_RPB3 RPB3 subu 30.7 26 0.00055 24.1 0.9 20 26-45 13-32 (265)
13 cd07032 RNAP_I_II_AC40 AC40 su 29.1 29 0.00063 24.7 1.0 20 26-45 13-32 (291)
14 KOG1521 RNA polymerase I and I 27.7 30 0.00066 26.1 0.9 15 31-45 63-77 (338)
15 KOG2801 Probable Rab-GAPs [Int 26.0 25 0.00055 27.6 0.3 17 7-23 85-101 (559)
16 PRK10178 D-alanyl-D-alanine di 25.5 53 0.0012 22.1 1.7 38 6-46 110-148 (184)
17 PF01427 Peptidase_M15: D-ala- 24.5 48 0.001 21.9 1.3 38 6-46 125-163 (198)
18 PRK00783 DNA-directed RNA poly 23.8 43 0.00094 22.2 1.0 15 31-45 18-32 (263)
19 PF07621 DUF1582: Protein of u 23.0 37 0.00081 17.5 0.5 19 11-29 2-23 (29)
20 PHA02682 ORF080 virion core pr 22.9 43 0.00092 24.7 0.9 12 34-45 245-256 (280)
21 PF09802 Sec66: Preprotein tra 21.4 42 0.00091 22.9 0.6 13 36-48 81-93 (190)
22 cd07030 RNAP_D D subunit of Ar 20.7 54 0.0012 21.7 1.0 14 32-45 19-32 (259)
23 PF07769 PsiF_repeat: psiF rep 20.3 30 0.00066 18.5 -0.2 11 23-33 9-19 (35)
No 1
>PF15365 PNRC: Proline-rich nuclear receptor coactivator
Probab=98.48 E-value=5.3e-08 Score=55.61 Aligned_cols=40 Identities=28% Similarity=0.321 Sum_probs=32.2
Q ss_pred cCCcccccccccccccc--ccchh-hhccCcchhHHHHHhhhc
Q 035434 8 SGDCYASGEFALRPKLI--SCNAE-AAGVDAGATDNLRRLLRL 47 (48)
Q Consensus 8 ~~~~lPlP~FSlk~K~~--~CnaE-aagvdd~atdnLRRLLRL 47 (48)
+|++||+|.|+.+++.. +|..| ....++.+|++||||||+
T Consensus 15 ~PssLP~P~f~~~~~~~~~~~~~~~~~~~~~~~T~~Lr~LL~v 57 (58)
T PF15365_consen 15 SPSSLPLPPFHWKSSPSSLSSCPESPSSDDESMTRQLRRLLKV 57 (58)
T ss_pred ChhhcCCCCcccccCccccccccccccccHHHHHHHHHHHHcc
Confidence 68899999999998663 33333 557889999999999997
No 2
>COG3807 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=91.69 E-value=0.072 Score=36.81 Aligned_cols=19 Identities=21% Similarity=0.260 Sum_probs=16.5
Q ss_pred ccccCCccccccc-cccccc
Q 035434 5 RTISGDCYASGEF-ALRPKL 23 (48)
Q Consensus 5 ~~~~~~~lPlP~F-Slk~K~ 23 (48)
-||.++-||+|+| |||++.
T Consensus 24 ~tig~sgLplPRfVSlKs~~ 43 (171)
T COG3807 24 TTIGASGLPLPRFVSLKSAE 43 (171)
T ss_pred CccCCCCCcccceEEecccc
Confidence 4788999999999 888876
No 3
>PRK11187 replication initiation regulator SeqA; Provisional
Probab=49.36 E-value=10 Score=26.11 Aligned_cols=15 Identities=53% Similarity=0.833 Sum_probs=12.2
Q ss_pred cCcchhHHHHHhhhc
Q 035434 33 VDAGATDNLRRLLRL 47 (48)
Q Consensus 33 vdd~atdnLRRLLRL 47 (48)
+-.+|-|=|||||.|
T Consensus 21 IGESASDILRRLL~l 35 (182)
T PRK11187 21 IGESASDILRRLLKL 35 (182)
T ss_pred cCCCHHHHHHHHhCC
Confidence 445688999999987
No 4
>PF08100 Dimerisation: Dimerisation domain; InterPro: IPR012967 This domain is found at the N terminus of a variety of plant O-methyltransferases. It has been shown to mediate dimerisation of these proteins [].; GO: 0008168 methyltransferase activity, 0046983 protein dimerization activity; PDB: 1ZGJ_A 1ZG3_A 1ZHF_A 1ZGA_A 2QYO_A 1KYW_A 1KYZ_A 3REO_D 1FPX_A 1FP2_A ....
Probab=44.52 E-value=14 Score=20.19 Aligned_cols=15 Identities=33% Similarity=0.539 Sum_probs=11.3
Q ss_pred cCcchhHHHHHhhhc
Q 035434 33 VDAGATDNLRRLLRL 47 (48)
Q Consensus 33 vdd~atdnLRRLLRL 47 (48)
.+..+.+.|+|+||+
T Consensus 35 ~~p~~~~~L~RimR~ 49 (51)
T PF08100_consen 35 SNPSAPPMLDRIMRL 49 (51)
T ss_dssp T-TTHHHHHHHHHHH
T ss_pred CCcchHHHHHHHHHH
Confidence 445678899999995
No 5
>PF14983 DUF4513: Domain of unknown function (DUF4513)
Probab=41.98 E-value=12 Score=25.17 Aligned_cols=31 Identities=26% Similarity=0.389 Sum_probs=22.3
Q ss_pred Ccccccccccccccc------------------ccchhhhccCcchhHH
Q 035434 10 DCYASGEFALRPKLI------------------SCNAEAAGVDAGATDN 40 (48)
Q Consensus 10 ~~lPlP~FSlk~K~~------------------~CnaEaagvdd~atdn 40 (48)
+..-+|+||++-..| -=|||++|+-.|.-++
T Consensus 29 ~~iHlPrFS~~~~~IPrrYVmpWK~dMkfR~~nlK~ae~~GIy~GPlee 77 (132)
T PF14983_consen 29 EEIHLPRFSLKQGMIPRRYVMPWKEDMKFRNVNLKNAELCGIYTGPLEE 77 (132)
T ss_pred cccccchhhhhcCCCcccccCchhhhhhhhHHhhhhhhhcccccCCchh
Confidence 345689999876554 4578899998877553
No 6
>PF03925 SeqA: SeqA protein; InterPro: IPR005621 The binding of SeqA protein to hemimethylated GATC sequences is important in the negative modulation of chromosomal initiation at oriC, and in the formation of SeqA foci necessary for Escherichia coli chromosome segregation []. SeqA tetramers are able to aggregate or multimerize in a reversible, concentration-dependent manner []. Apart from its function in the control of DNA replication, SeqA may also be a specific transcription factor []. The C-terminal domain binds DNA, binding to fully methylated and hemimethylated GATC sequences at oriC. The structure of the C-terminal domain consists of seven alpha-helices and three-stranded beta-sheet.; GO: 0003677 DNA binding, 0032297 negative regulation of DNA-dependent DNA replication initiation; PDB: 3FMT_A 1J3E_A 1XRX_D 1IU3_C 1LRR_D.
Probab=41.72 E-value=14 Score=25.41 Aligned_cols=15 Identities=53% Similarity=0.780 Sum_probs=10.7
Q ss_pred cCcchhHHHHHhhhc
Q 035434 33 VDAGATDNLRRLLRL 47 (48)
Q Consensus 33 vdd~atdnLRRLLRL 47 (48)
+-.+|-|=|||||.|
T Consensus 21 IGESASdILRRLL~l 35 (190)
T PF03925_consen 21 IGESASDILRRLLNL 35 (190)
T ss_dssp TT--HHHHHHHHHTH
T ss_pred cCCCHHHHHHHhcCC
Confidence 345678999999976
No 7
>PF01186 Lysyl_oxidase: Lysyl oxidase ; InterPro: IPR001695 Lysyl oxidase (1.4.3.13 from EC) (LOX) [] is an extracellular copper-dependent enzyme that catalyses the oxidative deamination of peptidyl lysine residues in precursors of various collagens and elastins, yielding alpha-aminoadipic-delta-semialdehyde. The deaminated lysines are then able to form semialdehyde cross-links, resulting in the formation of insoluble collagen and elastin fibres in the extracellular matrix []. The active site of LOX resides towards the C terminus: this region also binds a single copper atom in an octahedral coordination complex involving at least 3 His residues []. Four histidine residues are clustered in a central region of the enzyme. This region is thought to be involved in cooper-binding and is called the 'copper-talon' [].; GO: 0005507 copper ion binding, 0016641 oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor, 0055114 oxidation-reduction process
Probab=40.92 E-value=5.8 Score=27.65 Aligned_cols=23 Identities=39% Similarity=0.550 Sum_probs=18.3
Q ss_pred ccchhhhccCcchh------HHHHHhhhc
Q 035434 25 SCNAEAAGVDAGAT------DNLRRLLRL 47 (48)
Q Consensus 25 ~CnaEaagvdd~at------dnLRRLLRL 47 (48)
+|-+|-.++..+|. -+.|||||.
T Consensus 25 ~CA~eEnCl~~say~~~~~~~~~RrLLRF 53 (205)
T PF01186_consen 25 RCAAEENCLSSSAYRIQNWPYGERRLLRF 53 (205)
T ss_pred hhhhhcccccccccccCCCCCCcceEEec
Confidence 89999888888763 367999985
No 8
>TIGR01745 asd_gamma aspartate-semialdehyde dehydrogenase, gamma-proteobacterial.
Probab=39.46 E-value=14 Score=26.96 Aligned_cols=15 Identities=47% Similarity=0.740 Sum_probs=11.7
Q ss_pred cCcchhHHHHHhhhc
Q 035434 33 VDAGATDNLRRLLRL 47 (48)
Q Consensus 33 vdd~atdnLRRLLRL 47 (48)
+--||+-||||+|.+
T Consensus 350 lrkGAA~~~~~~~~~ 364 (366)
T TIGR01745 350 LLWGAAEPLRRMLRI 364 (366)
T ss_pred hhhhhHhHHHHHHHH
Confidence 335799999999874
No 9
>PF15148 Apolipo_F: Apolipoprotein F
Probab=36.73 E-value=8.9 Score=26.96 Aligned_cols=23 Identities=39% Similarity=0.395 Sum_probs=15.6
Q ss_pred CCccccccc----cccc--cccccchhhh
Q 035434 9 GDCYASGEF----ALRP--KLISCNAEAA 31 (48)
Q Consensus 9 ~~~lPlP~F----Slk~--K~~~CnaEaa 31 (48)
+.--|||+| +++. ..++|++||-
T Consensus 14 ~~~aPLp~~L~~LaLr~aLe~aGC~aea~ 42 (200)
T PF15148_consen 14 PHMAPLPEFLSGLALRVALEEAGCQAEAW 42 (200)
T ss_pred CCCCcchHHHHHHHHHHHHHHcCCcHHHH
Confidence 456689998 3343 2259999985
No 10
>COG3382 Solo B3/4 domain (OB-fold DNA/RNA-binding) of Phe-aaRS-beta [General function prediction only]
Probab=36.70 E-value=19 Score=25.46 Aligned_cols=22 Identities=41% Similarity=0.683 Sum_probs=17.0
Q ss_pred cccccccccccchhhhccCcchhHHHHHhhh
Q 035434 16 EFALRPKLISCNAEAAGVDAGATDNLRRLLR 46 (48)
Q Consensus 16 ~FSlk~K~~~CnaEaagvdd~atdnLRRLLR 46 (48)
+|-++|....|.+||- +||++|
T Consensus 72 ~~g~kp~k~r~S~EAL---------lrRv~k 93 (229)
T COG3382 72 RFGIKPTKTRPSAEAL---------LRRVLK 93 (229)
T ss_pred HhCCCcCCCCCcHHHH---------HHHHHc
Confidence 5777885459999987 888876
No 11
>PF05720 Dicty_CAD: Cell-cell adhesion domain; InterPro: IPR008601 This family is based on a group of Dictyostelium discoideum (Slime mould) proteins that are essential in early development []. P16642 from SWISSPROT and P16643 from SWISSPROT are located on the cell surface and mediate cell-cell adhesion.; GO: 0007155 cell adhesion
Probab=32.69 E-value=19 Score=22.14 Aligned_cols=15 Identities=33% Similarity=0.262 Sum_probs=12.9
Q ss_pred CccccccCCcccccc
Q 035434 2 LGLRTISGDCYASGE 16 (48)
Q Consensus 2 ~~~~~~~~~~lPlP~ 16 (48)
.|-.||||.+.|||.
T Consensus 5 ~GeStI~G~a~~lP~ 19 (82)
T PF05720_consen 5 DGESTISGKAIPLPT 19 (82)
T ss_pred CCeeEeecccccCCC
Confidence 477899999999997
No 12
>cd07031 RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polymerase II. The eukaryotic RPB3 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP II is responsible for the synthesis of mRNA precursor. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization, and the other is an inserted beta sheet subdomain. The RPB3 subunit heterodimerizes with the RPB11 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association.
Probab=30.70 E-value=26 Score=24.07 Aligned_cols=20 Identities=20% Similarity=0.346 Sum_probs=15.1
Q ss_pred cchhhhccCcchhHHHHHhh
Q 035434 26 CNAEAAGVDAGATDNLRRLL 45 (48)
Q Consensus 26 CnaEaagvdd~atdnLRRLL 45 (48)
+.-+.-|+|..-+|.|||+|
T Consensus 13 ~~F~l~~~~~s~aNALRRil 32 (265)
T cd07031 13 VKFILENTDLSVANSLRRVM 32 (265)
T ss_pred EEEEEEcCcHHHHHHHHHHH
Confidence 34445577788999999987
No 13
>cd07032 RNAP_I_II_AC40 AC40 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III. The eukaryotic AC40 subunit of RNA polymerase (RNAP) I and RNAP III is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP I is responsible for the synthesis of ribosomal RNA precursor, while RNAP III functions in the synthesis of 5S and tRNA. The AC40 subunit is the equivalent of the RPB3 subunit of RNAP II. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The RPB3 subun
Probab=29.11 E-value=29 Score=24.65 Aligned_cols=20 Identities=35% Similarity=0.587 Sum_probs=16.1
Q ss_pred cchhhhccCcchhHHHHHhh
Q 035434 26 CNAEAAGVDAGATDNLRRLL 45 (48)
Q Consensus 26 CnaEaagvdd~atdnLRRLL 45 (48)
+.-+--|+|.+-+|.|||++
T Consensus 13 ~~f~l~~~d~s~ANAlRRim 32 (291)
T cd07032 13 LEFDLIGVDASIANAFRRIL 32 (291)
T ss_pred EEEEEecCCHHHHHHHHHHH
Confidence 44455689999999999986
No 14
>KOG1521 consensus RNA polymerase I and III, subunit RPA40/RPC40 [Transcription]
Probab=27.65 E-value=30 Score=26.15 Aligned_cols=15 Identities=40% Similarity=0.806 Sum_probs=13.9
Q ss_pred hccCcchhHHHHHhh
Q 035434 31 AGVDAGATDNLRRLL 45 (48)
Q Consensus 31 agvdd~atdnLRRLL 45 (48)
.|||++-+|-+||+|
T Consensus 63 igIda~IANAfRRIL 77 (338)
T KOG1521|consen 63 IGIDASIANAFRRIL 77 (338)
T ss_pred eeccHHHHHHHHHHH
Confidence 499999999999997
No 15
>KOG2801 consensus Probable Rab-GAPs [Intracellular trafficking, secretion, and vesicular transport]
Probab=26.02 E-value=25 Score=27.61 Aligned_cols=17 Identities=24% Similarity=0.382 Sum_probs=12.4
Q ss_pred ccCCccccccccccccc
Q 035434 7 ISGDCYASGEFALRPKL 23 (48)
Q Consensus 7 ~~~~~lPlP~FSlk~K~ 23 (48)
-|.+|||+|.|--..+.
T Consensus 85 hsssclplpefvdntqv 101 (559)
T KOG2801|consen 85 HSSSCLPLPEFVDNTQV 101 (559)
T ss_pred CCcccccchhhcccCcC
Confidence 47789999999544443
No 16
>PRK10178 D-alanyl-D-alanine dipeptidase; Provisional
Probab=25.52 E-value=53 Score=22.10 Aligned_cols=38 Identities=26% Similarity=0.242 Sum_probs=20.8
Q ss_pred cccCCcccccc-ccccccccccchhhhccCcchhHHHHHhhh
Q 035434 6 TISGDCYASGE-FALRPKLISCNAEAAGVDAGATDNLRRLLR 46 (48)
Q Consensus 6 ~~~~~~lPlP~-FSlk~K~~~CnaEaagvdd~atdnLRRLLR 46 (48)
.-+|..++|+. |.--...+++.. .+++..+.+| |+|||
T Consensus 110 d~~G~~ldMGt~fD~f~~~s~~~~--~~~s~~~~~n-R~lL~ 148 (184)
T PRK10178 110 DAHGNILDMGTGFDEMHARSHHFH--PGVPPAAQRN-RLLLL 148 (184)
T ss_pred CCCCCEecCCCCcCcCCccccccC--CCCCHHHHHH-HHHHH
Confidence 34577788875 322222224432 3676666665 88876
No 17
>PF01427 Peptidase_M15: D-ala-D-ala dipeptidase This is family M15 in the peptidase classification. ; InterPro: IPR000755 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. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to MEROPS peptidase family M15 (clan MD), subfamily M15D (vanX D-Ala-D-Ala dipeptidase). The D-alanyl-D-alanine dipeptidase enzyme from Enterococcus faecalis is also known as the vancomycin resistance protein VanX, and hydrolyses D-ala-D-ala. It has a 250-fold differential in catalytic efficiency for hydrolysis of D-ala-D-ala versus D-ala-D-lactate. The latter therefore remains intact for subsequent incorporation into peptidoglycan precursors that terminate in the dipeptide D-ala-D-lactate rather than the dipeptide D-ala-D-ala, thereby preventing vancomycin from binding. The enzyme requires a metal cofactor, and is induced by vancomycin through regulation by VanS and VanR.; GO: 0008237 metallopeptidase activity, 0016805 dipeptidase activity, 0006508 proteolysis, 0005618 cell wall; PDB: 1R44_B.
Probab=24.47 E-value=48 Score=21.87 Aligned_cols=38 Identities=29% Similarity=0.391 Sum_probs=15.2
Q ss_pred cccCCcccccc-ccccccccccchhhhccCcchhHHHHHhhh
Q 035434 6 TISGDCYASGE-FALRPKLISCNAEAAGVDAGATDNLRRLLR 46 (48)
Q Consensus 6 ~~~~~~lPlP~-FSlk~K~~~CnaEaagvdd~atdnLRRLLR 46 (48)
.-.|..|+||+ |---...+.... .+++..+..| |+||+
T Consensus 125 ~~~G~~ldMGt~fD~f~~~s~~~~--~~i~~~~~~N-R~lL~ 163 (198)
T PF01427_consen 125 DATGEELDMGTPFDEFTERSHTDY--YGISPEARRN-RRLLR 163 (198)
T ss_dssp TTT--B---SS-TT--SGGGSTT---SSS-HHHHHH-HHHHH
T ss_pred cCCCCeeccCcCCCCCChhHHHhc--cCCCHHHHHH-HHHHH
Confidence 34577788875 221122212222 2367777777 88886
No 18
>PRK00783 DNA-directed RNA polymerase subunit D; Provisional
Probab=23.75 E-value=43 Score=22.21 Aligned_cols=15 Identities=27% Similarity=0.552 Sum_probs=13.1
Q ss_pred hccCcchhHHHHHhh
Q 035434 31 AGVDAGATDNLRRLL 45 (48)
Q Consensus 31 agvdd~atdnLRRLL 45 (48)
-|++..-+|.|||+|
T Consensus 18 ~g~~~t~~NalRRvl 32 (263)
T PRK00783 18 EGVTPAFANAIRRAM 32 (263)
T ss_pred eCCCHHHHHHHHHHH
Confidence 388888999999987
No 19
>PF07621 DUF1582: Protein of unknown function (DUF1582); InterPro: IPR011476 This is a family of hypothetical proteins found in Rhodopirellula baltica.
Probab=23.02 E-value=37 Score=17.53 Aligned_cols=19 Identities=32% Similarity=0.576 Sum_probs=12.9
Q ss_pred ccccccccccccc---cccchh
Q 035434 11 CYASGEFALRPKL---ISCNAE 29 (48)
Q Consensus 11 ~lPlP~FSlk~K~---~~CnaE 29 (48)
.||.|.||+.... ++|..|
T Consensus 2 ~lpsp~~l~~~ri~~~~nc~~~ 23 (29)
T PF07621_consen 2 ALPSPEFLLEARISTLSNCVQE 23 (29)
T ss_pred CcCCCCcChhhhcCCCcchhcc
Confidence 5788999876543 466554
No 20
>PHA02682 ORF080 virion core protein; Provisional
Probab=22.90 E-value=43 Score=24.72 Aligned_cols=12 Identities=58% Similarity=0.844 Sum_probs=9.7
Q ss_pred CcchhHHHHHhh
Q 035434 34 DAGATDNLRRLL 45 (48)
Q Consensus 34 dd~atdnLRRLL 45 (48)
..+|.|+|||||
T Consensus 245 Tq~AIdDLRrLl 256 (280)
T PHA02682 245 TQAAIDDLRRLL 256 (280)
T ss_pred HHHHHHHHHHHH
Confidence 346889999998
No 21
>PF09802 Sec66: Preprotein translocase subunit Sec66; InterPro: IPR018624 Members of this family of proteins are a component of the heterotetrameric Sec62/63 complex composed of SEC62, SEC63, SEC66 and SEC72. The Sec62/63 complex associates with the Sec61 complex to form the Sec complex. Sec 66 is involved in SRP-independent post-translational translocation across the endoplasmic reticulum and functions together with the Sec61 complex and KAR2 in a channel-forming translocon complex. Furthermore, Sec66 is also required for growth at elevated temperatures [, , , ].
Probab=21.38 E-value=42 Score=22.92 Aligned_cols=13 Identities=38% Similarity=0.910 Sum_probs=10.7
Q ss_pred chhHHHHHhhhcC
Q 035434 36 GATDNLRRLLRLR 48 (48)
Q Consensus 36 ~atdnLRRLLRLr 48 (48)
-|+.+|||+++||
T Consensus 81 RavedIrR~~klr 93 (190)
T PF09802_consen 81 RAVEDIRRIIKLR 93 (190)
T ss_pred HHHHHHHHHHHHH
Confidence 4678999999885
No 22
>cd07030 RNAP_D D subunit of Archaeal RNA polymerase. The D subunit of archaeal RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The D subunit is equivalent to the RPB3 subunit of eukaryotic RNAP II. It contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit w
Probab=20.73 E-value=54 Score=21.69 Aligned_cols=14 Identities=29% Similarity=0.574 Sum_probs=12.7
Q ss_pred ccCcchhHHHHHhh
Q 035434 32 GVDAGATDNLRRLL 45 (48)
Q Consensus 32 gvdd~atdnLRRLL 45 (48)
|++..-+|-|||+|
T Consensus 19 g~~~s~~NalRRil 32 (259)
T cd07030 19 GVPPAFANAIRRAI 32 (259)
T ss_pred CCCHHHHHHHHHHH
Confidence 88888999999987
No 23
>PF07769 PsiF_repeat: psiF repeat; InterPro: IPR011690 This region is approximately 35 residues long. It is found repeated in a number of putative phosphate starvation-inducible proteins expressed by various bacterial species. PsiF (Q7AH28 from SWISSPROT) is known to be an example of such phosphate starvation-inducible proteins [].
Probab=20.29 E-value=30 Score=18.46 Aligned_cols=11 Identities=45% Similarity=0.697 Sum_probs=8.4
Q ss_pred ccccchhhhcc
Q 035434 23 LISCNAEAAGV 33 (48)
Q Consensus 23 ~~~CnaEaagv 33 (48)
-..||+||.+.
T Consensus 9 M~~Cn~~A~~k 19 (35)
T PF07769_consen 9 MKTCNAEAKEK 19 (35)
T ss_pred HHHHHHHHHhC
Confidence 34799999865
Done!