Query 029312
Match_columns 195
No_of_seqs 22 out of 24
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 10:53:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029312.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029312hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0749 PolA DNA polymerase I 78.3 32 0.0007 34.5 11.4 128 43-174 436-574 (593)
2 PF03732 Retrotrans_gag: Retro 70.0 15 0.00033 25.2 5.2 66 35-100 26-92 (96)
3 KOG0005 Ubiquitin-like protein 65.0 6.4 0.00014 29.3 2.5 37 21-62 11-47 (70)
4 PF06456 Arfaptin: Arfaptin-li 60.9 1.1E+02 0.0025 26.6 11.1 29 142-170 168-197 (229)
5 KOG4077 Cytochrome c oxidase, 59.8 13 0.00027 31.4 3.7 46 11-57 98-143 (149)
6 PF11791 Aconitase_B_N: Aconit 55.7 27 0.00059 29.6 5.0 71 44-116 7-80 (154)
7 cd01043 DPS DPS protein, ferri 53.7 89 0.0019 23.9 7.3 94 4-109 38-132 (139)
8 PRK10455 periplasmic protein; 53.6 46 0.00099 27.7 6.0 37 25-61 91-139 (161)
9 TIGR02990 ectoine_eutA ectoine 50.9 9.7 0.00021 33.2 1.7 24 98-121 194-217 (239)
10 PF07813 LTXXQ: LTXXQ motif fa 50.7 46 0.001 23.5 5.0 51 8-58 18-94 (100)
11 PF05130 FlgN: FlgN protein; 43.5 1E+02 0.0022 22.6 6.0 48 2-49 6-53 (143)
12 KOG0994 Extracellular matrix g 42.8 4.4E+02 0.0096 29.7 12.3 175 11-190 1471-1674(1758)
13 PRK11519 tyrosine kinase; Prov 41.6 3.7E+02 0.0081 26.8 12.7 87 23-109 230-320 (719)
14 COG0783 Dps DNA-binding ferrit 41.5 85 0.0019 26.2 5.8 92 6-109 46-148 (156)
15 cd00923 Cyt_c_Oxidase_Va Cytoc 40.9 42 0.0009 26.9 3.7 44 12-56 57-100 (103)
16 PF11827 DUF3347: Protein of u 40.8 79 0.0017 26.3 5.5 59 23-81 56-119 (174)
17 COG3473 Maleate cis-trans isom 40.7 23 0.00049 31.9 2.4 33 99-138 193-225 (238)
18 COG2012 RPB5 DNA-directed RNA 39.7 15 0.00032 28.2 1.0 22 126-147 24-45 (80)
19 PF03564 DUF1759: Protein of u 38.0 98 0.0021 23.7 5.4 56 2-58 63-121 (145)
20 COG1529 CoxL Aerobic-type carb 37.9 44 0.00095 33.6 4.2 61 29-89 348-411 (731)
21 PF03704 BTAD: Bacterial trans 36.2 59 0.0013 24.5 3.9 29 32-61 113-141 (146)
22 PRK11546 zraP zinc resistance 36.0 1.8E+02 0.0039 24.2 6.9 37 28-68 84-120 (143)
23 PF07361 Cytochrom_B562: Cytoc 35.7 85 0.0018 24.1 4.6 35 118-163 59-93 (103)
24 PRK12750 cpxP periplasmic repr 35.6 1E+02 0.0022 25.8 5.4 33 28-60 101-145 (170)
25 PF06992 Phage_lambda_P: Repli 35.3 3.3E+02 0.0072 24.4 10.6 84 49-139 118-230 (233)
26 PRK09448 DNA starvation/statio 32.9 2.3E+02 0.005 23.2 7.0 75 20-109 78-153 (162)
27 PRK05883 acyl carrier protein; 32.0 99 0.0021 23.0 4.4 78 29-134 9-87 (91)
28 PRK08045 cystathionine gamma-s 31.1 17 0.00038 33.1 0.2 26 82-107 360-385 (386)
29 PF10123 Mu-like_Pro: Mu-like 30.5 66 0.0014 28.9 3.8 107 29-144 213-326 (326)
30 PF13438 DUF4113: Domain of un 29.9 46 0.001 22.7 2.1 16 123-138 3-18 (52)
31 PRK14181 bifunctional 5,10-met 28.4 1.7E+02 0.0038 26.7 6.1 62 4-67 11-81 (287)
32 PF12450 vWF_A: von Willebrand 27.5 54 0.0012 25.8 2.3 46 19-70 27-72 (99)
33 PLN02469 hydroxyacylglutathion 27.2 1.4E+02 0.003 26.0 5.1 49 26-76 186-237 (258)
34 PRK09841 cryptic autophosphory 27.1 6.5E+02 0.014 25.2 13.6 86 23-108 230-319 (726)
35 PRK14178 bifunctional 5,10-met 26.6 1.8E+02 0.0038 26.5 5.8 64 3-68 10-82 (279)
36 PF13801 Metal_resist: Heavy-m 26.5 2.2E+02 0.0049 20.1 5.3 21 28-48 82-102 (125)
37 cd07631 BAR_APPL1 The Bin/Amph 26.1 4.7E+02 0.01 23.3 8.3 23 114-136 100-122 (215)
38 PRK14182 bifunctional 5,10-met 25.8 2.1E+02 0.0045 26.1 6.1 64 4-68 12-86 (282)
39 PF02284 COX5A: Cytochrome c o 25.7 43 0.00093 27.0 1.5 12 53-64 62-73 (108)
40 PF02630 SCO1-SenC: SCO1/SenC; 25.6 76 0.0016 25.7 3.0 57 6-64 75-133 (174)
41 PRK14180 bifunctional 5,10-met 25.3 1.9E+02 0.0042 26.2 5.8 48 20-68 31-87 (282)
42 PRK10363 cpxP periplasmic repr 24.9 1.2E+02 0.0025 26.0 4.1 36 25-60 85-132 (166)
43 COG1938 Archaeal enzymes of AT 24.0 2.3E+02 0.005 25.6 5.9 59 113-177 181-239 (244)
44 PRK08249 cystathionine gamma-s 23.6 30 0.00064 31.7 0.3 28 82-109 371-398 (398)
45 TIGR02215 phage_chp_gp8 phage 23.5 1.3E+02 0.0028 25.4 4.1 39 78-116 15-56 (188)
46 PRK10241 hydroxyacylglutathion 23.4 1.5E+02 0.0033 25.4 4.6 49 27-77 178-229 (251)
47 PF05731 TROVE: TROVE domain; 23.0 2.3E+02 0.005 26.3 6.0 93 28-129 51-143 (385)
48 TIGR02144 LysX_arch Lysine bio 22.8 1.4E+02 0.0031 24.9 4.2 43 15-58 63-107 (280)
49 PRK12751 cpxP periplasmic stre 22.6 1.4E+02 0.0031 25.0 4.1 35 27-61 93-139 (162)
50 PF13871 Helicase_C_4: Helicas 22.5 96 0.0021 28.2 3.3 54 23-81 188-242 (278)
51 TIGR03017 EpsF chain length de 22.4 5.9E+02 0.013 23.1 12.1 70 24-93 135-208 (444)
52 PRK04778 septation ring format 22.3 5.6E+02 0.012 24.9 8.6 95 4-106 448-550 (569)
53 PF12244 DUF3606: Protein of u 22.3 1.3E+02 0.0029 20.9 3.3 43 26-77 14-56 (57)
54 PRK14194 bifunctional 5,10-met 22.0 2.5E+02 0.0055 25.8 5.9 64 4-68 15-89 (301)
55 PLN02897 tetrahydrofolate dehy 21.8 1.4E+02 0.0031 28.1 4.3 65 3-68 66-142 (345)
56 PF04614 Pex19: Pex19 protein 21.7 1.8E+02 0.0038 25.6 4.7 134 5-151 9-177 (248)
57 TIGR02778 ligD_pol DNA polymer 21.4 1E+02 0.0022 27.6 3.2 31 24-54 118-151 (245)
58 PRK14168 bifunctional 5,10-met 21.3 2.8E+02 0.0061 25.4 6.0 64 4-68 14-89 (297)
59 cd04865 LigD_Pol_like_2 LigD_P 21.0 1.1E+02 0.0023 27.2 3.3 31 24-54 103-136 (228)
60 COG0420 SbcD DNA repair exonuc 20.6 1.6E+02 0.0036 26.4 4.4 49 4-53 20-78 (390)
61 cd04863 MtLigD_Pol_like MtLigD 20.5 1.1E+02 0.0024 27.2 3.2 30 25-54 107-139 (231)
62 TIGR01428 HAD_type_II 2-haloal 20.4 2.4E+02 0.0052 22.3 4.9 98 42-141 65-167 (198)
63 PF03732 Retrotrans_gag: Retro 20.4 2.1E+02 0.0045 19.4 4.0 33 33-65 61-94 (96)
64 TIGR02684 dnstrm_HI1420 probab 20.1 2.7E+02 0.0059 20.9 4.9 67 60-138 19-85 (89)
No 1
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=78.34 E-value=32 Score=34.47 Aligned_cols=128 Identities=20% Similarity=0.244 Sum_probs=104.2
Q ss_pred HHHHHhcCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHHHcC-----------CCchhhHHHHHHHHHHHHHHhhCC
Q 029312 43 KTVREKADLFSESQRIAYTIETRTAGIPDARTYLLTLKEIRERRG-----------LIDEHGAEAMMMDALEKVEKEIKK 111 (195)
Q Consensus 43 ~~ir~k~gl~s~~e~I~~tie~~~~~~~dvR~yL~~~~EiR~~~G-----------l~D~~g~~a~mm~ALdkvEK~igk 111 (195)
.-+.+.+|||- .-.+..|+..+.+.|.|+.|++...+.=+.-| +.+-..--...-.|-+ =-.++.
T Consensus 436 fgLa~~L~I~~--~eA~~~I~~YF~rypgv~~ym~~~~~~ar~~GyV~Tl~gRRry~p~i~s~n~~~R~~aE--R~AiNa 511 (593)
T COG0749 436 FGLAQQLGIPR--KEAKEYIDRYFERYPGVKEYMERTKEEAREDGYVETLFGRRRYLPDINSSNRVVRAAAE--RAAINA 511 (593)
T ss_pred hhHHHHcCCCh--HHHHHHHHHHHHhChHHHHHHHHHHHHHHHcCceeecccccccCcccccCCHHHHHHHH--HHHhcC
Confidence 45677899987 55778899999999999999998887655544 4444433333333433 457899
Q ss_pred ccccccHhhHHHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 029312 112 PLMRNDKKGMALLTAEFDKINKKLGIRKEDLPKYEEQLELKIAKAQLEELKKDALEAMETQKK 174 (195)
Q Consensus 112 pL~r~DkkGM~ll~ae~~ki~kklGi~~eDl~K~~ee~el~~aK~~L~elk~~a~e~m~~~kk 174 (195)
|+--+-+-=+++-+=.+++.-+.-+++.-.+=-+--|+.++.-+.+++++++-.-+.|+..-.
T Consensus 512 PIQGTAADiiK~AMI~vd~~l~~~~~~~rllLQVHDELvfEv~~~e~e~~~~~v~~~Me~a~~ 574 (593)
T COG0749 512 PIQGTAADIIKLAMIKVDKALKEEKLKARLLLQVHDELVFEVPKEELEEVKKLLKAIMENAVN 574 (593)
T ss_pred cCcccHHHHHHHHHHhHHHHHhhcchhhhhHHhhhhhhhhcCcHhHHHHHHHHHHHHHHHhhc
Confidence 999999999999999999999999888778889999999999999999999999999999855
No 2
>PF03732 Retrotrans_gag: Retrotransposon gag protein ; InterPro: IPR005162 Transposable elements (TEs) promote various chromosomal rearrangements more efficiently, and often more specifically, than other cellular processes. Retrotransposons are structurally similar to retroviruses and are bounded by long terminal repeats. This entry represents eukaryotic Gag or capsid-related retrotranspon-related proteins. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.
Probab=69.95 E-value=15 Score=25.21 Aligned_cols=66 Identities=12% Similarity=0.180 Sum_probs=52.5
Q ss_pred HHHHHHHHHHHHHhcCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHHHcCC-CchhhHHHHHHH
Q 029312 35 VSQYANVMKTVREKADLFSESQRIAYTIETRTAGIPDARTYLLTLKEIRERRGL-IDEHGAEAMMMD 100 (195)
Q Consensus 35 V~~YA~~~~~ir~k~gl~s~~e~I~~tie~~~~~~~dvR~yL~~~~EiR~~~Gl-~D~~g~~a~mm~ 100 (195)
+.-|.+....++...+=+.........+..++|+..+|+.|+....++....+- -++.......+.
T Consensus 26 ~~~W~~~~~~~~~~f~~~~~~~~~~~~l~~l~Q~~esv~~y~~rf~~l~~~~~~~~~e~~~v~~f~~ 92 (96)
T PF03732_consen 26 FITWEEFKDAFRKRFFPPDRKEQARQELNSLRQGNESVREYVNRFRELARRAPPPMDEEMLVERFIR 92 (96)
T ss_pred CCCHHHHHHHHHHHHhhhhccccchhhhhhhhccCCcHHHHHHHHHHHHHHCCCCcCHHHHHHHHHH
Confidence 556888888899998888888888888999999999999999999999999983 333333333443
No 3
>KOG0005 consensus Ubiquitin-like protein [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=64.96 E-value=6.4 Score=29.26 Aligned_cols=37 Identities=27% Similarity=0.444 Sum_probs=28.1
Q ss_pred hccccccCCCCHHHHHHHHHHHHHHHHhcCCCChHHHHHHHH
Q 029312 21 RKEKITIAPEDPAAVSQYANVMKTVREKADLFSESQRIAYTI 62 (195)
Q Consensus 21 kk~ki~id~~D~aAV~~YA~~~~~ir~k~gl~s~~e~I~~ti 62 (195)
+.+.|.|+|.|. -....+.+-++-||||+.||+-++=
T Consensus 11 KeIeidIep~Dk-----verIKErvEEkeGIPp~qqrli~~g 47 (70)
T KOG0005|consen 11 KEIEIDIEPTDK-----VERIKERVEEKEGIPPQQQRLIYAG 47 (70)
T ss_pred ceEEEeeCcchH-----HHHHHHHhhhhcCCCchhhhhhhcc
Confidence 456778888874 2345677888999999999997753
No 4
>PF06456 Arfaptin: Arfaptin-like domain; InterPro: IPR010504 Arfaptin interacts with ARF1, a small GTPase involved in vesicle budding at the Golgi complex and immature secretory granules. The structure of arfaptin shows that upon binding to a small GTPase, arfaptin forms a an elongated, crescent-shaped dimer of three-helix coiled-coils []. The N-terminal region of ICA69 is similar to arfaptin [].; PDB: 1I4D_B 1I4L_B 1I49_B 1I4T_A 4DCN_D.
Probab=60.91 E-value=1.1e+02 Score=26.62 Aligned_cols=29 Identities=28% Similarity=0.477 Sum_probs=23.6
Q ss_pred hhhHHH-HHHHHHHHHHHHHHHHHHHHHHH
Q 029312 142 LPKYEE-QLELKIAKAQLEELKKDALEAME 170 (195)
Q Consensus 142 l~K~~e-e~el~~aK~~L~elk~~a~e~m~ 170 (195)
.|++++ +.++..+|...+.||.|++.-|+
T Consensus 168 ~~~~r~~q~~~~~~k~rf~kLr~Dv~~Kl~ 197 (229)
T PF06456_consen 168 EPKFRVAQGNYQEAKERFDKLRSDVLVKLD 197 (229)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred cchHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 566653 56779999999999999998776
No 5
>KOG4077 consensus Cytochrome c oxidase, subunit Va/COX6 [Energy production and conversion]
Probab=59.85 E-value=13 Score=31.38 Aligned_cols=46 Identities=17% Similarity=0.203 Sum_probs=36.3
Q ss_pred HHHHHHHhhhhccccccCCCCHHHHHHHHHHHHHHHHhcCCCChHHH
Q 029312 11 KKFETALGVLRKEKITIAPEDPAAVSQYANVMKTVREKADLFSESQR 57 (195)
Q Consensus 11 kkF~~~l~~lkk~ki~id~~D~aAV~~YA~~~~~ir~k~gl~s~~e~ 57 (195)
+.|-+++-+|-.+|+-. |.-.+.-..|-+..+-++.++|||+++|.
T Consensus 98 NDfa~aVRilE~iK~K~-g~~k~~Y~y~v~elkpvl~ELGI~t~EeL 143 (149)
T KOG4077|consen 98 NDFATAVRILEAIKDKC-GAQKQVYPYYVKELKPVLNELGIPTPEEL 143 (149)
T ss_pred ccHHHHHHHHHHHHHhc-ccHHHHHHHHHHHHHHHHHHhCCCCHHHh
Confidence 56888888888888885 44344466778888999999999999985
No 6
>PF11791 Aconitase_B_N: Aconitate B N-terminal domain; InterPro: IPR015933 Aconitase (aconitate hydratase; 4.2.1.3 from EC) is an iron-sulphur protein that contains a [4Fe-4S]-cluster and catalyses the interconversion of isocitrate and citrate via a cis-aconitate intermediate. Aconitase functions in both the TCA and glyoxylate cycles, however unlike the majority of iron-sulphur proteins that function as electron carriers, the [4Fe-4S]-cluster of aconitase reacts directly with an enzyme substrate. In eukaryotes there is a cytosolic form (cAcn) and a mitochondrial form (mAcn) of the enzyme. In bacteria there are also 2 forms, aconitase A (AcnA) and B (AcnB). Several aconitases are known to be multi-functional enzymes with a second non-catalytic, but essential function that arises when the cellular environment changes, such as when iron levels drop [, ]. Eukaryotic cAcn and mAcn, and bacterial AcnA have the same domain organisation, consisting of three N-terminal alpha/beta/alpha domains, a linker region, followed by a C-terminal 'swivel' domain with a beta/beta/alpha structure (1-2-3-linker-4), although mAcn is small than cAcn. However, bacterial AcnB has a different organisation: it contains an N-terminal HEAT-like domain, followed by the 'swivel' domain, then the three alpha/beta/alpha domains (HEAT-4-1-2-3) []. Below is a description of some of the multi-functional activities associated with different aconitases. Eukaryotic mAcn catalyses the second step of the mitochondrial TCA cycle, which is important for energy production, providing high energy electrons in the form of NADH and FADH2 to the mitochondrial oxidative phosphorylation pathway []. The TCA cycle also provides precursors for haem and amino acid production. This enzyme has a second, non-catalytic but essential role in mitochondrial DNA (mtDNA) maintenance: mAcn acts to stabilise mtDNA, forming part of mtDNA protein-DNA complexes known as nucleoids. mAcn is thought to reversibly model nucleoids to directly influence mitochondrial gene expression in response to changes in the cellular environment. Therefore, mAcn can influence the expression of components of the oxidative phosphorylation pathway encoded in mtDNA. Eukaryotic cAcn enzyme balances the amount of citrate and isocitrate in the cytoplasm, which in turn creates a balance between the amount of NADPH generated from isocitrate by isocitrate dehydrogenase with the amount of acetyl-CoA generated from citrate by citrate lyase. Fatty acid synthesis requires both NADPH and acetyl-CoA, as do other metabolic processes, including the need for NADPH to combat oxidative stress. The enzymatic form of cAcn predominates when iron levels are normal, but if they drop sufficiently to cause the disassembly of the [4Fe-4S]-cluster, then cAcn undergoes a conformational change from a compact enzyme to a more open L-shaped protein known as iron regulatory protein 1 (IRP1; or IRE-binding protein 1, IREBP1) [, ]. As IRP1, the catalytic site and the [4Fe-4S]-cluster are lost, and two new RNA-binding sites appear. IRP1 functions in the post-transcriptional regulation of genes involved in iron metabolism - it binds to mRNA iron-responsive elements (IRE), 30-nucleotide stem-loop structures at the 3' or 5' end of specific transcripts. Transcripts containing an IRE include ferritin L and H subunits (iron storage), transferrin (iron plasma chaperone), transferrin receptor (iron uptake into cells), ferroportin (iron exporter), mAcn, succinate dehydrogenase, erythroid aminolevulinic acid synthetase (tetrapyrrole biosynthesis), among others. If the IRE is in the 5'-UTR of the transcript (e.g. in ferritin mRNA), then IRP1-binding prevents its translation by blocking the transcript from binding to the ribosome. If the IRE is in the 3'-UTR of the transcript (e.g. transferrin receptor), then IRP1-binding protects it from endonuclease degradation, thereby prolonging the half-life of the transcript and enabling it to be translated []. IRP2 is another IRE-binding protein that binds to the same transcripts as IRP1. However, since IRP1 is predominantly in the enzymatic cAcn form, it is IRP2 that acts as the major metabolic regulator that maintains iron homeostasis []. Although IRP2 is homologous to IRP1, IRP2 lacks aconitase activity, and is known only to have a single function in the post-transcriptional regulation of iron metabolism genes []. In iron-replete cells, IRP2 activity is regulated primarily by iron-dependent degradation through the ubiquitin-proteasomal system. Bacterial AcnB is also known to be multi-functional. In addition to its role in the TCA cycle, AcnB was shown to be a post-transcriptional regulator of gene expression in Escherichia coli and Salmonella enterica [, ]. In S. enterica, AcnB initiates a regulatory cascade controlling flagella biosynthesis through an interaction with the ftsH transcript, an alternative RNA polymerase sigma factor. This binding lowers the intracellular concentration of FtsH protease, which in turn enhances the amount of RNA polymerase sigma32 factor (normally degraded by FtsH protease), and sigma32 then increases the synthesis of chaperone DnaK, which in turn promotes the synthesis of the flagellar protein FliC. AcnB regulates the synthesis of other proteins as well, such as superoxide dismutase (SodA) and other enzymes involved in oxidative stress. This entry represents the N-terminal HEAT-like domain, which is present in bacterial aconitase (AcnB), but not in AcnA or eukaryotic cAcn/IRP2 or mAcn. This domain is multi-helical, forming two curved layers in a right-handed alpha-alpha superhelix. HEAT-like domains are usually implicated in protein-protein interactions. The HEAT-like domain and the 'swivel' domain that follows it were shown to be sufficient for dimerisation and for AcnB binding to mRNA. An iron-mediated dimerisation mechanism may be responsible for switching AcnB between its catalytic and regulatory roles, as dimerisation requires iron while mRNA binding is inhibited by iron. More information about these proteins can be found at Protein of the Month: Aconitase [].; GO: 0003994 aconitate hydratase activity, 0006099 tricarboxylic acid cycle; PDB: 1L5J_B.
Probab=55.72 E-value=27 Score=29.56 Aligned_cols=71 Identities=23% Similarity=0.259 Sum_probs=48.8
Q ss_pred HHHHhcCCCC---hHHHHHHHHHHhhcCCCcHHHHHHHHHHHHHHcCCCchhhHHHHHHHHHHHHHHhhCCccccc
Q 029312 44 TVREKADLFS---ESQRIAYTIETRTAGIPDARTYLLTLKEIRERRGLIDEHGAEAMMMDALEKVEKEIKKPLMRN 116 (195)
Q Consensus 44 ~ir~k~gl~s---~~e~I~~tie~~~~~~~dvR~yL~~~~EiR~~~Gl~D~~g~~a~mm~ALdkvEK~igkpL~r~ 116 (195)
.=|...|||| ..++....++-+..+...=+.||..+-..|..-|..+...++|.-+.++-+ +++.-|+.+.
T Consensus 7 ~eRa~~GipPlPL~a~Qt~~lielLk~~~~~~~~~lldLL~~RV~PGVD~AA~VKA~FL~~ia~--g~~~~~~Is~ 80 (154)
T PF11791_consen 7 AERAALGIPPLPLNAEQTAELIELLKNPPAGEEAFLLDLLTNRVPPGVDEAAYVKAEFLAAIAK--GEISSPLISP 80 (154)
T ss_dssp HHHHCTT-------HHHHHHHHHHHHS--TT-HHHHHHHHHHSS--TT-HHHHHHHHHHHHHHT--TSS-BTTB-H
T ss_pred HHHHHCCCCCCCCCHHHHHHHHHHHhCCCCccHHHHHHHHHhcCCCCCChHHHHHHHHHHHHHc--CCccCCCcCH
Confidence 3477889987 478888999999888888889999999999999999999999988888754 3455566553
No 7
>cd01043 DPS DPS protein, ferritin-like diiron-binding domain. DPS (DNA Protecting protein under Starved conditions) domain is a member of a broad superfamily of ferritin-like diiron-carboxylate proteins. Some DPS proteins nonspecifically bind DNA, protecting it from cleavage caused by reactive oxygen species such as the hydroxyl radicals produced during oxidation of Fe(II) by hydrogen peroxide. These proteins assemble into dodecameric structures, some form DPS-DNA co-crystalline complexes, and possess iron and H2O2 detoxification capabilities. Expression of DPS is induced by oxidative or nutritional stress, including metal ion starvation. Members of the DPS family are homopolymers formed by 12 four-helix bundle subunits that assemble with 23 symmetry into a hollow shell. The DPS ferroxidase site is unusual in that it is not located in a four-helix bundle as in ferritin, but is shared by 2-fold symmetry-related subunits providing the iron ligands. Many DPS sequences (e.g., E. coli) disp
Probab=53.71 E-value=89 Score=23.88 Aligned_cols=94 Identities=11% Similarity=0.197 Sum_probs=59.2
Q ss_pred HHHHHHHHHHHHHHhhhhccccccCCCCHHHHHHHHHHHHHHHHhc-CCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHH
Q 029312 4 NIFLDVKKKFETALGVLRKEKITIAPEDPAAVSQYANVMKTVREKA-DLFSESQRIAYTIETRTAGIPDARTYLLTLKEI 82 (195)
Q Consensus 4 ~vF~~vqkkF~~~l~~lkk~ki~id~~D~aAV~~YA~~~~~ir~k~-gl~s~~e~I~~tie~~~~~~~dvR~yL~~~~Ei 82 (195)
..+.+..+.+..+-+-+....-. .+++|+.+.+++... ..- +-.++.+.+...++.+.+-+...|.=...+.+
T Consensus 38 e~~~~~~~~~D~lAERi~~lgg~-P~~~~~~~~~~s~l~----~~~~~~~~~~~~l~~~~~~~~~~i~~~~~~i~~a~~- 111 (139)
T cd01043 38 ELYDELREAIDEIAERIRALGGK-PLGTLKEYAELSTIK----EEPAGVLSAKEMVAELLEDYETLIEELREAIELADE- 111 (139)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCC-CCCCHHHHHhHCCCC----CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH-
Confidence 44555566666666666666666 378888888886642 222 55677777777777665544444433333332
Q ss_pred HHHcCCCchhhHHHHHHHHHHHHHHhh
Q 029312 83 RERRGLIDEHGAEAMMMDALEKVEKEI 109 (195)
Q Consensus 83 R~~~Gl~D~~g~~a~mm~ALdkvEK~i 109 (195)
..+-++..+|.+-+...||.+
T Consensus 112 ------~~D~~t~~ll~~il~~~ek~~ 132 (139)
T cd01043 112 ------AGDPATADLLTEIIRELEKQA 132 (139)
T ss_pred ------cCCHHHHHHHHHHHHHHHHHH
Confidence 456777888888888888764
No 8
>PRK10455 periplasmic protein; Reviewed
Probab=53.59 E-value=46 Score=27.67 Aligned_cols=37 Identities=16% Similarity=0.227 Sum_probs=27.2
Q ss_pred cccCCCCHHHHHHHHHHHHHHHHh------------cCCCChHHHHHHH
Q 029312 25 ITIAPEDPAAVSQYANVMKTVREK------------ADLFSESQRIAYT 61 (195)
Q Consensus 25 i~id~~D~aAV~~YA~~~~~ir~k------------~gl~s~~e~I~~t 61 (195)
|.-++-|+++|..++..+-.+... ..+.+|+|+-+..
T Consensus 91 i~ad~FDeaavra~~~k~~~~~~~~~~~~~~~~~qiy~vLTPEQr~q~~ 139 (161)
T PRK10455 91 IASDTFDKAKAEAQITKMEAQRKARMLAHMETQNKIYNVLTPEQKKQFN 139 (161)
T ss_pred HccCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHH
Confidence 455788999999999876555443 5788888886543
No 9
>TIGR02990 ectoine_eutA ectoine utilization protein EutA. Members of this protein family are EutA, a predicted arylmalonate decarboxylase found in a conserved ectoine utilization operon of species that include Sinorhizobium meliloti 1021 (where it is known to be induced by ectoine), Mesorhizobium loti and Silicibacter pomeroyi. It is missing from two other species with the other ectoine transport and utilization genes: Pseudomonas putida and Agrobacterium tumefaciens.
Probab=50.93 E-value=9.7 Score=33.18 Aligned_cols=24 Identities=17% Similarity=0.415 Sum_probs=20.4
Q ss_pred HHHHHHHHHHhhCCccccccHhhH
Q 029312 98 MMDALEKVEKEIKKPLMRNDKKGM 121 (195)
Q Consensus 98 mm~ALdkvEK~igkpL~r~DkkGM 121 (195)
..+.++++|.++|||+++||-.-+
T Consensus 194 t~~vi~~lE~~lGkPVlsSNqat~ 217 (239)
T TIGR02990 194 AATCAQRIEQAIGKPVVTSNQATA 217 (239)
T ss_pred hHHHHHHHHHHHCCCEEEHHHHHH
Confidence 457889999999999999997653
No 10
>PF07813 LTXXQ: LTXXQ motif family protein; InterPro: IPR012899 This five residue motif is found in a number of bacterial proteins bearing similarity to the protein CpxP (P32158 from SWISSPROT). This is a periplasmic protein that aids in combating extracytoplasmic protein-mediated toxicity, and may also be involved in the response to alkaline pH []. Another member of this family, Spy (P77754 from SWISSPROT) is also a periplasmic protein that may be involved in the response to stress []. The homology between CpxP and Spy may indicate that these two proteins are functionally related []. The motif is found repeated twice in many members of this entry. ; GO: 0042597 periplasmic space; PDB: 3ITF_B 3QZC_B 3OEO_D 3O39_A.
Probab=50.66 E-value=46 Score=23.49 Aligned_cols=51 Identities=18% Similarity=0.221 Sum_probs=27.4
Q ss_pred HHHHHHHHHHhhhhcccccc------------CCCCHHHHHHHH--HHHHHHHHh------------cCCCChHHHH
Q 029312 8 DVKKKFETALGVLRKEKITI------------APEDPAAVSQYA--NVMKTVREK------------ADLFSESQRI 58 (195)
Q Consensus 8 ~vqkkF~~~l~~lkk~ki~i------------d~~D~aAV~~YA--~~~~~ir~k------------~gl~s~~e~I 58 (195)
+|+.+|+++...++...-++ .+-|.+++..++ ..+..++.+ .++.+|+|+-
T Consensus 18 eQ~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vLt~eQk~ 94 (100)
T PF07813_consen 18 EQKAKWRAIRQAMKAKMKPLKAMREQLRALRDPSFDEAAPEALAAMAEMMELRAEMMEERAKAQHALYAVLTPEQKE 94 (100)
T ss_dssp HHHHHHHHHHHHHCTTS------HHHHHHHHHSS--HHHHHHHH--HHCHHHHHHHHHHHHHHHHHHHTTS-HHHHH
T ss_pred HHHHHHHHHHHHHHHHHHhhcccHHHHHHhccccCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHH
Confidence 57777777777776666665 345666666666 444444433 4666666654
No 11
>PF05130 FlgN: FlgN protein; InterPro: IPR007809 Flagella synthesis protein FlgN is an export chaperone involved in flagellar synthesis []. This entry represents a FlgN-like domain, consisting of a 4 long helices bundle, where the last helix is shorter than the three others.; GO: 0009296 flagellum assembly, 0019861 flagellum; PDB: 2FUP_A 3OPC_A.
Probab=43.53 E-value=1e+02 Score=22.63 Aligned_cols=48 Identities=13% Similarity=0.207 Sum_probs=40.0
Q ss_pred hhHHHHHHHHHHHHHHhhhhccccccCCCCHHHHHHHHHHHHHHHHhc
Q 029312 2 LKNIFLDVKKKFETALGVLRKEKITIAPEDPAAVSQYANVMKTVREKA 49 (195)
Q Consensus 2 vK~vF~~vqkkF~~~l~~lkk~ki~id~~D~aAV~~YA~~~~~ir~k~ 49 (195)
|..+..++..-|+.+++.+.++.=-|..+|+..+..+...+..+..++
T Consensus 6 L~~~L~~~~~~~~~L~~ll~~e~~~l~~~d~~~l~~~~~~k~~l~~~l 53 (143)
T PF05130_consen 6 LIELLEEQIELLQELLELLEEEREALISGDIDELEELVEEKQELLEEL 53 (143)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH
Confidence 567788889999999999999888888999999988888777666553
No 12
>KOG0994 consensus Extracellular matrix glycoprotein Laminin subunit beta [Extracellular structures]
Probab=42.79 E-value=4.4e+02 Score=29.70 Aligned_cols=175 Identities=17% Similarity=0.126 Sum_probs=0.0
Q ss_pred HHHHHHHhhhhccccccCCCCHHHHHHHHHHHHHHHHhcCCCChHHHHHHH-------------HHH-hhcCCCcHHHHH
Q 029312 11 KKFETALGVLRKEKITIAPEDPAAVSQYANVMKTVREKADLFSESQRIAYT-------------IET-RTAGIPDARTYL 76 (195)
Q Consensus 11 kkF~~~l~~lkk~ki~id~~D~aAV~~YA~~~~~ir~k~gl~s~~e~I~~t-------------ie~-~~~~~~dvR~yL 76 (195)
+--+.++..++++=-- ..-||..|...|+.++ ++.||+..+.|+.. +|. +....+|++---
T Consensus 1471 ~el~~Li~~v~~Flt~-~~adp~si~~vA~~vL----~l~lp~tpeqi~~L~~~I~e~v~sL~nVd~IL~~T~~di~ra~ 1545 (1758)
T KOG0994|consen 1471 RELRNLIQQVRDFLTQ-PDADPDSIEEVAEEVL----ALELPLTPEQIQQLTGEIQERVASLPNVDAILSRTKGDIARAE 1545 (1758)
T ss_pred HHHHHHHHHHHHHhcC-CCCCHHHHHHHHHHHH----hccCCCCHHHHHHHHHHHHHHHHhcccHHHHHHhhhhhHHHHH
Q ss_pred HHHHHHHHHcCC-CchhhHHHHHHHHHHHHHHhhCCc------------cccccHhhHHHHHHHHHHHHHHhCCCCCChh
Q 029312 77 LTLKEIRERRGL-IDEHGAEAMMMDALEKVEKEIKKP------------LMRNDKKGMALLTAEFDKINKKLGIRKEDLP 143 (195)
Q Consensus 77 ~~~~EiR~~~Gl-~D~~g~~a~mm~ALdkvEK~igkp------------L~r~DkkGM~ll~ae~~ki~kklGi~~eDl~ 143 (195)
+-.++-++.+.- +|..+...++.+||++.+...|.. +...+=.-..--++..++.....+-+-++|.
T Consensus 1546 ~L~s~A~~a~~~A~~v~~~ae~V~eaL~~Ad~Aq~~a~~ai~~a~~~~~~a~~~l~kv~~~t~~aE~~~~~a~q~~~eL~ 1625 (1758)
T KOG0994|consen 1546 NLQSEAERARSRAEDVKGQAEDVVEALEEADVAQGEAQDAIQGADRDIRLAQQLLAKVQEETAAAEKLATSATQQLGELE 1625 (1758)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_pred hHHHHHHHHHHHHHHH--HHHHHHHHHHHHHhhhhhhhhhhhccccccc
Q 029312 144 KYEEQLELKIAKAQLE--ELKKDALEAMETQKKREEFKDEEMVEVKSLD 190 (195)
Q Consensus 144 K~~ee~el~~aK~~L~--elk~~a~e~m~~~kkre~~k~~~~~dvk~Ld 190 (195)
+..|++..+++++-.+ +.-++|-.+-..+..-++.-+.++-++...+
T Consensus 1626 ~~~e~lk~~~~qns~~A~~a~~~a~sa~~~A~~a~q~~~~lq~~~~~~~ 1674 (1758)
T KOG0994|consen 1626 TRMEELKHKAAQNSAEAKQAEKTAGSAKEQALSAEQGLEILQKYYELVD 1674 (1758)
T ss_pred HHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
No 13
>PRK11519 tyrosine kinase; Provisional
Probab=41.61 E-value=3.7e+02 Score=26.83 Aligned_cols=87 Identities=13% Similarity=0.226 Sum_probs=63.5
Q ss_pred cccccCCCCHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHhhcCCCcHHHHHHHH----HHHHHHcCCCchhhHHHHH
Q 029312 23 EKITIAPEDPAAVSQYANVMKTVREKADLFSESQRIAYTIETRTAGIPDARTYLLTL----KEIRERRGLIDEHGAEAMM 98 (195)
Q Consensus 23 ~ki~id~~D~aAV~~YA~~~~~ir~k~gl~s~~e~I~~tie~~~~~~~dvR~yL~~~----~EiR~~~Gl~D~~g~~a~m 98 (195)
+.|.....||.-....+|..-..--+-.+-.-.+....+++.+.+..+.+|+=|..+ .++|.+.|+-|...--...
T Consensus 230 i~Is~~~~dP~~Aa~iaN~l~~~Yi~~~~~~k~~~a~~a~~fL~~ql~~l~~~L~~aE~~l~~fr~~~~~vd~~~ea~~~ 309 (719)
T PRK11519 230 LSLTYTGEDREQIRDILNSITRNYLEQNIERKSEEASKSLAFLAQQLPEVRSRLDVAENKLNAFRQDKDSVDLPLEAKAV 309 (719)
T ss_pred EEEEEEcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCchHHHHHH
Confidence 456777889999999999887776666666666777788888888888888777664 8899999997754433335
Q ss_pred HHHHHHHHHhh
Q 029312 99 MDALEKVEKEI 109 (195)
Q Consensus 99 m~ALdkvEK~i 109 (195)
.+.+.++++++
T Consensus 310 l~~~~~l~~ql 320 (719)
T PRK11519 310 LDSMVNIDAQL 320 (719)
T ss_pred HHHHHHHHHHH
Confidence 55666555543
No 14
>COG0783 Dps DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]
Probab=41.53 E-value=85 Score=26.16 Aligned_cols=92 Identities=18% Similarity=0.376 Sum_probs=53.0
Q ss_pred HHHHHHHHHHHHhhhh-------ccccccCCCCHH-HHHHHHHHHHHHHHhcCCCChHHHHHHHHHHhhcCCCcHHHHHH
Q 029312 6 FLDVKKKFETALGVLR-------KEKITIAPEDPA-AVSQYANVMKTVREKADLFSESQRIAYTIETRTAGIPDARTYLL 77 (195)
Q Consensus 6 F~~vqkkF~~~l~~lk-------k~ki~id~~D~a-AV~~YA~~~~~ir~k~gl~s~~e~I~~tie~~~~~~~dvR~yL~ 77 (195)
|+.+-.+|+.+.+.+. --=+.| +|.|- ..+.|+.. -.+.+.-|-++..+.+...++. |-.
T Consensus 46 F~~lHe~~ee~y~el~~~~DeiAERi~~L-Gg~p~~t~~~~~~~-s~ike~~~~~~~~~~l~~l~~~----------~~~ 113 (156)
T COG0783 46 FFALHEKLEELYEELAEHVDEIAERIRAL-GGVPLGTLSEYLKL-SSIKEEPGDYTAREMLKELVED----------YEY 113 (156)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHc-CCCCcccHHHHHHh-CCCcccCCCCCHHHHHHHHHHH----------HHH
Confidence 5555555555544422 112233 44443 44444432 2344444447788877777654 444
Q ss_pred HHHHHHHHcCC---CchhhHHHHHHHHHHHHHHhh
Q 029312 78 TLKEIRERRGL---IDEHGAEAMMMDALEKVEKEI 109 (195)
Q Consensus 78 ~~~EiR~~~Gl---~D~~g~~a~mm~ALdkvEK~i 109 (195)
-+..+|...++ ..+.++-.+|-+++.++||.+
T Consensus 114 l~~~~r~~~~~a~e~gD~~Tadl~~~~~~~~EK~~ 148 (156)
T COG0783 114 LIKELRKGIELADEAGDEVTADLLTDIIRELEKTL 148 (156)
T ss_pred HHHHHHHHHHhhhhcCChhHHHHHHHHHHHHHHHH
Confidence 45566666666 455677888888999999864
No 15
>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Va is one of three mammalian subunits that lacks a transmembrane region. Subunit Va is located on the matrix side of the membrane and binds thyroid hormone T2, releasing allosteric inhibition caused by the binding of ATP to subunit IV and allowing high turnover at elevated intramitochondrial ATP/ADP ratios.
Probab=40.94 E-value=42 Score=26.86 Aligned_cols=44 Identities=11% Similarity=0.092 Sum_probs=24.4
Q ss_pred HHHHHHhhhhccccccCCCCHHHHHHHHHHHHHHHHhcCCCChHH
Q 029312 12 KFETALGVLRKEKITIAPEDPAAVSQYANVMKTVREKADLFSESQ 56 (195)
Q Consensus 12 kF~~~l~~lkk~ki~id~~D~aAV~~YA~~~~~ir~k~gl~s~~e 56 (195)
.|-.++-.|-..|.-. ++...--..|-+..+-.++++||+++++
T Consensus 57 D~alAVR~lE~vK~K~-~~~~~~y~~~lqeikp~l~ELGI~t~Ee 100 (103)
T cd00923 57 DFALAVRILEAIKDKC-GAHKEIYPYILQEIKPTLKELGISTPEE 100 (103)
T ss_pred hHHHHHHHHHHHHHHc-cCchhhHHHHHHHHhHHHHHHCCCCHHH
Confidence 4445555555444442 3333344455566666677777777765
No 16
>PF11827 DUF3347: Protein of unknown function (DUF3347); InterPro: IPR021782 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 169 to 570 amino acids in length.
Probab=40.80 E-value=79 Score=26.30 Aligned_cols=59 Identities=19% Similarity=0.183 Sum_probs=43.5
Q ss_pred cccccCCCCHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHhhc-----CCCcHHHHHHHHHH
Q 029312 23 EKITIAPEDPAAVSQYANVMKTVREKADLFSESQRIAYTIETRTA-----GIPDARTYLLTLKE 81 (195)
Q Consensus 23 ~ki~id~~D~aAV~~YA~~~~~ir~k~gl~s~~e~I~~tie~~~~-----~~~dvR~yL~~~~E 81 (195)
++=-|..+|.+++++.|..+.+....++.+.........+..... ++...|..+..|++
T Consensus 56 lk~ALv~dd~~~a~~aA~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~di~~qR~~F~~lS~ 119 (174)
T PF11827_consen 56 LKDALVADDLKAAKAAAKALLAALKAVDMAELSASLAKALMEAAEDAKEHDIEHQREAFESLSE 119 (174)
T ss_pred HHHHHHhcCHHHHHHHHHHHHHHHHhcccccccHHHHHHHHHHHHhhhhCCHHHHHHHHHHHHH
Confidence 334456899999999999999999999988555444444444332 77777888877777
No 17
>COG3473 Maleate cis-trans isomerase [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=40.74 E-value=23 Score=31.95 Aligned_cols=33 Identities=18% Similarity=0.507 Sum_probs=25.1
Q ss_pred HHHHHHHHHhhCCccccccHhhHHHHHHHHHHHHHHhCCC
Q 029312 99 MDALEKVEKEIKKPLMRNDKKGMALLTAEFDKINKKLGIR 138 (195)
Q Consensus 99 m~ALdkvEK~igkpL~r~DkkGM~ll~ae~~ki~kklGi~ 138 (195)
.+.++++|..+|+|+.+||-.-|-. ..+.+|++
T Consensus 193 ~eii~~lE~~~G~PVvsSN~AT~W~-------~Lr~~g~~ 225 (238)
T COG3473 193 FEIIEKLERDTGVPVVSSNQATLWM-------ALRLIGLR 225 (238)
T ss_pred HHHHHHHHHHhCCceeeccHHHHHH-------HHHHcCCc
Confidence 5789999999999999999765432 34556665
No 18
>COG2012 RPB5 DNA-directed RNA polymerase, subunit H, RpoH/RPB5 [Transcription]
Probab=39.74 E-value=15 Score=28.21 Aligned_cols=22 Identities=41% Similarity=0.632 Sum_probs=19.1
Q ss_pred HHHHHHHHHhCCCCCChhhHHH
Q 029312 126 AEFDKINKKLGIRKEDLPKYEE 147 (195)
Q Consensus 126 ae~~ki~kklGi~~eDl~K~~e 147 (195)
+|...+.++|||+|++||++..
T Consensus 24 eE~~~vLk~l~i~~~qLPkI~~ 45 (80)
T COG2012 24 EEAKEVLKELGIEPEQLPKIKA 45 (80)
T ss_pred HHHHHHHHHhCCCHHHCCcccc
Confidence 5668899999999999999764
No 19
>PF03564 DUF1759: Protein of unknown function (DUF1759); InterPro: IPR005312 This is a small family of proteins of unknown function.
Probab=38.05 E-value=98 Score=23.68 Aligned_cols=56 Identities=14% Similarity=0.238 Sum_probs=40.9
Q ss_pred hhHHHHHHHHHHHHHHhhhhccccccCCCCHHHHHHHHHHHHHHHHh---cCCCChHHHH
Q 029312 2 LKNIFLDVKKKFETALGVLRKEKITIAPEDPAAVSQYANVMKTVREK---ADLFSESQRI 58 (195)
Q Consensus 2 vK~vF~~vqkkF~~~l~~lkk~ki~id~~D~aAV~~YA~~~~~ir~k---~gl~s~~e~I 58 (195)
|++-|-.-..-.+++++.|.+.+. +..+|+.++..+...+..+... +|.+..+..+
T Consensus 63 L~~~yg~~~~i~~~~~~~l~~l~~-~~~~d~~~L~~~~~~v~~~i~~L~~lg~~~~~~~l 121 (145)
T PF03564_consen 63 LEERYGNPRRIIQALLEELRNLPP-ISNDDPEALRSLVDKVNNCIRALKALGVNVDDPLL 121 (145)
T ss_pred HHHHhCCchHHHHHHHHHHhcccc-ccchhHHHHHHHHHHHHHHHHHHHHcCCCCCCHHH
Confidence 556666666677888888987775 4699999999999888776544 6665554433
No 20
>COG1529 CoxL Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]
Probab=37.86 E-value=44 Score=33.60 Aligned_cols=61 Identities=20% Similarity=0.217 Sum_probs=51.7
Q ss_pred CCCHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHhhcC---CCcHHHHHHHHHHHHHHcCCC
Q 029312 29 PEDPAAVSQYANVMKTVREKADLFSESQRIAYTIETRTAG---IPDARTYLLTLKEIRERRGLI 89 (195)
Q Consensus 29 ~~D~aAV~~YA~~~~~ir~k~gl~s~~e~I~~tie~~~~~---~~dvR~yL~~~~EiR~~~Gl~ 89 (195)
+|+|.+.-..---|..+.++|||++.+-|+.+++.+.--+ ..+.+.|...+.+..+++|..
T Consensus 348 ~g~~~~~~a~E~~~d~lA~~Lgidp~eiR~~n~~~~g~~~~~~~~~~~~~~~~~~~~ak~~~~~ 411 (731)
T COG1529 348 AGRPEGTFALERAVDELAEELGIDPVEIRLRNLIRGGPFGLGRRYDSGDYLEELDEAAKRFGWS 411 (731)
T ss_pred CCCchhHHHHHHHHHHHHHHhCCCHHHHhhhhccccCCCCCcccccCccHHHHHHHHHHhcCcc
Confidence 6777777777778899999999999999999999965444 888899999999999888853
No 21
>PF03704 BTAD: Bacterial transcriptional activator domain; InterPro: IPR005158 Found in the DNRI/REDD/AFSR family of regulators, this region of AFSR (P25941 from SWISSPROT) along with the C-terminal region is capable of independently directing actinorhodin production. It is important for the formation of secondary metabolites.; PDB: 2FF4_B 2FEZ_A.
Probab=36.25 E-value=59 Score=24.47 Aligned_cols=29 Identities=17% Similarity=0.196 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHHHHHHhcCCCChHHHHHHH
Q 029312 32 PAAVSQYANVMKTVREKADLFSESQRIAYT 61 (195)
Q Consensus 32 ~aAV~~YA~~~~~ir~k~gl~s~~e~I~~t 61 (195)
.+|+..|......+++++|++ |+..+...
T Consensus 113 ~~A~~~Y~~~~~~l~~elg~~-Ps~~~~~l 141 (146)
T PF03704_consen 113 AEALRVYERYRRRLREELGIE-PSPETRAL 141 (146)
T ss_dssp HHHHHHHHHHHHHHHHHHS-----HHHHHH
T ss_pred HHHHHHHHHHHHHHHHHhCcC-cCHHHHHH
Confidence 467778888888888888884 44444433
No 22
>PRK11546 zraP zinc resistance protein; Provisional
Probab=36.05 E-value=1.8e+02 Score=24.22 Aligned_cols=37 Identities=27% Similarity=0.454 Sum_probs=22.5
Q ss_pred CCCCHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHhhcC
Q 029312 28 APEDPAAVSQYANVMKTVREKADLFSESQRIAYTIETRTAG 68 (195)
Q Consensus 28 d~~D~aAV~~YA~~~~~ir~k~gl~s~~e~I~~tie~~~~~ 68 (195)
.+-|+++|++-++.+-++|.++. +++++.-++...+.
T Consensus 84 ~~pD~~kI~aL~kEI~~Lr~kL~----e~r~~~~~~~~k~G 120 (143)
T PRK11546 84 NPPDSSKINAVAKEMENLRQSLD----ELRVKRDIAMAEAG 120 (143)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHcC
Confidence 45677777777777777776653 55555555544433
No 23
>PF07361 Cytochrom_B562: Cytochrome b562; InterPro: IPR009155 Cytochrome b562 is a haem-containing protein that is expressed in the periplasm of Escherichia coli. In b-type cytochromes, the haem atom is not covalently attached to the polypeptide. Cytochrome b562 has a four-helical bundle structure that is structurally similar to that found in members of the cytochrome c family (IPR002321 from INTERPRO). Cytochrome b562 has a reduction potential of 167 mV, which sets the energy yield possible in metabolism and is also a key determinant of the rate at which redox reactions proceed [].; GO: 0005506 iron ion binding, 0009055 electron carrier activity, 0020037 heme binding, 0042597 periplasmic space; PDB: 4ER9_A 3IQ6_G 2QLA_B 3FOO_A 3M79_C 256B_A 3NMI_F 3HNK_A 3NMK_D 2BC5_A ....
Probab=35.67 E-value=85 Score=24.09 Aligned_cols=35 Identities=29% Similarity=0.344 Sum_probs=22.7
Q ss_pred HhhHHHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHHHHHHHHHHH
Q 029312 118 KKGMALLTAEFDKINKKLGIRKEDLPKYEEQLELKIAKAQLEELKK 163 (195)
Q Consensus 118 kkGM~ll~ae~~ki~kklGi~~eDl~K~~ee~el~~aK~~L~elk~ 163 (195)
..||..|..+++.+...+-- =.|+-||++|.+|..
T Consensus 59 ~~Gl~~li~~id~a~~~~~~-----------G~l~~AK~~l~~l~~ 93 (103)
T PF07361_consen 59 QEGLDKLIDQIDKAEALAEA-----------GKLDEAKAALKKLDD 93 (103)
T ss_dssp HHHHHHHHHHHHHHHHHHHT-----------THHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHC-----------CCHHHHHHHHHHHHH
Confidence 46777777777776665432 256678887777654
No 24
>PRK12750 cpxP periplasmic repressor CpxP; Reviewed
Probab=35.59 E-value=1e+02 Score=25.80 Aligned_cols=33 Identities=18% Similarity=0.243 Sum_probs=23.1
Q ss_pred CCCCHHHHHHHHHHHHHHHHh------------cCCCChHHHHHH
Q 029312 28 APEDPAAVSQYANVMKTVREK------------ADLFSESQRIAY 60 (195)
Q Consensus 28 d~~D~aAV~~YA~~~~~ir~k------------~gl~s~~e~I~~ 60 (195)
+|=||++|..+++.+.+...+ ..+.+|+|+-..
T Consensus 101 ~~FDeaavral~~~~~~~~~e~~v~~~~~~~~~~~vLTpEQRak~ 145 (170)
T PRK12750 101 DDFDEAAANDLAKQMVEKQVERRVKMLEKRHQMLSILTPEQKAKF 145 (170)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHH
Confidence 788999999997665544222 567777777553
No 25
>PF06992 Phage_lambda_P: Replication protein P; InterPro: IPR009731 This family consists of several Bacteriophage lambda replication protein P like proteins. The bacteriophage lambda P protein promoters replication of the phage chromosome by recruiting a key component of the cellular replication machinery to the viral origin. Specifically, P protein delivers one or more molecules of Escherichia coli DnaB helicase to a nucleoprotein structure formed by the lambda O initiator at the lambda replication origin [].; GO: 0006270 DNA-dependent DNA replication initiation
Probab=35.29 E-value=3.3e+02 Score=24.43 Aligned_cols=84 Identities=17% Similarity=0.175 Sum_probs=50.5
Q ss_pred cCCCChHHHHHHHHHHhhc--CCCcHHHH----------HHHHHHHHHHcCCCchhhHHHHHHHHHHHHHH---------
Q 029312 49 ADLFSESQRIAYTIETRTA--GIPDARTY----------LLTLKEIRERRGLIDEHGAEAMMMDALEKVEK--------- 107 (195)
Q Consensus 49 ~gl~s~~e~I~~tie~~~~--~~~dvR~y----------L~~~~EiR~~~Gl~D~~g~~a~mm~ALdkvEK--------- 107 (195)
+||||++|.+...-.+.+. .-++...| ++.+-+-=...+++|.. +....-..|+...+
T Consensus 118 lGLP~~del~~~~~~y~~~rg~y~~~e~f~w~s~v~YwlvtdLy~~~r~~~lt~~e-Lrk~a~~~L~~makRi~sGE~IP 196 (233)
T PF06992_consen 118 LGLPSVDELYQRYKRYCRYRGFYPSIEEFPWRSNVEYWLVTDLYRRMRQRQLTDEE-LRKRAKKELKAMAKRIASGEPIP 196 (233)
T ss_pred cCCCCHHHHHHHHHHHHHHhCCCCChhhCCCcchhHHHHHHHHHHHHHHccCCHHH-HHHHHHHHHHHHHHHHHCCCcCC
Confidence 7899999888877777442 22343333 34444444456676654 22223344444433
Q ss_pred --------hhCCccccccHhhHHHHHHHHHHHHHHhCCCC
Q 029312 108 --------EIKKPLMRNDKKGMALLTAEFDKINKKLGIRK 139 (195)
Q Consensus 108 --------~igkpL~r~DkkGM~ll~ae~~ki~kklGi~~ 139 (195)
..+.|+ ++++|+ +.+++|-.++|++.
T Consensus 197 ePv~qLp~~~~~P~--s~e~~l----~~iA~lr~k~glk~ 230 (233)
T PF06992_consen 197 EPVKQLPKLHSIPV--SREKAL----EIIAELRAKFGLKG 230 (233)
T ss_pred cHHHHhhhhcCCCC--CHHHHH----HHHHHHHHHhCCCc
Confidence 334555 778887 55788999999975
No 26
>PRK09448 DNA starvation/stationary phase protection protein Dps; Provisional
Probab=32.86 E-value=2.3e+02 Score=23.18 Aligned_cols=75 Identities=9% Similarity=0.080 Sum_probs=44.4
Q ss_pred hhccccccCCCCHHHHHHHHHHHHHHHH-hcCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHHHcCCCchhhHHHHH
Q 029312 20 LRKEKITIAPEDPAAVSQYANVMKTVRE-KADLFSESQRIAYTIETRTAGIPDARTYLLTLKEIRERRGLIDEHGAEAMM 98 (195)
Q Consensus 20 lkk~ki~id~~D~aAV~~YA~~~~~ir~-k~gl~s~~e~I~~tie~~~~~~~dvR~yL~~~~EiR~~~Gl~D~~g~~a~m 98 (195)
++.+.-. .|+.++.+.+|+. +.+ --+-++..+.|...++.+..-+..+|.-. .=.++.++..+|
T Consensus 78 i~~lGg~-p~~t~~e~~~~s~----i~e~~~~~~~~~~~l~~l~~d~~~~~~~~r~~i----------~e~~D~~T~dll 142 (162)
T PRK09448 78 AVQLGGV-ALGTTQVVASKTP----LKSYPLDIHNVQDHLKALADRYAIVANDVRKAI----------DEAGDEDTADIF 142 (162)
T ss_pred HHHcCCC-CCCCHHHHHHhCC----CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH----------hhcCChhHHHHH
Confidence 5555544 2777777777763 333 22333556666666665544333333322 223468888989
Q ss_pred HHHHHHHHHhh
Q 029312 99 MDALEKVEKEI 109 (195)
Q Consensus 99 m~ALdkvEK~i 109 (195)
-+-+..+||.+
T Consensus 143 ~~~~~~~eK~~ 153 (162)
T PRK09448 143 TAASRDLDKFL 153 (162)
T ss_pred HHHHHHHHHHH
Confidence 89999999864
No 27
>PRK05883 acyl carrier protein; Validated
Probab=31.98 E-value=99 Score=23.05 Aligned_cols=78 Identities=15% Similarity=0.237 Sum_probs=50.8
Q ss_pred CCCHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHHHcCCCchhhHHHHH-HHHHHHHHH
Q 029312 29 PEDPAAVSQYANVMKTVREKADLFSESQRIAYTIETRTAGIPDARTYLLTLKEIRERRGLIDEHGAEAMM-MDALEKVEK 107 (195)
Q Consensus 29 ~~D~aAV~~YA~~~~~ir~k~gl~s~~e~I~~tie~~~~~~~dvR~yL~~~~EiR~~~Gl~D~~g~~a~m-m~ALdkvEK 107 (195)
|.|+++| |.+.+.-+++.+|+++.. |.-...+.++.|...+- ++.+-.+|.
T Consensus 9 ~~~~~~I--~~~l~~iia~~l~v~~~~--------------------------I~~d~~l~~dlg~DSL~~v~lv~~lE~ 60 (91)
T PRK05883 9 TSSPSTV--SATLLSILRDDLNVDLTR--------------------------VTPDARLVDDVGLDSVAFAVGMVAIEE 60 (91)
T ss_pred CCCHHHH--HHHHHHHHHHHhCCChhh--------------------------CCCCCchhhccCCChHHHHHHHHHHHH
Confidence 4566665 566666666666665421 12233445556666655 677778889
Q ss_pred hhCCccccccHhhHHHHHHHHHHHHHH
Q 029312 108 EIKKPLMRNDKKGMALLTAEFDKINKK 134 (195)
Q Consensus 108 ~igkpL~r~DkkGM~ll~ae~~ki~kk 134 (195)
..|-.+--.+-.++.+...=++-+..+
T Consensus 61 ~fgI~i~~ee~~~~~TV~dl~~~v~~~ 87 (91)
T PRK05883 61 RLGVALSEEDLLSCDTVGDLEAAIAAK 87 (91)
T ss_pred HHCCCcCHHHHHhCCCHHHHHHHHHHH
Confidence 999888888888887777776666654
No 28
>PRK08045 cystathionine gamma-synthase; Provisional
Probab=31.12 E-value=17 Score=33.05 Aligned_cols=26 Identities=19% Similarity=0.267 Sum_probs=24.0
Q ss_pred HHHHcCCCchhhHHHHHHHHHHHHHH
Q 029312 82 IRERRGLIDEHGAEAMMMDALEKVEK 107 (195)
Q Consensus 82 iR~~~Gl~D~~g~~a~mm~ALdkvEK 107 (195)
||-+.||+|.+..-+-+.+||+++||
T Consensus 360 iR~svGlE~~~dl~~dl~~al~~~~~ 385 (386)
T PRK08045 360 LRISTGIEDGEDLIADLENGFRAANK 385 (386)
T ss_pred EEEEeCcCCHHHHHHHHHHHHHHhhc
Confidence 67889999999999999999999986
No 29
>PF10123 Mu-like_Pro: Mu-like prophage I protein; InterPro: IPR012106 This entry is represented by the Bacteriophage Mu, Gp32. The characteristics of the protein distribution suggest prophage matches.
Probab=30.49 E-value=66 Score=28.89 Aligned_cols=107 Identities=20% Similarity=0.218 Sum_probs=58.5
Q ss_pred CCCHHHHHHHHHH---HHHHHHhcCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHHHcCCCchhhHHHHHHHHHHHH
Q 029312 29 PEDPAAVSQYANV---MKTVREKADLFSESQRIAYTIETRTAGIPDARTYLLTLKEIRERRGLIDEHGAEAMMMDALEKV 105 (195)
Q Consensus 29 ~~D~aAV~~YA~~---~~~ir~k~gl~s~~e~I~~tie~~~~~~~dvR~yL~~~~EiR~~~Gl~D~~g~~a~mm~ALdkv 105 (195)
|.--..+..|... ..+++.+..=-..+..|..-|...+- .|.-|.|+..+. ..|..+.++.+ ++.-.|
T Consensus 213 ~a~~~~~~~~~al~~qlaaL~~~~~~~~~e~lV~~Ai~~Gki-~Pa~r~~~~~l~-------~~d~~a~~~~l-~~~p~i 283 (326)
T PF10123_consen 213 PAKFVPVATVNALQAQLAALKAQLAEAEAEALVDAAIKDGKI-TPAQRDWARALA-------KQDPAAFKAFL-AAAPPI 283 (326)
T ss_pred HHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCC-CHHHHHHHHHHH-------hcCHHHHHHHH-HhCCcc
Confidence 4443344444443 33344443333334444444444332 577788776554 45666666643 332222
Q ss_pred HHhhCCcc----ccccHhhHHHHHHHHHHHHHHhCCCCCChhh
Q 029312 106 EKEIKKPL----MRNDKKGMALLTAEFDKINKKLGIRKEDLPK 144 (195)
Q Consensus 106 EK~igkpL----~r~DkkGM~ll~ae~~ki~kklGi~~eDl~K 144 (195)
=.-.+... -.....|-..|.++=-++.+.+||++||+-|
T Consensus 284 aa~~~~~~~~~~~~~~~~~~~~Lt~ee~av~~~lGis~edf~K 326 (326)
T PF10123_consen 284 AALSGLQTGGAKPPGPADGSAALTAEELAVCRQLGISPEDFAK 326 (326)
T ss_pred ccCccccccccCCCCCCCCCCCCCHHHHHHHHHcCCCHHHhcC
Confidence 11111111 1234468889999999999999999999865
No 30
>PF13438 DUF4113: Domain of unknown function (DUF4113)
Probab=29.94 E-value=46 Score=22.66 Aligned_cols=16 Identities=31% Similarity=0.515 Sum_probs=13.5
Q ss_pred HHHHHHHHHHHHhCCC
Q 029312 123 LLTAEFDKINKKLGIR 138 (195)
Q Consensus 123 ll~ae~~ki~kklGi~ 138 (195)
.|+..+|+||.++|-.
T Consensus 3 ~LM~~iD~iN~r~G~~ 18 (52)
T PF13438_consen 3 RLMQAIDAINRRFGRG 18 (52)
T ss_pred HHHHHHHHHHHhcCCC
Confidence 5888999999999854
No 31
>PRK14181 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=28.42 E-value=1.7e+02 Score=26.65 Aligned_cols=62 Identities=15% Similarity=0.197 Sum_probs=44.4
Q ss_pred HHHHHHHHHHHHHHhhhhccccccCCCCHHHHHHHHHHHHHHHHhcCCCC---------hHHHHHHHHHHhhc
Q 029312 4 NIFLDVKKKFETALGVLRKEKITIAPEDPAAVSQYANVMKTVREKADLFS---------ESQRIAYTIETRTA 67 (195)
Q Consensus 4 ~vF~~vqkkF~~~l~~lkk~ki~id~~D~aAV~~YA~~~~~ir~k~gl~s---------~~e~I~~tie~~~~ 67 (195)
.+..++++....+ +..+++-+.+.++|| |-..|++......+++||.+ .++.+...|+.+-.
T Consensus 11 ~i~~~~k~~v~~l-~~~P~LaiI~vg~d~-as~~Yv~~k~k~~~~~Gi~~~~~~l~~~~t~~el~~~I~~lN~ 81 (287)
T PRK14181 11 HILATIKENISAS-STAPGLAVVLIGNDP-ASEVYVGMKVKKATDLGMVSKAHRLPSDATLSDILKLIHRLNN 81 (287)
T ss_pred HHHHHHHHHHHHh-CCCCcEEEEEeCCCH-HHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhC
Confidence 4555666666665 777778788867776 55689999999999999865 23456677777643
No 32
>PF12450 vWF_A: von Willebrand factor ; InterPro: IPR022156 This domain family is found in bacteria, and is approximately 100 amino acids in length. The family is found in association with PF00092 from PFAM. There are two conserved sequence motifs: STF and DVD. There are two completely conserved residues (E and N) that may be functionally important. In hemostasis, platelet adhesion to the damaged vessel wall is mediated by several proteins, including von Willebrand factor. In solution vWF becomes immobilized via its A3 domain on the fibrillar collagen of the vessel wall and acts as an intermediary between collagen and the platelet receptor glycoprotein Ibalpha (GPIbalpha), which is the only platelet receptor that does not require prior activation for bond formation.
Probab=27.51 E-value=54 Score=25.76 Aligned_cols=46 Identities=20% Similarity=0.188 Sum_probs=37.6
Q ss_pred hhhccccccCCCCHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHhhcCCC
Q 029312 19 VLRKEKITIAPEDPAAVSQYANVMKTVREKADLFSESQRIAYTIETRTAGIP 70 (195)
Q Consensus 19 ~lkk~ki~id~~D~aAV~~YA~~~~~ir~k~gl~s~~e~I~~tie~~~~~~~ 70 (195)
-+..++|.+|.++ |++++.-|...-=.|+...||.++|+||.-+-|
T Consensus 27 plSTFSiDVDtaS------Ys~vRr~L~~G~lPp~~aVR~EE~iNyF~YdY~ 72 (99)
T PF12450_consen 27 PLSTFSIDVDTAS------YSNVRRFLNQGQLPPPDAVRIEEMINYFDYDYP 72 (99)
T ss_pred CccceeEEcCccc------HHHHHHHHHCCCCCCcCceeHHHHhhcccCCCC
Confidence 3677888887654 889999999988888889999999999876543
No 33
>PLN02469 hydroxyacylglutathione hydrolase
Probab=27.17 E-value=1.4e+02 Score=26.01 Aligned_cols=49 Identities=20% Similarity=0.320 Sum_probs=31.1
Q ss_pred ccCCCCHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHH---hhcCCCcHHHHH
Q 029312 26 TIAPEDPAAVSQYANVMKTVREKADLFSESQRIAYTIET---RTAGIPDARTYL 76 (195)
Q Consensus 26 ~id~~D~aAV~~YA~~~~~ir~k~gl~s~~e~I~~tie~---~~~~~~dvR~yL 76 (195)
.|+|++++ +.+|.+.....|. -|.|+.---|.....+ ++++.++++..+
T Consensus 186 ~vep~n~~-~~~~~~~~~~~~~-~~~~t~pstl~~E~~~Npflr~~~~~~~~~~ 237 (258)
T PLN02469 186 TVEPDNEK-LKQKLEWAEKQRQ-AGLPTVPSTIEEELETNPFMRVDLPEIQEKV 237 (258)
T ss_pred hhCCCCHH-HHHHHHHHHHHHH-CCCCcCCccHHHHHhhCCeecCCCHHHHHHh
Confidence 45677764 6666666665554 4777665555555555 677777777665
No 34
>PRK09841 cryptic autophosphorylating protein tyrosine kinase Etk; Provisional
Probab=27.06 E-value=6.5e+02 Score=25.21 Aligned_cols=86 Identities=14% Similarity=0.270 Sum_probs=58.9
Q ss_pred cccccCCCCHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHhhcCCCcHHHHHHHH----HHHHHHcCCCchhhHHHHH
Q 029312 23 EKITIAPEDPAAVSQYANVMKTVREKADLFSESQRIAYTIETRTAGIPDARTYLLTL----KEIRERRGLIDEHGAEAMM 98 (195)
Q Consensus 23 ~ki~id~~D~aAV~~YA~~~~~ir~k~gl~s~~e~I~~tie~~~~~~~dvR~yL~~~----~EiR~~~Gl~D~~g~~a~m 98 (195)
+.|.....||.-.+..+|..-.+=-+-.+-.-.+....+++.+.+..+.+++=|..+ ..+|.+.|+-|...--...
T Consensus 230 i~Is~~~~dP~~Aa~ilN~la~~Yi~~~l~~k~~~a~~a~~fL~~qL~~l~~~L~~aE~~l~~fr~~~~~~d~~~ea~~~ 309 (726)
T PRK09841 230 LELTMTGDDPQLITRILNSIANNYLQQNIARQAAQDSQSLEFLQRQLPEVRSELDQAEEKLNVYRQQRDSVDLNLEAKAV 309 (726)
T ss_pred EEEEEeCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHH
Confidence 346667889999999888766655444555556677777888888888888777764 8899999997743222334
Q ss_pred HHHHHHHHHh
Q 029312 99 MDALEKVEKE 108 (195)
Q Consensus 99 m~ALdkvEK~ 108 (195)
.+-+.+++.+
T Consensus 310 l~~~~~l~~q 319 (726)
T PRK09841 310 LEQIVNVDNQ 319 (726)
T ss_pred HHHHHHHHHH
Confidence 4555555544
No 35
>PRK14178 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=26.62 E-value=1.8e+02 Score=26.48 Aligned_cols=64 Identities=16% Similarity=0.227 Sum_probs=46.9
Q ss_pred hHHHHHHHHHHHHHHhhhhccccccCCCCHHHHHHHHHHHHHHHHhcCCCC---------hHHHHHHHHHHhhcC
Q 029312 3 KNIFLDVKKKFETALGVLRKEKITIAPEDPAAVSQYANVMKTVREKADLFS---------ESQRIAYTIETRTAG 68 (195)
Q Consensus 3 K~vF~~vqkkF~~~l~~lkk~ki~id~~D~aAV~~YA~~~~~ir~k~gl~s---------~~e~I~~tie~~~~~ 68 (195)
+.+..+++++...+ +..+++-+.+.++||+ -..|.+......+++||.+ .++.+...|+.+-.+
T Consensus 10 ~~i~~~~~~~v~~l-g~~P~Laii~vg~d~a-s~~Yv~~k~k~~~~~Gi~~~~~~l~~~~~~~el~~~I~~lN~D 82 (279)
T PRK14178 10 EKRLELLKEEIIES-GLYPRLATVIVGDDPA-SQMYVRMKHRACERVGIGSVGIELPGDATTRTVLERIRRLNED 82 (279)
T ss_pred HHHHHHHHHHHHHh-CCCCeEEEEEeCCChh-HHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCC
Confidence 45666777777665 7788888888666665 5679999999999999975 335567777776443
No 36
>PF13801 Metal_resist: Heavy-metal resistance; PDB: 3EPV_C 2Y3D_A 2Y3H_D 2Y3G_B 2Y3B_A 2Y39_A 3LAY_H.
Probab=26.54 E-value=2.2e+02 Score=20.05 Aligned_cols=21 Identities=19% Similarity=0.401 Sum_probs=14.3
Q ss_pred CCCCHHHHHHHHHHHHHHHHh
Q 029312 28 APEDPAAVSQYANVMKTVREK 48 (195)
Q Consensus 28 d~~D~aAV~~YA~~~~~ir~k 48 (195)
+|-|+++|..-.+.+-+++.+
T Consensus 82 ~~~D~~~i~a~~~~~~~~~~~ 102 (125)
T PF13801_consen 82 PPPDEAAIEALLEEIREAQAE 102 (125)
T ss_dssp SSS-HHHHHHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHHHHH
Confidence 355788888877777776665
No 37
>cd07631 BAR_APPL1 The Bin/Amphiphysin/Rvs (BAR) domain of Adaptor protein, Phosphotyrosine interaction, PH domain and Leucine zipper containing 1. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Adaptor protein, Phosphotyrosine interaction, PH domain and Leucine zipper containing (APPL) proteins are effectors of the small GTPase Rab5 that function in endosome-mediated signaling. They contain BAR, pleckstrin homology (PH) and phosphotyrosine binding (PTB) domains. They form homo- and hetero-oligomers that are mediated by their BAR domains. Vertebrates contain two APPL proteins, APPL1 and APPL2. APPL1 interacts with diverse receptors (e.g. NGF receptor TrkA, FSHR, adiponectin receptors) and signaling proteins (e.g. Akt, PI3K), and may function as an adaptor linked to many distinct signaling pathways. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be invo
Probab=26.13 E-value=4.7e+02 Score=23.27 Aligned_cols=23 Identities=17% Similarity=0.174 Sum_probs=15.8
Q ss_pred ccccHhhHHHHHHHHHHHHHHhC
Q 029312 114 MRNDKKGMALLTAEFDKINKKLG 136 (195)
Q Consensus 114 ~r~DkkGM~ll~ae~~ki~kklG 136 (195)
...|=.+.+-....|+++..++.
T Consensus 100 ~kedL~~~Ke~KK~FdK~Se~~d 122 (215)
T cd07631 100 KERDLKEILTLKEVFQIASNDHD 122 (215)
T ss_pred HHHHHHHHHHHHHHHHHhhhHHH
Confidence 45566777778888887766554
No 38
>PRK14182 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=25.75 E-value=2.1e+02 Score=26.08 Aligned_cols=64 Identities=17% Similarity=0.174 Sum_probs=43.7
Q ss_pred HHHHHHHHHHHHHH--hhhhccccccCCCCHHHHHHHHHHHHHHHHhcCCCC---------hHHHHHHHHHHhhcC
Q 029312 4 NIFLDVKKKFETAL--GVLRKEKITIAPEDPAAVSQYANVMKTVREKADLFS---------ESQRIAYTIETRTAG 68 (195)
Q Consensus 4 ~vF~~vqkkF~~~l--~~lkk~ki~id~~D~aAV~~YA~~~~~ir~k~gl~s---------~~e~I~~tie~~~~~ 68 (195)
.+..+.++....+- +..+++-+.+.++|| |-..|.+......+++||.+ .++.+..+|+.+-++
T Consensus 12 ~i~~~ik~~v~~l~~~g~~P~LaiI~vg~d~-as~~Yv~~k~k~a~~~Gi~~~~~~l~~~~t~~~l~~~I~~lN~d 86 (282)
T PRK14182 12 KVKGEVATEVRALAARGVQTGLTVVRVGDDP-ASAIYVRGKRKDCEEVGITSVEHHLPATTTQAELLALIARLNAD 86 (282)
T ss_pred HHHHHHHHHHHHHHhCCCCCeEEEEEeCCCH-HHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCC
Confidence 45555555555543 335566677756666 56789999999999999976 345677888877554
No 39
>PF02284 COX5A: Cytochrome c oxidase subunit Va; InterPro: IPR003204 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits is known as Va.; GO: 0004129 cytochrome-c oxidase activity; PDB: 2DYR_R 3AG1_E 3ABL_E 1V54_R 2EIJ_R 1OCR_E 2DYS_E 2EIM_E 2OCC_E 3ASN_R ....
Probab=25.67 E-value=43 Score=26.98 Aligned_cols=12 Identities=25% Similarity=0.191 Sum_probs=5.6
Q ss_pred ChHHHHHHHHHH
Q 029312 53 SESQRIAYTIET 64 (195)
Q Consensus 53 s~~e~I~~tie~ 64 (195)
+...||...|..
T Consensus 62 a~AVR~lE~iK~ 73 (108)
T PF02284_consen 62 ALAVRILEGIKD 73 (108)
T ss_dssp HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHH
Confidence 334445555544
No 40
>PF02630 SCO1-SenC: SCO1/SenC; InterPro: IPR003782 This family is involved in biogenesis of respiratory and photosynthetic systems. In yeast the SCO1 protein is specifically required for a post-translational step in the accumulation of subunits 1 and 2 of cytochrome c oxidase (COXI and COX-II) []. It is a mitochondrion-associated cytochrome c oxidase assembly factor. The purple nonsulphur photosynthetic eubacterium Rhodobacter capsulatus is a versatile organism that can obtain cellular energy by several means, including the capture of light energy for photosynthesis as well as the use of light-independent respiration, in which molecular oxygen serves as a terminal electron acceptor. The SenC protein is required for optimal cytochrome c oxidase activity in aerobically grown R. capsulatus cells and is involved in the induction of structural polypeptides of the light-harvesting and reaction centre complexes [].; PDB: 2K6V_A 3ME8_A 3ME7_A 2GT6_A 2GQL_A 2GQK_A 2GGT_B 1WP0_C 2HRN_A 2GQM_A ....
Probab=25.58 E-value=76 Score=25.74 Aligned_cols=57 Identities=16% Similarity=0.237 Sum_probs=33.9
Q ss_pred HHHHHHHHHHHHhhhhccccccCCC--CHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHH
Q 029312 6 FLDVKKKFETALGVLRKEKITIAPE--DPAAVSQYANVMKTVREKADLFSESQRIAYTIET 64 (195)
Q Consensus 6 F~~vqkkF~~~l~~lkk~ki~id~~--D~aAV~~YA~~~~~ir~k~gl~s~~e~I~~tie~ 64 (195)
+.++++++..--..++=..|++||+ .|++.++|+...-. .-.|+-...+.|....+.
T Consensus 75 l~~~~~~l~~~~~~v~~v~ISvDP~~DTp~~L~~Y~~~~~~--~~~~ltg~~~~i~~l~~~ 133 (174)
T PF02630_consen 75 LSQLQKQLGEEGKDVQFVFISVDPERDTPEVLKKYAKKFGP--DFIGLTGSREEIEELAKQ 133 (174)
T ss_dssp HHHHHHHHHHTTTTEEEEEEESSTTTC-HHHHHHHHHCHTT--TCEEEEEEHHHHHHHHHH
T ss_pred HHHHHHHhhhccCceEEEEEEeCCCCCCHHHHHHHHHhcCC--CcceeEeCHHHHHHHHHH
Confidence 4455665555422455667999996 59999999986531 113333445555555554
No 41
>PRK14180 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=25.33 E-value=1.9e+02 Score=26.24 Aligned_cols=48 Identities=17% Similarity=0.167 Sum_probs=34.2
Q ss_pred hhccccccCCCCHHHHHHHHHHHHHHHHhcCCCCh---------HHHHHHHHHHhhcC
Q 029312 20 LRKEKITIAPEDPAAVSQYANVMKTVREKADLFSE---------SQRIAYTIETRTAG 68 (195)
Q Consensus 20 lkk~ki~id~~D~aAV~~YA~~~~~ir~k~gl~s~---------~e~I~~tie~~~~~ 68 (195)
.+++-+.+.++||| -..|.+......+++||.+. ++.+...|+.+-++
T Consensus 31 ~P~La~I~vg~d~a-s~~Yv~~k~k~~~~~Gi~~~~~~l~~~~~~~el~~~I~~lN~D 87 (282)
T PRK14180 31 TPKLVAIIVGNDPA-SKTYVASKEKACAQVGIDSQVITLPEHTTESELLELIDQLNND 87 (282)
T ss_pred CCeEEEEEeCCCHH-HHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCC
Confidence 44555666566665 56699999999999998653 35677888776543
No 42
>PRK10363 cpxP periplasmic repressor CpxP; Reviewed
Probab=24.86 E-value=1.2e+02 Score=26.01 Aligned_cols=36 Identities=22% Similarity=0.174 Sum_probs=30.1
Q ss_pred cccCCCCHHHHHHHHHHHHHHHHh------------cCCCChHHHHHH
Q 029312 25 ITIAPEDPAAVSQYANVMKTVREK------------ADLFSESQRIAY 60 (195)
Q Consensus 25 i~id~~D~aAV~~YA~~~~~ir~k------------~gl~s~~e~I~~ 60 (195)
|+=|+-|++||..-+..|-..... ..|.+|+|+-+.
T Consensus 85 I~ad~FDEaavra~a~kma~~~~e~~Vem~k~~nqmy~lLTPEQKaq~ 132 (166)
T PRK10363 85 VTAENFDENAVRAQAEKMAQEQVARQVEMAKVRNQMYRLLTPEQQAVL 132 (166)
T ss_pred HhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHH
Confidence 344899999999999998877665 789999998775
No 43
>COG1938 Archaeal enzymes of ATP-grasp superfamily [General function prediction only]
Probab=24.03 E-value=2.3e+02 Score=25.57 Aligned_cols=59 Identities=31% Similarity=0.374 Sum_probs=41.5
Q ss_pred cccccHhhHHHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 029312 113 LMRNDKKGMALLTAEFDKINKKLGIRKEDLPKYEEQLELKIAKAQLEELKKDALEAMETQKKREE 177 (195)
Q Consensus 113 L~r~DkkGM~ll~ae~~ki~kklGi~~eDl~K~~ee~el~~aK~~L~elk~~a~e~m~~~kkre~ 177 (195)
..+-|-.+-+.+ ++.+|+-+|+. =|-+++++|++ +...||++|-++..+.++.+++..+
T Consensus 181 ~~~PDP~AAa~v---ve~lnk~~~l~-V~td~L~keAe--~i~~~lekl~eq~~~~~~~~~~~~e 239 (244)
T COG1938 181 GDRPDPRAAARV---VEALNKMLGLN-VDTDKLEKEAE--EIEEQLEKLAEQLEKEEERVEREEE 239 (244)
T ss_pred CCCCChHHHHHH---HHHHHHHhcCc-cCHHHHHHHHH--HHHHHHHHHHHHHHHHHHhhhcccc
Confidence 344577766555 45889989987 46778888774 5677888888887777777655543
No 44
>PRK08249 cystathionine gamma-synthase; Provisional
Probab=23.61 E-value=30 Score=31.70 Aligned_cols=28 Identities=25% Similarity=0.344 Sum_probs=25.2
Q ss_pred HHHHcCCCchhhHHHHHHHHHHHHHHhh
Q 029312 82 IRERRGLIDEHGAEAMMMDALEKVEKEI 109 (195)
Q Consensus 82 iR~~~Gl~D~~g~~a~mm~ALdkvEK~i 109 (195)
||-+.||+|.+..-+-+..||+.+|+++
T Consensus 371 iR~svGlE~~~dl~~dl~~al~~~~~~~ 398 (398)
T PRK08249 371 VRISVGIEDTEDLIADLEQAFAHLESEL 398 (398)
T ss_pred EEEEeccCCHHHHHHHHHHHHHHhhhcC
Confidence 6788999999999999999999998763
No 45
>TIGR02215 phage_chp_gp8 phage conserved hypothetical protein, phiE125 gp8 family. This model describes a family of proteins found exclusively in phage or in prophage regions of bacterial genomes, including the phage-like Rhodobacter capsulatus gene transfer agent, which packages DNA. Members of this family show some similarity to members of pfam05135, a putative DNA packaging protein family.
Probab=23.53 E-value=1.3e+02 Score=25.45 Aligned_cols=39 Identities=15% Similarity=0.201 Sum_probs=29.1
Q ss_pred HHHHHHHHcCC--C-chhhHHHHHHHHHHHHHHhhCCccccc
Q 029312 78 TLKEIRERRGL--I-DEHGAEAMMMDALEKVEKEIKKPLMRN 116 (195)
Q Consensus 78 ~~~EiR~~~Gl--~-D~~g~~a~mm~ALdkvEK~igkpL~r~ 116 (195)
++.|.+.-.++ . |+.=..+.+..|.+.+|..+|++|++.
T Consensus 15 tl~e~K~~LRi~~~~eDa~l~~li~aA~~~iE~~tgr~l~~q 56 (188)
T TIGR02215 15 TVADFKAFLRLGTEVQDEVLRSLLTAARAAIEARTGKILISQ 56 (188)
T ss_pred CHHHHHHhcCCCCCccHHHHHHHHHHHHHHHHHHhCceeeee
Confidence 35566666666 2 344456778899999999999999874
No 46
>PRK10241 hydroxyacylglutathione hydrolase; Provisional
Probab=23.41 E-value=1.5e+02 Score=25.39 Aligned_cols=49 Identities=14% Similarity=0.148 Sum_probs=34.8
Q ss_pred cCCCCHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHH---hhcCCCcHHHHHH
Q 029312 27 IAPEDPAAVSQYANVMKTVREKADLFSESQRIAYTIET---RTAGIPDARTYLL 77 (195)
Q Consensus 27 id~~D~aAV~~YA~~~~~ir~k~gl~s~~e~I~~tie~---~~~~~~dvR~yL~ 77 (195)
++|+++ ++.+|.+.....| +-|.|+.---|.....+ ++++.|++|..+.
T Consensus 178 ~~p~n~-~l~~~~~~~~~~~-~~~~~t~pstl~~E~~~Npflr~~~~~~~~~~~ 229 (251)
T PRK10241 178 ILPHDL-SINDYYRKVKELR-AKNQITLPVILKNERQINLFLRTEDIDLINVIN 229 (251)
T ss_pred hCCCCH-HHHHHHHHHHHHH-HCCCCcCCccHHHHHhhCCeecCCCHHHHHHhc
Confidence 346665 5777777777666 45677776677777766 7889999997763
No 47
>PF05731 TROVE: TROVE domain; InterPro: IPR008858 The TROVE (Telomerase, Ro and Vault) domain is a module of ~300-500 residues that is found in TEP1 and Ro60 the protein components of three ribonucleoprotein particles. The TROVE domain is also found in bacterial ribonucleoproteins suggesting an ancient origin of these ribonucleoproteins. The TROVE domain can be found associated with other domains, such as the VWFA domain, the TEP1 N-terminal domain, the NACHT-NTPase domain, and WD-40 repeats. The TROVE domain may be involved in binding the RNA components of the three RNPs, which are telomerase RNA, Y RNA and vault RNA []. The TROVE domain contains a few absolutely conserved residues. As none of these conserved residues are the polar type of amino acids found in active sites, it seems unlikely that this region has an enzymatic function [].; GO: 0003723 RNA binding, 0030529 ribonucleoprotein complex; PDB: 2NVO_A 2I91_B 1YVP_A 1YVR_A.
Probab=23.03 E-value=2.3e+02 Score=26.34 Aligned_cols=93 Identities=18% Similarity=0.155 Sum_probs=64.5
Q ss_pred CCCCHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHHHcCCCchhhHHHHHHHHHHHHHH
Q 029312 28 APEDPAAVSQYANVMKTVREKADLFSESQRIAYTIETRTAGIPDARTYLLTLKEIRERRGLIDEHGAEAMMMDALEKVEK 107 (195)
Q Consensus 28 d~~D~aAV~~YA~~~~~ir~k~gl~s~~e~I~~tie~~~~~~~dvR~yL~~~~EiR~~~Gl~D~~g~~a~mm~ALdkvEK 107 (195)
..+||.-|. +...-+|++..|++....+....=......+-++.|+..+=. ..++......+-+.+..-..
T Consensus 51 ~~~dpefvl---k~avy~r~~~~lr~~~~~L~Alaa~~~~~r~~~~~~~~~Vvr------~p~dl~ef~~~~q~~~~~~~ 121 (385)
T PF05731_consen 51 AEGDPEFVL---KLAVYARQEGNLRKTPNFLLALAACAPSCRPAARRYFPRVVR------RPSDLFEFVQYYQSLARKGV 121 (385)
T ss_dssp HCCTHHHHH---HHHHHHHHCT-SS-SHHHHHHHHHHCCCSHHHHHHHHHHH--------SHHHHHHHHHH--HHHHHHH
T ss_pred HhcChHHHH---HHHHHHHHhCCCCCchHHHHHHHHhCcccHHHHHHHHHHHHc------CcchHHHHHHHHHHHHhccc
Confidence 378898884 455889999999999999998887777677888888777644 56666666666544443334
Q ss_pred hhCCccccccHhhHHHHHHHHH
Q 029312 108 EIKKPLMRNDKKGMALLTAEFD 129 (195)
Q Consensus 108 ~igkpL~r~DkkGM~ll~ae~~ 129 (195)
..++++=+.=++||+-+..+|+
T Consensus 122 ~~~~~lg~~lRkav~~wf~~~d 143 (385)
T PF05731_consen 122 RGRRGLGRALRKAVADWFNQFD 143 (385)
T ss_dssp TTT-S-SHHHHHHHHHHHHCS-
T ss_pred cCCCCcCHHHHHHHHHHHhcCC
Confidence 5578999999999999988775
No 48
>TIGR02144 LysX_arch Lysine biosynthesis enzyme LysX. The family of proteins found in this equivalog include the characterized LysX from Thermus thermophilus which is part of a well-organized lysine biosynthesis gene cluster. LysX is believed to carry out an ATP-dependent acylation of the amino group of alpha-aminoadipate in the prokaryotic version of the fungal AAA lysine biosynthesis pathway. No species having a sequence in this equivalog contains the elements of the more common diaminopimelate lysine biosythesis pathway, and none has been shown to be a lysine auxotroph. These sequences have mainly recieved the name of the related enzyme, "ribosomal protein S6 modification protein RimK". RimK has been characterized in E. coli, and acts by ATP-dependent condensation of S6 with glutamate residues.
Probab=22.79 E-value=1.4e+02 Score=24.90 Aligned_cols=43 Identities=7% Similarity=0.040 Sum_probs=32.6
Q ss_pred HHHhhhhccccccCCCCHHHHHHHHHH--HHHHHHhcCCCChHHHH
Q 029312 15 TALGVLRKEKITIAPEDPAAVSQYANV--MKTVREKADLFSESQRI 58 (195)
Q Consensus 15 ~~l~~lkk~ki~id~~D~aAV~~YA~~--~~~ir~k~gl~s~~e~I 58 (195)
.....+....+|+ -+++.++....++ ++.+.+++|+|.|.-.+
T Consensus 63 ~~~~~le~~g~~~-~n~~~~~~~~~dK~~~~~~l~~~gip~P~t~~ 107 (280)
T TIGR02144 63 YSARLLEALGVPV-INSSHVIEACGDKIFTYLKLAKAGVPTPRTYL 107 (280)
T ss_pred HHHHHHHHCCCcE-ECcHHHHHHHhhHHHHHHHHHHCCcCCCCeEe
Confidence 3344455567776 5689999999999 88888999999886543
No 49
>PRK12751 cpxP periplasmic stress adaptor protein CpxP; Reviewed
Probab=22.60 E-value=1.4e+02 Score=25.00 Aligned_cols=35 Identities=26% Similarity=0.205 Sum_probs=28.0
Q ss_pred cCCCCHHHHHHHHHHHHHHHHh------------cCCCChHHHHHHH
Q 029312 27 IAPEDPAAVSQYANVMKTVREK------------ADLFSESQRIAYT 61 (195)
Q Consensus 27 id~~D~aAV~~YA~~~~~ir~k------------~gl~s~~e~I~~t 61 (195)
=+|=||+||..-+..|-..... +.+.+|+|+-...
T Consensus 93 Ad~FDeaAvra~~~kma~~~~e~~v~~~~~~~qmy~lLTPEQra~l~ 139 (162)
T PRK12751 93 ADKFDEAAVRAQAEKMSQNQIERHVEMAKVRNQMYNLLTPEQKEALN 139 (162)
T ss_pred cCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHH
Confidence 4789999999998888766553 7899999987653
No 50
>PF13871 Helicase_C_4: Helicase_C-like
Probab=22.47 E-value=96 Score=28.16 Aligned_cols=54 Identities=20% Similarity=0.284 Sum_probs=37.0
Q ss_pred cccccCCCCHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHhh-cCCCcHHHHHHHHHH
Q 029312 23 EKITIAPEDPAAVSQYANVMKTVREKADLFSESQRIAYTIETRT-AGIPDARTYLLTLKE 81 (195)
Q Consensus 23 ~ki~id~~D~aAV~~YA~~~~~ir~k~gl~s~~e~I~~tie~~~-~~~~dvR~yL~~~~E 81 (195)
..+|+ |+-|.....+...+.+....+||.+.+..=. .+. ..-++|.+||+.+.=
T Consensus 188 ~~~~~-~~~~~~~~~F~~~~~~~L~~VGL~~~~~~~g----~~~~~k~~~V~kFLNRLLG 242 (278)
T PF13871_consen 188 PPVPP-PGYPGSLGEFFEDMRTALEGVGLLSEDDESG----GLKLDKDPSVPKFLNRLLG 242 (278)
T ss_pred CccCC-CCccccHHHHHHHHHHHHhhcccccccccCC----cccccccccHHHHHHHhhC
Confidence 34555 7777788889999999999999964321111 111 234599999999864
No 51
>TIGR03017 EpsF chain length determinant protein EpsF. Sequences in this family of proteins are members of the chain length determinant family (pfam02706) which includes the wzc protein from E.coli. This family of proteins are homologous to the EpsF protein of the methanolan biosynthesis operon of Methylobacillus species strain 12S. The distribution of this protein appears to be restricted to a subset of exopolysaccharide operons containing a syntenic grouping of genes including a variant of the EpsH exosortase protein. Exosortase has been proposed to be involved in the targetting and processing of proteins containing the PEP-CTERM domain to the exopolysaccharide layer.
Probab=22.42 E-value=5.9e+02 Score=23.11 Aligned_cols=70 Identities=14% Similarity=0.156 Sum_probs=47.1
Q ss_pred ccccCCCCHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHhhcCCCcHHHHHH----HHHHHHHHcCCCchhh
Q 029312 24 KITIAPEDPAAVSQYANVMKTVREKADLFSESQRIAYTIETRTAGIPDARTYLL----TLKEIRERRGLIDEHG 93 (195)
Q Consensus 24 ki~id~~D~aAV~~YA~~~~~ir~k~gl~s~~e~I~~tie~~~~~~~dvR~yL~----~~~EiR~~~Gl~D~~g 93 (195)
.|.....||.-....+|.+-+.--+..+-.-......+++.+....+.+|+=|. .+..+|.+.|+.+..+
T Consensus 135 ~is~~~~dp~~A~~i~n~~~~~y~~~~~~~~~~~~~~~~~fl~~ql~~~~~~l~~ae~~l~~fr~~~~i~~~~~ 208 (444)
T TIGR03017 135 SIEFSGVDPRFAATVANAFAQAYIDTNIELKVEPAQKAALWFVQQIAALREDLARAQSKLSAYQQEKGIVSSDE 208 (444)
T ss_pred EEEEeCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCcccCc
Confidence 345556799999988887776655555544445555566666666666665554 4678999999976543
No 52
>PRK04778 septation ring formation regulator EzrA; Provisional
Probab=22.35 E-value=5.6e+02 Score=24.92 Aligned_cols=95 Identities=21% Similarity=0.228 Sum_probs=59.1
Q ss_pred HHHHHHHHHHHHHHhhhhccccccCCCCHHHHH-HHHHHHHHH---HHh-cCCCChHHHHHHHHHH---hhcCCCcHHHH
Q 029312 4 NIFLDVKKKFETALGVLRKEKITIAPEDPAAVS-QYANVMKTV---REK-ADLFSESQRIAYTIET---RTAGIPDARTY 75 (195)
Q Consensus 4 ~vF~~vqkkF~~~l~~lkk~ki~id~~D~aAV~-~YA~~~~~i---r~k-~gl~s~~e~I~~tie~---~~~~~~dvR~y 75 (195)
.-|..++..-+.+...+.. .|| +..||. .|......+ ..+ -+|-.--..+..+|.+ ++..-+.|..-
T Consensus 448 ~~~~~~~~~i~~l~~~L~~--g~V---Nm~ai~~e~~e~~~~~~~L~~q~~dL~~~a~~lE~~Iqy~nRfr~~~~~V~~~ 522 (569)
T PRK04778 448 EMFFEVSDEIEALAEELEE--KPI---NMEAVNRLLEEATEDVETLEEETEELVENATLTEQLIQYANRYRSDNEEVAEA 522 (569)
T ss_pred HHHHHHHHHHHHHHHHhcc--CCC---CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCHHHHHH
Confidence 4567777777777777776 444 567777 665443332 111 2222222333333333 77788888888
Q ss_pred HHHHHHHHHHcCCCchhhHHHHHHHHHHHHH
Q 029312 76 LLTLKEIRERRGLIDEHGAEAMMMDALEKVE 106 (195)
Q Consensus 76 L~~~~EiR~~~Gl~D~~g~~a~mm~ALdkvE 106 (195)
+..+.. -+-=.++..+-..+-+||++||
T Consensus 523 f~~Ae~---lF~~~~Y~~al~~~~~alE~ve 550 (569)
T PRK04778 523 LNEAER---LFREYDYKAALEIIATALEKVE 550 (569)
T ss_pred HHHHHH---HHHhCChHHHHHHHHHHHHhhC
Confidence 888877 4433678888887888888886
No 53
>PF12244 DUF3606: Protein of unknown function (DUF3606); InterPro: IPR022037 This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=22.30 E-value=1.3e+02 Score=20.87 Aligned_cols=43 Identities=16% Similarity=0.261 Sum_probs=31.3
Q ss_pred ccCCCCHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHhhcCCCcHHHHHH
Q 029312 26 TIAPEDPAAVSQYANVMKTVREKADLFSESQRIAYTIETRTAGIPDARTYLL 77 (195)
Q Consensus 26 ~id~~D~aAV~~YA~~~~~ir~k~gl~s~~e~I~~tie~~~~~~~dvR~yL~ 77 (195)
.|++++|..|..+|. ++|++ .+++...|...--.+.+||.||.
T Consensus 14 ~I~~~e~~ev~ywa~-------~~gvt--~~~L~~AV~~vG~~~~~V~~~L~ 56 (57)
T PF12244_consen 14 RIDLSEPYEVRYWAK-------RFGVT--EEQLREAVRAVGNSRAAVRAYLG 56 (57)
T ss_pred hcCCCCHHHHHHHHH-------HHCcC--HHHHHHHHHHHCcCHHHHHHHHc
Confidence 356788888887764 56664 46677777777777888888885
No 54
>PRK14194 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=22.04 E-value=2.5e+02 Score=25.75 Aligned_cols=64 Identities=20% Similarity=0.249 Sum_probs=43.1
Q ss_pred HHHHHHHHHHHHHH--hhhhccccccCCCCHHHHHHHHHHHHHHHHhcCCCC---------hHHHHHHHHHHhhcC
Q 029312 4 NIFLDVKKKFETAL--GVLRKEKITIAPEDPAAVSQYANVMKTVREKADLFS---------ESQRIAYTIETRTAG 68 (195)
Q Consensus 4 ~vF~~vqkkF~~~l--~~lkk~ki~id~~D~aAV~~YA~~~~~ir~k~gl~s---------~~e~I~~tie~~~~~ 68 (195)
.+..++++....+- +..+++-+.+.++|| |-..|++......+++||.+ .++.+...|+.+-++
T Consensus 15 ~i~~~lk~~i~~l~~~g~~P~LaiI~vg~d~-as~~Yv~~k~k~a~~~Gi~~~~~~l~~~~t~~~l~~~I~~lN~D 89 (301)
T PRK14194 15 RVLAQVREDVRTLKAAGIEPALAVILVGNDP-ASQVYVRNKILRAEEAGIRSLEHRLPADTSQARLLALIAELNAD 89 (301)
T ss_pred HHHHHHHHHHHHHHhCCCCCeEEEEEeCCCh-hHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHcCC
Confidence 34455555555433 334556666655555 66889999999999999976 355677888877554
No 55
>PLN02897 tetrahydrofolate dehydrogenase/cyclohydrolase, putative
Probab=21.82 E-value=1.4e+02 Score=28.06 Aligned_cols=65 Identities=9% Similarity=0.098 Sum_probs=46.0
Q ss_pred hHHHHHHHHHHHHHH---hhhhccccccCCCCHHHHHHHHHHHHHHHHhcCCCCh---------HHHHHHHHHHhhcC
Q 029312 3 KNIFLDVKKKFETAL---GVLRKEKITIAPEDPAAVSQYANVMKTVREKADLFSE---------SQRIAYTIETRTAG 68 (195)
Q Consensus 3 K~vF~~vqkkF~~~l---~~lkk~ki~id~~D~aAV~~YA~~~~~ir~k~gl~s~---------~e~I~~tie~~~~~ 68 (195)
+.+..+++++...+- +...++-+.+.++||+.- .|.+......+++||.+. ++.+...|+.+-.+
T Consensus 66 ~~i~~~lk~~v~~l~~~~g~~P~LaiIlvGddpaS~-~Yv~~k~K~a~~~GI~~~~~~l~~~~te~ell~~I~~lN~D 142 (345)
T PLN02897 66 EEIRTKIASEVRKMKKAVGKVPGLAVVLVGQQRDSQ-TYVRNKIKACEETGIKSLLAELPEDCTEGQILSALRKFNED 142 (345)
T ss_pred HHHHHHHHHHHHHHHhccCCCCeEEEEEeCCChHHH-HHHHHHHHHHHhcCCEEEEEECCCCCCHHHHHHHHHHHhCC
Confidence 345556666655542 445677778878888776 899999999999998652 34577788777555
No 56
>PF04614 Pex19: Pex19 protein family; InterPro: IPR006708 Peroxisome(s) form an intracellular compartment, bounded by a typical lipid bilayer membrane. Peroxisome functions are often specialised by organism and cell type; two widely distributed and well-conserved functions are H2O2-based respiration and fatty acid beta-oxidation. Other functions include ether lipid (plasmalogen) synthesis and cholesterol synthesis in animals, the glyoxylate cycle in germinating seeds ("glyoxysomes"), photorespiration in leaves, glycolysis in trypanosomes ("glycosomes"), and methanol and/or amine oxidation and assimilation in some yeasts. PEX genes encode the machinery ("peroxins") required to assemble the peroxisome. Membrane assembly and maintenance requires three of these (peroxins 3, 16, and 19) and may occur without the import of the matrix (lumen) enzymes. Matrix protein import follows a branched pathway of soluble recycling receptors, with one branch for each class of peroxisome targeting sequence (two are well characterised), and a common trunk for all. At least one of these receptors, Pex5p, enters and exits peroxisomes as it functions. Proliferation of the organelle is regulated by Pex11p. Peroxisome biogenesis is remarkably conserved among eukaryotes. A group of fatal, inherited neuropathologies are recognised as peroxisome biogenesis diseases. ; GO: 0005777 peroxisome; PDB: 2WL8_B 2W85_B.
Probab=21.67 E-value=1.8e+02 Score=25.63 Aligned_cols=134 Identities=19% Similarity=0.277 Sum_probs=36.5
Q ss_pred HHHHHHHHHHHHHhhhhccccccCCCCHHHHHHHHHHHHHHHHh---------cCCC----------ChHHHHHHHHHHh
Q 029312 5 IFLDVKKKFETALGVLRKEKITIAPEDPAAVSQYANVMKTVREK---------ADLF----------SESQRIAYTIETR 65 (195)
Q Consensus 5 vF~~vqkkF~~~l~~lkk~ki~id~~D~aAV~~YA~~~~~ir~k---------~gl~----------s~~e~I~~tie~~ 65 (195)
...+.++.|..+|+ -. .+.+|++...+...+..+... .... +-...|+.||+.+
T Consensus 9 ~~~~l~~~m~~Lm~------~~-~~~~~e~~~~fe~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~F~~~I~~TL~~L 81 (248)
T PF04614_consen 9 FAKQLQDEMAELMG------GD-EEEDPEAAEQFEKLLKELGEAESEALSASGSKPSSASSESATDESFQSTISETLERL 81 (248)
T ss_dssp ----HHHHHHHHHH------------------------------------------------------------------
T ss_pred HHHHHHHHHHHHHh------cc-cccCHHHHHHHHHHHHHHhcccccccccccccccccccCCCcchhHHHHHHHHHHHH
Confidence 44677888999998 22 366788888888887766652 1111 3335677777777
Q ss_pred hcCCCcHHHHHHH--------HHHHHHHcCC------CchhhHHHHHHHHHHHHHHhhCCccccccHhhHHHHHHHHHHH
Q 029312 66 TAGIPDARTYLLT--------LKEIRERRGL------IDEHGAEAMMMDALEKVEKEIKKPLMRNDKKGMALLTAEFDKI 131 (195)
Q Consensus 66 ~~~~~dvR~yL~~--------~~EiR~~~Gl------~D~~g~~a~mm~ALdkvEK~igkpL~r~DkkGM~ll~ae~~ki 131 (195)
.+.+.++-+=... +..+=..++. .++.+...+|..-+. .=+-|.++- .-|+-|..++-+.
T Consensus 82 ~es~~~~~~~~~~~~~~~dd~l~~ll~~m~~~~~~~~~~~~~~~~~l~~mm~---qL~SKevLY---ePmKel~~kyP~w 155 (248)
T PF04614_consen 82 KESGDNADAAAAEDSSNSDDMLAQLLKQMGGGGDGGGGGDEDFDKMLQGMMQ---QLLSKEVLY---EPMKELRDKYPEW 155 (248)
T ss_dssp -------------------------------------------HHHHHHHHH---HHTSHHHHH---HHHHHHHHHHHHH
T ss_pred HhCcccccccccccccCCHHHHHHHHHHHhccccccCCCchhHHHHHHHHHH---HhccHhhhh---hhHHHHHHHhHHH
Confidence 7766655443311 1111113322 233333333322221 112222221 4677777888877
Q ss_pred HHHhC--CCCCChhhHHHHHHH
Q 029312 132 NKKLG--IRKEDLPKYEEQLEL 151 (195)
Q Consensus 132 ~kklG--i~~eDl~K~~ee~el 151 (195)
.++.+ +.+||+.+|+.|.++
T Consensus 156 L~~n~~~l~~ed~~rY~~Q~~~ 177 (248)
T PF04614_consen 156 LEENKSKLSAEDYERYEKQYEL 177 (248)
T ss_dssp HHHHCCCS-HHHHHHHHHHHHH
T ss_pred HHhCcCcCCHHHHHHHHHHHHH
Confidence 66655 667788888887654
No 57
>TIGR02778 ligD_pol DNA polymerase LigD, polymerase domain. DNA repair of double-stranded breaks by non-homologous end joining (NHEJ) is accomplished by a two-protein system that is present in a minority of prokaryotes. One component is the Ku protein (see TIGR02772), which binds DNA ends. The other is a DNA ligase, a protein that is a multidomain polypeptide in most of those bacteria that have NHEJ, a permuted polypeptide in Mycobacterium tuberculosis and a few other species, and the product of tandem genes in some other bacteria. This model represents the polymerase domain.
Probab=21.42 E-value=1e+02 Score=27.65 Aligned_cols=31 Identities=16% Similarity=0.189 Sum_probs=26.2
Q ss_pred ccccCCCCH---HHHHHHHHHHHHHHHhcCCCCh
Q 029312 24 KITIAPEDP---AAVSQYANVMKTVREKADLFSE 54 (195)
Q Consensus 24 ki~id~~D~---aAV~~YA~~~~~ir~k~gl~s~ 54 (195)
-+.|||+++ +.|..=|..+..+..++||.|.
T Consensus 118 vfDLDP~~~~~f~~v~~~A~~~r~~L~~lgL~~f 151 (245)
T TIGR02778 118 VFDLDPGPGVAWKLVVEAAQLIRELLDELGLESF 151 (245)
T ss_pred EEECCCCCCCCHHHHHHHHHHHHHHHHHcCCccc
Confidence 356899886 7888899999999999999873
No 58
>PRK14168 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=21.32 E-value=2.8e+02 Score=25.42 Aligned_cols=64 Identities=11% Similarity=0.194 Sum_probs=43.5
Q ss_pred HHHHHHHHHHHHHH---hhhhccccccCCCCHHHHHHHHHHHHHHHHhcCCCC---------hHHHHHHHHHHhhcC
Q 029312 4 NIFLDVKKKFETAL---GVLRKEKITIAPEDPAAVSQYANVMKTVREKADLFS---------ESQRIAYTIETRTAG 68 (195)
Q Consensus 4 ~vF~~vqkkF~~~l---~~lkk~ki~id~~D~aAV~~YA~~~~~ir~k~gl~s---------~~e~I~~tie~~~~~ 68 (195)
.+..+++++...+. +..+++-+.+.++|| |-..|++......+++||.+ .++.+...|+.+-.+
T Consensus 14 ~i~~~lk~~v~~l~~~~g~~P~LaiI~vg~d~-as~~Yv~~k~k~~~~~Gi~~~~~~l~~~~t~~el~~~I~~lN~D 89 (297)
T PRK14168 14 EILEEIRGEVAELKEKYGKVPGLVTILVGESP-ASLSYVTLKIKTAHRLGFHEIQDNQSVDITEEELLALIDKYNND 89 (297)
T ss_pred HHHHHHHHHHHHHHHcCCCCCeEEEEEeCCCH-HHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCC
Confidence 45556666666654 345667777755555 66889999999999999864 345566777776543
No 59
>cd04865 LigD_Pol_like_2 LigD_Pol_like_2: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD, subgroup 2. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The Pol domains of PaeLigD and Mycobacterium tuberculosis (Mt)LigD are stimulated by manganese, are error-prone, and prefer adding rNTPs to dNTPs in vitro; however PaeLigD and MtLigD belong to other subgroups, proteins in this subgroup await functional characterization.
Probab=20.99 E-value=1.1e+02 Score=27.24 Aligned_cols=31 Identities=19% Similarity=0.243 Sum_probs=26.1
Q ss_pred ccccCCCCH---HHHHHHHHHHHHHHHhcCCCCh
Q 029312 24 KITIAPEDP---AAVSQYANVMKTVREKADLFSE 54 (195)
Q Consensus 24 ki~id~~D~---aAV~~YA~~~~~ir~k~gl~s~ 54 (195)
-+.|||+++ +.|..=|..+..+..++||.|.
T Consensus 103 vfDLDP~~~~~f~~v~~~A~~vr~~L~~lgL~sf 136 (228)
T cd04865 103 VIDLDPQPGTSFEDVVEVALLVREVLDELGLRGY 136 (228)
T ss_pred EEECCCCCCCCHHHHHHHHHHHHHHHHHcCCccc
Confidence 367899965 8888999999999999999874
No 60
>COG0420 SbcD DNA repair exonuclease [DNA replication, recombination, and repair]
Probab=20.62 E-value=1.6e+02 Score=26.42 Aligned_cols=49 Identities=22% Similarity=0.464 Sum_probs=38.5
Q ss_pred HHHHHHHHHHHHHHhhhhcccc--ccCCCC--------HHHHHHHHHHHHHHHHhcCCCC
Q 029312 4 NIFLDVKKKFETALGVLRKEKI--TIAPED--------PAAVSQYANVMKTVREKADLFS 53 (195)
Q Consensus 4 ~vF~~vqkkF~~~l~~lkk~ki--~id~~D--------~aAV~~YA~~~~~ir~k~gl~s 53 (195)
.-+-++++.|.++|+..++.++ .|-.|| +.|+..+.+.+..++. +|||-
T Consensus 20 ~r~~d~~~~f~~~l~~a~~~~vD~vliAGDlFd~~~Ps~~a~~~~~~~l~~l~~-~~Ipv 78 (390)
T COG0420 20 SRLEDQKKAFDELLEIAKEEKVDFVLIAGDLFDTNNPSPRALKLFLEALRRLKD-AGIPV 78 (390)
T ss_pred cchHHHHHHHHHHHHHHHHccCCEEEEccccccCCCCCHHHHHHHHHHHHHhcc-CCCcE
Confidence 3577899999999999999998 444554 7888888888888776 66663
No 61
>cd04863 MtLigD_Pol_like MtLigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Mycobacterium tuberculosis (Mt)LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. MtLigD is monomeric and contains an N-terminal Pol domain, a central phosphoesterase module, and a C-terminal ligase domain. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The MtLigD Pol domain is stimulated by manganese, is error-prone, and prefers adding rNTPs to dNTPs in vitro. The MtLigD Pol domain has been shown to prefer DNA gapped substrates
Probab=20.47 E-value=1.1e+02 Score=27.20 Aligned_cols=30 Identities=17% Similarity=0.211 Sum_probs=25.8
Q ss_pred cccCCCCH---HHHHHHHHHHHHHHHhcCCCCh
Q 029312 25 ITIAPEDP---AAVSQYANVMKTVREKADLFSE 54 (195)
Q Consensus 25 i~id~~D~---aAV~~YA~~~~~ir~k~gl~s~ 54 (195)
+.|||++. +.|..=|..+..+..++||.|.
T Consensus 107 fDLDP~~~~~f~~v~~~A~~~r~~L~~lgL~s~ 139 (231)
T cd04863 107 FDLDPGEPAGLVECARVALWLRDRLAALGLASF 139 (231)
T ss_pred EECCCCCCCCHHHHHHHHHHHHHHHHHcCCccc
Confidence 56888875 8899999999999999999873
No 62
>TIGR01428 HAD_type_II 2-haloalkanoic acid dehalogenase, type II. Note that the Type I HAD enzymes have not yet been fully characterized, but clearly utilize a substantially different catalytic mechanism and are thus unlikely to be related.
Probab=20.39 E-value=2.4e+02 Score=22.25 Aligned_cols=98 Identities=16% Similarity=0.240 Sum_probs=47.7
Q ss_pred HHHHHHhcCCCChHHHHHHHHHH--hhcCCCcHHHHHHHHHHHHHHcCCCchhhHHHHHHHHHHHH--HHhhCCcccccc
Q 029312 42 MKTVREKADLFSESQRIAYTIET--RTAGIPDARTYLLTLKEIRERRGLIDEHGAEAMMMDALEKV--EKEIKKPLMRND 117 (195)
Q Consensus 42 ~~~ir~k~gl~s~~e~I~~tie~--~~~~~~dvR~yL~~~~EiR~~~Gl~D~~g~~a~mm~ALdkv--EK~igkpL~r~D 117 (195)
...+.+..|++...+.+....+. .....|+|+.+|..+.+.-...++-.- +....+...|... ..-.- ....++
T Consensus 65 ~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~~~g~~~~i~Sn-~~~~~~~~~l~~~gl~~~fd-~i~~s~ 142 (198)
T TIGR01428 65 LRYLLGRLGLEDDESAADRLAEAYLRLPPHPDVPAGLRALKERGYRLAILSN-GSPAMLKSLVKHAGLDDPFD-AVLSAD 142 (198)
T ss_pred HHHHHHHcCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHCCCeEEEEeC-CCHHHHHHHHHHCCChhhhh-eeEehh
Confidence 44566778887554444444443 244678999999988863233444111 2222222222211 11111 122333
Q ss_pred HhhHH-HHHHHHHHHHHHhCCCCCC
Q 029312 118 KKGMA-LLTAEFDKINKKLGIRKED 141 (195)
Q Consensus 118 kkGM~-ll~ae~~ki~kklGi~~eD 141 (195)
.-|.. --..-+..+.+++|+.|++
T Consensus 143 ~~~~~KP~~~~~~~~~~~~~~~p~~ 167 (198)
T TIGR01428 143 AVRAYKPAPQVYQLALEALGVPPDE 167 (198)
T ss_pred hcCCCCCCHHHHHHHHHHhCCChhh
Confidence 32321 1223456677778888765
No 63
>PF03732 Retrotrans_gag: Retrotransposon gag protein ; InterPro: IPR005162 Transposable elements (TEs) promote various chromosomal rearrangements more efficiently, and often more specifically, than other cellular processes. Retrotransposons are structurally similar to retroviruses and are bounded by long terminal repeats. This entry represents eukaryotic Gag or capsid-related retrotranspon-related proteins. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.
Probab=20.36 E-value=2.1e+02 Score=19.44 Aligned_cols=33 Identities=18% Similarity=0.269 Sum_probs=27.9
Q ss_pred HHHHHHHHHHHHHHHhcCC-CChHHHHHHHHHHh
Q 029312 33 AAVSQYANVMKTVREKADL-FSESQRIAYTIETR 65 (195)
Q Consensus 33 aAV~~YA~~~~~ir~k~gl-~s~~e~I~~tie~~ 65 (195)
.-|..|.+....+...++- .+++..|..-++|+
T Consensus 61 esv~~y~~rf~~l~~~~~~~~~e~~~v~~f~~GL 94 (96)
T PF03732_consen 61 ESVREYVNRFRELARRAPPPMDEEMLVERFIRGL 94 (96)
T ss_pred CcHHHHHHHHHHHHHHCCCCcCHHHHHHHHHHCC
Confidence 4588999999999999995 88888888877765
No 64
>TIGR02684 dnstrm_HI1420 probable addiction module antidote protein. gene pairs, when found on the bacterial chromosome, are located often with prophage regions, but also both in integrated plasmid regions and in housekeeping gene regions. Analysis suggests that the gene pair may serve as an addiction module.
Probab=20.13 E-value=2.7e+02 Score=20.89 Aligned_cols=67 Identities=18% Similarity=0.185 Sum_probs=38.6
Q ss_pred HHHHHhhcCCCcHHHHHHHHHHHHHHcCCCchhhHHHHHHHHHHHHHHhhCCccccccHhhHHHHHHHHHHHHHHhCCC
Q 029312 60 YTIETRTAGIPDARTYLLTLKEIRERRGLIDEHGAEAMMMDALEKVEKEIKKPLMRNDKKGMALLTAEFDKINKKLGIR 138 (195)
Q Consensus 60 ~tie~~~~~~~dvR~yL~~~~EiR~~~Gl~D~~g~~a~mm~ALdkvEK~igkpL~r~DkkGM~ll~ae~~ki~kklGi~ 138 (195)
.-|+..-+++ ....++..+.++|+..|++.-.-..-+=-..|-.+|+--+.|= + ..+-+|.+.+|++
T Consensus 19 ~~l~~~le~~-~~~~~~~~l~~~r~~~glSqLAe~~GIs~stLs~iE~g~~~Ps-------~----~tL~kI~~aLgi~ 85 (89)
T TIGR02684 19 EYLAQALEDG-DPAYIAHALGYIARARGMTQLARKTGLSRESLYKALSGKGNPT-------F----DTILKVTKALGLK 85 (89)
T ss_pred HHHHHHHHcC-CHHHHHHHHHHHHHHCChHHHHHHHCCCHHHHHHHHcCCCCCC-------H----HHHHHHHHHcCCc
Confidence 3344433333 5557888899999999997311111111356777886655552 2 3445666667665
Done!