Query 028429
Match_columns 209
No_of_seqs 124 out of 324
Neff 6.5
Searched_HMMs 46136
Date Fri Mar 29 11:24:11 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028429.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028429hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2536 MAM33, mitochondrial m 100.0 3.1E-47 6.7E-52 324.3 18.7 185 13-202 57-263 (263)
2 PF02330 MAM33: Mitochondrial 100.0 6.1E-43 1.3E-47 293.2 14.7 172 23-200 1-204 (204)
3 KOG4024 Complement component 1 100.0 1.4E-30 3E-35 216.8 21.3 185 11-203 65-266 (266)
4 TIGR01881 cas_Cmr5 CRISPR-asso 81.0 6.1 0.00013 30.9 6.2 43 155-197 70-121 (127)
5 PF08513 LisH: LisH; InterPro 69.4 8 0.00017 21.9 3.1 25 154-178 1-25 (27)
6 KOG4233 DNA-bridging protein B 66.4 8.9 0.00019 27.9 3.4 36 161-196 32-67 (90)
7 PF00123 Hormone_2: Peptide ho 64.7 17 0.00037 21.0 3.8 24 171-194 4-27 (28)
8 PF02961 BAF: Barrier to autoi 57.5 15 0.00031 27.2 3.3 38 159-196 30-67 (89)
9 smart00070 GLUCA Glucagon like 47.8 31 0.00068 19.7 3.0 22 172-193 5-26 (27)
10 PRK11814 cysteine desulfurase 47.4 35 0.00075 32.6 5.0 51 145-199 424-479 (486)
11 PF13154 DUF3991: Protein of u 47.3 11 0.00023 26.5 1.2 18 162-179 1-19 (77)
12 PF08275 Toprim_N: DNA primase 39.2 25 0.00054 27.2 2.2 18 158-175 12-29 (128)
13 PHA01623 hypothetical protein 38.6 1.1E+02 0.0024 20.3 5.1 30 151-182 19-48 (56)
14 PHA02360 hypothetical protein 37.7 35 0.00075 23.7 2.5 17 154-170 29-45 (70)
15 PF10929 DUF2811: Protein of u 37.3 30 0.00065 23.5 2.1 31 150-180 4-41 (57)
16 PF00070 Pyr_redox: Pyridine n 37.1 35 0.00075 23.4 2.5 22 150-171 36-57 (80)
17 PF13376 OmdA: Bacteriocin-pro 35.6 74 0.0016 21.3 3.9 40 150-197 4-43 (63)
18 KOG2635 Medium subunit of clat 35.5 1.6E+02 0.0035 28.1 7.2 29 101-130 446-475 (512)
19 PF13495 Phage_int_SAM_4: Phag 35.4 77 0.0017 21.6 4.2 34 156-201 1-34 (85)
20 PF07063 DUF1338: Domain of un 30.4 1.1E+02 0.0024 27.4 5.2 46 150-195 100-180 (302)
21 smart00667 LisH Lissencephaly 29.8 72 0.0016 17.6 2.7 27 153-179 3-29 (34)
22 PF09862 DUF2089: Protein of u 29.4 79 0.0017 24.3 3.5 58 115-177 2-59 (113)
23 PF08321 PPP5: PPP5 TPR repeat 28.5 50 0.0011 24.4 2.3 24 141-164 39-64 (95)
24 PF14265 DUF4355: Domain of un 28.4 1.2E+02 0.0025 22.9 4.4 40 155-195 69-108 (125)
25 TIGR03420 DnaA_homol_Hda DnaA 27.1 1.5E+02 0.0033 24.0 5.2 55 147-204 157-213 (226)
26 PF12122 DUF3582: Protein of u 27.0 60 0.0013 24.3 2.5 22 153-174 9-30 (101)
27 smart00777 Mad3_BUB1_I Mad3/BU 25.5 1.1E+02 0.0024 23.8 3.8 30 158-187 83-112 (125)
28 PF13434 K_oxygenase: L-lysine 25.5 42 0.00091 30.2 1.7 33 159-194 70-105 (341)
29 PF13034 DUF3895: Protein of u 25.2 1.1E+02 0.0023 22.1 3.4 28 152-179 1-30 (78)
30 PF10915 DUF2709: Protein of u 24.9 1E+02 0.0022 26.3 3.6 39 156-194 196-235 (238)
31 cd04739 DHOD_like Dihydroorota 23.6 1.1E+02 0.0025 27.2 4.1 50 141-194 268-324 (325)
32 PRK10416 signal recognition pa 23.5 2.9E+02 0.0062 24.7 6.6 35 150-184 42-76 (318)
33 TIGR01981 sufD FeS assembly pr 23.2 84 0.0018 28.6 3.2 37 145-185 316-352 (366)
34 TIGR01446 DnaD_dom DnaD and ph 23.1 2E+02 0.0044 19.3 4.5 34 151-184 12-45 (73)
35 PRK13031 preprotein translocas 23.0 1.9E+02 0.0042 23.3 4.8 31 95-126 57-88 (149)
36 PF12826 HHH_2: Helix-hairpin- 22.7 68 0.0015 21.6 1.9 42 149-190 23-64 (64)
37 COG5559 Uncharacterized conser 22.6 52 0.0011 22.6 1.3 29 149-187 8-36 (65)
38 PF09701 Cas_Cmr5: CRISPR-asso 22.6 2E+02 0.0044 21.8 4.8 42 156-197 66-118 (122)
39 PF10281 Ish1: Putative stress 21.8 74 0.0016 19.2 1.8 15 158-172 7-21 (38)
40 TIGR02793 nikR nickel-responsi 21.8 2E+02 0.0044 22.4 4.6 20 151-170 6-25 (129)
41 PF02268 TFIIA_gamma_N: Transc 21.3 1.5E+02 0.0032 19.4 3.2 32 150-181 9-40 (49)
42 PF09373 PMBR: Pseudomurein-bi 21.2 1E+02 0.0022 18.1 2.2 21 187-207 8-28 (33)
43 PF07671 DUF1601: Protein of u 20.8 1.2E+02 0.0026 18.7 2.5 17 162-178 6-22 (37)
44 PF12123 Amidase02_C: N-acetyl 20.6 1.1E+02 0.0023 19.7 2.4 18 152-169 24-41 (45)
45 PF04726 Microvir_J: Microviru 20.6 50 0.0011 18.2 0.7 13 2-14 2-14 (24)
46 PF08311 Mad3_BUB1_I: Mad3/BUB 20.4 1.3E+02 0.0029 23.0 3.4 30 158-187 83-112 (126)
47 PF01458 UPF0051: Uncharacteri 20.3 57 0.0012 27.4 1.4 32 145-180 196-227 (229)
48 PHA02115 hypothetical protein 20.1 1.1E+02 0.0024 22.5 2.6 43 23-65 3-47 (105)
49 PRK13658 hypothetical protein; 20.1 1.4E+02 0.0029 20.2 2.8 27 20-47 32-59 (59)
No 1
>KOG2536 consensus MAM33, mitochondrial matrix glycoprotein [Energy production and conversion]
Probab=100.00 E-value=3.1e-47 Score=324.26 Aligned_cols=185 Identities=32% Similarity=0.561 Sum_probs=152.8
Q ss_pred chhHHHHHHHHHHHHHHHHhcCCCCC-----CCC-CCCCEEEeCCCCCCceEEEEeeCCeEEEEEEeecC--CCCCCCCC
Q 028429 13 AVVDSILLRSLRDHYEEVAKMTPPPK-----VSP-PSSFTIVKGALDTHGPVLKRMYGSEQISIYVTRLG--NIIRGGDD 84 (209)
Q Consensus 13 ~~~d~~Ll~~L~~Ei~~~~~~~~~~~-----~~~-~~~F~i~~~~gd~~~v~L~R~~~~E~I~V~~~~~~--~~~~~~~e 84 (209)
++.++.|++.+.+||+++.+..++.+ +|. +.||+|+++||. ++|+|+|+|++|+|+|.++|.. ...+.++.
T Consensus 57 ss~t~~~~r~i~~EI~s~~~~~~~~~~~~~~~~~~~~pf~ied~PG~-q~V~L~r~~~GE~i~V~v~v~~~~~~~~~e~~ 135 (263)
T KOG2536|consen 57 SSFTQNLLRVILSEIKSEKKHDPPHQVLEEEIPLSKFPFEIEDRPGE-QWVVLTRKFEGETIKVEVDVTQLVTDEPEEDE 135 (263)
T ss_pred cccccchHHHHHHHHHHhhhcCCchhhhhhccccCCCCcceecCCCc-eEEEEEeecCCceEEEEEeeehhccCCcchhc
Confidence 44578999999999998777666554 444 489999999996 9999999999999999888532 11111110
Q ss_pred -------CCCC-------CCCCcceeEEEEEEcCCCCceEEEEEeeeCCeEEEeEEEeecCccccCcccCCCCcCCCCCC
Q 028429 85 -------DDDD-------DDGINQLFLHVEMSKPGQKNSLLFLCGLYPDALGIHSVSMRPNLESEGILVVPSQYTGPSFQ 150 (209)
Q Consensus 85 -------~e~d-------~e~~~~~~~~V~ItK~~~~~~L~f~c~~~~~e~~I~~v~~~~~~~~~~~~~~~~~Y~GP~F~ 150 (209)
++++ .+...+++|+|+|+|++ |.+|+|.|++++|+|.|++++++++... ...+.+|.||.|.
T Consensus 136 de~e~~~~~~~~~~~~~~~~~~~~iplvV~vsK~~-~~sLef~cta~pD~i~Idslsv~~~~d~---~~~~l~Y~GP~F~ 211 (263)
T KOG2536|consen 136 DETEEEDEDEDQEDDDPLSDNISNIPLVVTVSKGD-GVSLEFLCTAFPDEIVIDSLSVRPPIDA---SEDQLAYEGPSFE 211 (263)
T ss_pred cccccccccccccccccCCCcceeeEEEEEEecCC-CceEEEEeecCCCceEEeeeEecCCCCc---cchhhhccCCChh
Confidence 0111 12346799999999965 8999999999999999999999997643 2344799999999
Q ss_pred CccHHHHHHHHHHHHHcCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhhcC
Q 028429 151 DLDERMRDALHSYIEERGVNESLFPFLQAWLYVKDNRNLMHWFRQVGQYISG 202 (209)
Q Consensus 151 ~LDe~Lq~~~~~YLeeRGId~~la~fl~~y~~~KEq~eYi~WL~~v~~Fv~~ 202 (209)
+||++||++||.|||+|||+++|+.|||+||.+|+++||++||++||+||+.
T Consensus 212 eLDe~Lqd~fh~fLEeRGI~esl~~FL~~ym~~Kd~rEYl~WlksvK~Fv~~ 263 (263)
T KOG2536|consen 212 ELDEELQDSFHRFLEERGIKESLASFLHAYMKNKDSREYLRWLKSVKSFVEQ 263 (263)
T ss_pred HHhHHHHHHHHHHHHHcCCCHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhcC
Confidence 9999999999999999999999999999999999999999999999999974
No 2
>PF02330 MAM33: Mitochondrial glycoprotein; InterPro: IPR003428 This mitochondrial matrix protein family contains members of the MAM33 family which bind to the globular 'heads' of C1Q.; GO: 0005759 mitochondrial matrix; PDB: 3QV0_A 1YQF_F 3JV1_A 1P32_A 3RPX_A.
Probab=100.00 E-value=6.1e-43 Score=293.21 Aligned_cols=172 Identities=28% Similarity=0.557 Sum_probs=132.6
Q ss_pred HHHHHHHHHhcCCC----CCCCCCCCCEEEeCCCCCCceEEEEeeCCeEEEEEEeecCCCC----CCCCCCC---CCC--
Q 028429 23 LRDHYEEVAKMTPP----PKVSPPSSFTIVKGALDTHGPVLKRMYGSEQISIYVTRLGNII----RGGDDDD---DDD-- 89 (209)
Q Consensus 23 L~~Ei~~~~~~~~~----~~~~~~~~F~i~~~~gd~~~v~L~R~~~~E~I~V~~~~~~~~~----~~~~e~e---~d~-- 89 (209)
|++||+++++...+ .+..++.+|+|.+.+|+ +.|+|+|+|++|+|+|.|++.. .+ +++.+.+ +++
T Consensus 1 L~~EI~~E~~~~~~~~~~~~~l~~~~f~i~d~~g~-~~V~L~r~~~~E~I~V~f~v~~-~~~~~~~~~~~~~~~~e~~~~ 78 (204)
T PF02330_consen 1 LKSEIKYEKENYESPDSLKEFLPPSPFEIEDKPGG-SEVTLTREFGGEKIRVTFNVND-SVDPPFDEDEDEEEGEEEEEE 78 (204)
T ss_dssp HHHHHHHHHHHCT-HHHHCCHHHHTTTCEEEECCT-TEEEEEEEETTEEEEEEEECCC-H--------------------
T ss_pred ChHHHHHHHHcccccHHHHhhCCCCCCEEEEcCCC-cEEEEEEecCCcEEEEEEECCc-cCCCCCCccccchhccccccc
Confidence 78899877665442 12335678999999885 9999999999999999998543 22 1111100 000
Q ss_pred ---------C-----CCcceeEEEEEEcCCCCceEEEEEeeeCCeEEEeEEEeecCccc-c----CcccCCCCcCCCCCC
Q 028429 90 ---------D-----GINQLFLHVEMSKPGQKNSLLFLCGLYPDALGIHSVSMRPNLES-E----GILVVPSQYTGPSFQ 150 (209)
Q Consensus 90 ---------e-----~~~~~~~~V~ItK~~~~~~L~f~c~~~~~e~~I~~v~~~~~~~~-~----~~~~~~~~Y~GP~F~ 150 (209)
+ ..+.+.++|.|+||+ ++|.|.|++++|+|.|++|+++++... . +.| ...|.||.|+
T Consensus 79 ~~~~~~fe~~~~~~~~~~~~~~~v~~~k~~--~~l~f~~~~~~d~~~I~~v~~~~~~~~~~~~~~~e~--~~~y~gp~f~ 154 (204)
T PF02330_consen 79 EISEPDFEVEIPKEDEVSFPFFVVVISKPG--DGLEFDCSAQDDEFSIDNVSFYPDGDSTKDSAEAEW--EDAYYGPDFD 154 (204)
T ss_dssp ------CEEECCCCCCCEEEEEEEEEECTC--EEEEEEEECCTTEEEEEEEEEESSHHHH--SHHHHH--HCSS-ECEGG
T ss_pred ccccccchhcccccccccceeEEEEEEcCC--CceEEeEeccCceEEEEEEEEecCccccccccchhc--cccccCCccc
Confidence 0 012457899999984 569999999999999999999986433 1 112 4689999999
Q ss_pred CccHHHHHHHHHHHHHcCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 028429 151 DLDERMRDALHSYIEERGVNESLFPFLQAWLYVKDNRNLMHWFRQVGQYI 200 (209)
Q Consensus 151 ~LDe~Lq~~~~~YLeeRGId~~la~fl~~y~~~KEq~eYi~WL~~v~~Fv 200 (209)
+||++||++|++||++||||.+||+||++||++|||++|++||++|++||
T Consensus 155 ~LDe~Lq~~~~~yLeeRGId~~la~fl~~y~~~kEq~eYi~wL~~l~~Fv 204 (204)
T PF02330_consen 155 ELDENLQDAFMNYLEERGIDEELANFLHDYSTDKEQREYIRWLKNLKKFV 204 (204)
T ss_dssp GSBHHHHHHHHHHHHHTT-SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred cCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 99999999999999999999999999999999999999999999999997
No 3
>KOG4024 consensus Complement component 1, Q subcomponent binding protein/mRNA splicing factor SF2, subunit P32 [Defense mechanisms]
Probab=99.98 E-value=1.4e-30 Score=216.80 Aligned_cols=185 Identities=19% Similarity=0.258 Sum_probs=144.0
Q ss_pred CCchhHHHHHHHHHHHHHHHHhcCCCCCCC-CCCCCEEEeCCCCCCceEEEEeeCCeEEEEEEeecCCCCCCCCC--C-C
Q 028429 11 GFAVVDSILLRSLRDHYEEVAKMTPPPKVS-PPSSFTIVKGALDTHGPVLKRMYGSEQISIYVTRLGNIIRGGDD--D-D 86 (209)
Q Consensus 11 ~~~~~d~~Ll~~L~~Ei~~~~~~~~~~~~~-~~~~F~i~~~~gd~~~v~L~R~~~~E~I~V~~~~~~~~~~~~~e--~-e 86 (209)
-++.++++|.++|.+||+.+.+..+.+..| ...||.+.-+ |.+|.|+|+.++|+|.|+|| ++|++|.+++ + .
T Consensus 65 vht~~~~alv~fl~~Ei~~erk~qkgkt~Pkt~~Gf~v~l~---gaev~Ltkk~~~Eki~V~FN-vNhsvd~~e~~e~eP 140 (266)
T KOG4024|consen 65 VHTELQQALVRFLEAEIQLERKNQKGKTAPKTFAGFQVTLK---GAEVRLTKKNGSEKILVVFN-VNHSVDMDEGFEDEP 140 (266)
T ss_pred cchHHHHHHHHHHHHHHHHHHHhhcCCccCccccceEEEec---CceeEEeeccCCceEEEEEe-cCCccCcccCCccCc
Confidence 367889999999999999888887777666 6799999986 58999999999999999999 5566543322 1 1
Q ss_pred CCC-----CCCcceeEEEEEEcCCCCceEEEEEeeeCCe-------EEEeEEEeecCccc-cCcccCCCCcCCCCCCCcc
Q 028429 87 DDD-----DGINQLFLHVEMSKPGQKNSLLFLCGLYPDA-------LGIHSVSMRPNLES-EGILVVPSQYTGPSFQDLD 153 (209)
Q Consensus 87 ~d~-----e~~~~~~~~V~ItK~~~~~~L~f~c~~~~~e-------~~I~~v~~~~~~~~-~~~~~~~~~Y~GP~F~~LD 153 (209)
..+ +..+.++|+|.|.|+ +++|.|+|.+.+++ +.|..+++.+.... ..+|. ...|. -.-+.||
T Consensus 141 sq~~~~~pe~tS~P~F~VeiiKG--~~~L~f~c~~~~~e~QedEy~~~~~~~~~a~f~~~gn~~~~-d~vYa-~~gd~lD 216 (266)
T KOG4024|consen 141 SQAVAPVPEATSMPPFTVEIIKG--DQRLCFHCELVPVEDQEDEYDFRVEEFYVAPFAKNGNEDVP-DEVYA-SSGDYLD 216 (266)
T ss_pred cccCCCCcccccCCCeEEEEEeC--CeeEEEEeecCCcccCcccccceeeeEEeeecccCCCccCC-cceee-ccCcccC
Confidence 111 123679999999996 58999999995442 34444443332111 11233 35674 3348999
Q ss_pred HHHHHHHHHHHHHcCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCC
Q 028429 154 ERMRDALHSYIEERGVNESLFPFLQAWLYVKDNRNLMHWFRQVGQYISGK 203 (209)
Q Consensus 154 e~Lq~~~~~YLeeRGId~~la~fl~~y~~~KEq~eYi~WL~~v~~Fv~~~ 203 (209)
..|++.|+.||++||||.+||+-|.+|++..||.+||.+|++||+|++++
T Consensus 217 ~~LyDlL~~~LeerG~d~~Fa~~Lv~laTa~EH~~YIglLeklkkF~~~q 266 (266)
T KOG4024|consen 217 PDLYDLLFVYLEERGLDARFAKTLVALATAYEHSQYIGLLEKLKKFISKQ 266 (266)
T ss_pred HHHHHHHHHHHHHcCccHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhcCC
Confidence 99999999999999999999999999999999999999999999999874
No 4
>TIGR01881 cas_Cmr5 CRISPR-associated protein, Cmr5 family. CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This family, represented by TM1791.1 of Thermotoga maritima, is found in both archaeal and bacterial species as part of the 6-gene CRISPR RAMP module.
Probab=80.99 E-value=6.1 Score=30.88 Aligned_cols=43 Identities=9% Similarity=0.285 Sum_probs=30.0
Q ss_pred HHHHHHHHHHHHcCCChh---HHHHHHH-----HH-HHHHHHHHHHHHHHHH
Q 028429 155 RMRDALHSYIEERGVNES---LFPFLQA-----WL-YVKDNRNLMHWFRQVG 197 (209)
Q Consensus 155 ~Lq~~~~~YLeeRGId~~---la~fl~~-----y~-~~KEq~eYi~WL~~v~ 197 (209)
-|...+..||.++|+-+. +...|.+ |+ ...|=-+|..||+++.
T Consensus 70 ~l~~~l~~~L~~~~~~~~~~~l~~~il~~~~~~y~~~T~eaL~~l~WLKRfA 121 (127)
T TIGR01881 70 KYYAHILYWLKERELVDKFKNALKELMEKDYSDSRIATEEALRYLNWLKRLA 121 (127)
T ss_pred HHHHHHHHHHHHcccccchHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHH
Confidence 478899999999987654 3333322 33 4567778999999865
No 5
>PF08513 LisH: LisH; InterPro: IPR013720 The LisH motif is found in a large number of eukaryotic proteins, from metazoa, fungi and plants that have a wide range of functions. The recently solved structure of the LisH domain in the N-terminal region of LIS1 depicted it as a novel dimerization motif, and that other structural elements are likely to play an important role in dimerisation [, , ]. The LisH (lis homology) domain mediates protein dimerisation and tetramerisation. The LisH domain is found in Sif2, a component of the Set3 complex which is responsible for repressing meiotic genes. It has been shown that the LisH domain helps mediate interaction with components of the Set3 complex []. ; PDB: 2XTE_L 2XTC_B 2XTD_A 1UUJ_B.
Probab=69.43 E-value=8 Score=21.89 Aligned_cols=25 Identities=24% Similarity=0.468 Sum_probs=19.8
Q ss_pred HHHHHHHHHHHHHcCCChhHHHHHH
Q 028429 154 ERMRDALHSYIEERGVNESLFPFLQ 178 (209)
Q Consensus 154 e~Lq~~~~~YLeeRGId~~la~fl~ 178 (209)
++|...+++||.++|-......|..
T Consensus 1 ~~Ln~lI~~YL~~~Gy~~tA~~f~~ 25 (27)
T PF08513_consen 1 EELNQLIYDYLVENGYKETAKAFAK 25 (27)
T ss_dssp HHHHHHHHHHHHHCT-HHHHHHHHH
T ss_pred CHHHHHHHHHHHHCCcHHHHHHHHh
Confidence 4678899999999999888777754
No 6
>KOG4233 consensus DNA-bridging protein BAF [Chromatin structure and dynamics; Replication, recombination and repair]
Probab=66.37 E-value=8.9 Score=27.86 Aligned_cols=36 Identities=17% Similarity=0.314 Sum_probs=29.0
Q ss_pred HHHHHHcCCChhHHHHHHHHHHHHHHHHHHHHHHHH
Q 028429 161 HSYIEERGVNESLFPFLQAWLYVKDNRNLMHWFRQV 196 (209)
Q Consensus 161 ~~YLeeRGId~~la~fl~~y~~~KEq~eYi~WL~~v 196 (209)
-.=|.++|+|---.-+=+-+...|...++..||+..
T Consensus 32 g~~L~~~GfdkAYvllGQfLllkKdE~lF~~Wlk~~ 67 (90)
T KOG4233|consen 32 GIKLVDAGFDKAYVLLGQFLLLKKDEDLFQEWLKET 67 (90)
T ss_pred hhhHHhccccHHHHHHHHHHHhcccHHHHHHHHHHH
Confidence 445789999988666666667889999999999875
No 7
>PF00123 Hormone_2: Peptide hormone; InterPro: IPR000532 A number of polypeptidic hormones, mainly expressed in the intestine or the pancreas, belong to a group of structurally related peptides [, ]. Once such hormone, glucagon is widely distributed and produced in the alpha-cells of pancreatic islets []. It affects glucose metabolism in the liver [] by inhibiting glycogen synthesis, stimulating glycogenolysis and enchancing gluconeogenesis. It also increases mobilisation of glucose, free fatty acids and ketone bodies, which are metabolites produced in excess in diabetes mellitus. Glucagon is produced, like other peptide hormones, as part of a larger precursor (preproglucagon), which is cleaved to produce glucagon, glucagon-like protein I and glucagon-like protein II []. The structure of glucagon itself is fully conserved in all known mammalian species []. Other members of the structurally similar group include glicentin precursor, secretin, gastric inhibitory protein, vasoactive intestinal peptide (VIP), prealbumin, peptide HI-27 and growth hormone releasing factor.; GO: 0005179 hormone activity, 0005576 extracellular region; PDB: 1T5Q_A 2OBU_A 2QKH_B 2L70_A 2L71_A 2B4N_A 1GCN_A 1D0R_A 3IOL_B 2RRI_A ....
Probab=64.72 E-value=17 Score=21.01 Aligned_cols=24 Identities=8% Similarity=0.297 Sum_probs=18.3
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHH
Q 028429 171 ESLFPFLQAWLYVKDNRNLMHWFR 194 (209)
Q Consensus 171 ~~la~fl~~y~~~KEq~eYi~WL~ 194 (209)
.-|.+-+..|+...--++|++||-
T Consensus 4 g~ftsdys~~L~~~aak~fl~~L~ 27 (28)
T PF00123_consen 4 GTFTSDYSKYLDQLAAKKFLQWLM 27 (28)
T ss_dssp TTHHHHHHHHHHHHHHHHHHHHHC
T ss_pred ccccHHHHHHHHHHHHHHHHHHHh
Confidence 346666677777788899999984
No 8
>PF02961 BAF: Barrier to autointegration factor; InterPro: IPR004122 Barrier-to-autointegration factor (BAF) is an essential protein that is highly conserved in metazoan evolution, and which may act as a DNA-bridging protein []. BAF binds directly to double-stranded DNA, to transcription activators, and to inner nuclear membrane proteins, including lamin A filament proteins that anchor nuclear-pore complexes in place, and nuclear LEM-domain proteins that bind to laminins filaments and chromatin. New findings suggest that BAF has structural roles in nuclear assembly and chromatin organisation, represses gene expression and might interlink chromatin structure, nuclear architecture and gene regulation in metazoans []. BAF can be exploited by retroviruses to act as a host component of pre-integration complexes, which promote the integration of the retroviral DNA into the host chromosome by preventing autointegration of retroviral DNA []. BAF might contribute to the assembly or activity of retroviral pre-integration complexes through direct binding to the retroviral proteins p55 Gag and matrix, as well as to DNA.; GO: 0003677 DNA binding; PDB: 2ODG_A 2BZF_A 2EZX_B 2EZY_B 1QCK_B 1CI4_B 2EZZ_B.
Probab=57.54 E-value=15 Score=27.20 Aligned_cols=38 Identities=24% Similarity=0.441 Sum_probs=23.8
Q ss_pred HHHHHHHHcCCChhHHHHHHHHHHHHHHHHHHHHHHHH
Q 028429 159 ALHSYIEERGVNESLFPFLQAWLYVKDNRNLMHWFRQV 196 (209)
Q Consensus 159 ~~~~YLeeRGId~~la~fl~~y~~~KEq~eYi~WL~~v 196 (209)
.+-.=|++.|++---.-.=+-+...|.+..+..||++.
T Consensus 30 ~lg~~L~~~GfdKAy~vLGqfLll~kde~~F~~WLk~~ 67 (89)
T PF02961_consen 30 VLGKRLEEKGFDKAYVVLGQFLLLKKDEELFQDWLKDT 67 (89)
T ss_dssp HHHHHHHHTT--BHHHHHHHHHHTTT-HHHHHHHHHHH
T ss_pred HHHHHHHHCCCcHHHHHhhhhhhccCcHHHHHHHHHHH
Confidence 44567899999984222222235788899999999985
No 9
>smart00070 GLUCA Glucagon like hormones.
Probab=47.77 E-value=31 Score=19.74 Aligned_cols=22 Identities=9% Similarity=0.362 Sum_probs=15.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHH
Q 028429 172 SLFPFLQAWLYVKDNRNLMHWF 193 (209)
Q Consensus 172 ~la~fl~~y~~~KEq~eYi~WL 193 (209)
.|.+-...|+...--+.|++||
T Consensus 5 ~ftsdysk~L~~~~ar~fl~~L 26 (27)
T smart00070 5 TFTSDYSKYLDQLAAKKFLQWL 26 (27)
T ss_pred cccHHHHHHHHHHHHHHHHHHh
Confidence 3444555666666778899998
No 10
>PRK11814 cysteine desulfurase activator complex subunit SufB; Provisional
Probab=47.41 E-value=35 Score=32.55 Aligned_cols=51 Identities=12% Similarity=0.066 Sum_probs=38.7
Q ss_pred CCCCCCCccHHHHHHHHHHHHHcCCChhHHHHHHHHHHHHHH-----HHHHHHHHHHHHh
Q 028429 145 TGPSFQDLDERMRDALHSYIEERGVNESLFPFLQAWLYVKDN-----RNLMHWFRQVGQY 199 (209)
Q Consensus 145 ~GP~F~~LDe~Lq~~~~~YLeeRGId~~la~fl~~y~~~KEq-----~eYi~WL~~v~~F 199 (209)
.|.-...||++ -.-||..|||+.+-|.-|.-+..-.|- -++++|++++=+.
T Consensus 424 HgATvG~idee----qLFYL~SRGi~e~eA~~Llv~gF~~evi~~ip~e~~~e~~~~i~~ 479 (486)
T PRK11814 424 HEATTSKISED----QLFYCRQRGISEEDAVSMIVNGFCKEVFQELPMEFAVEAQKLLAI 479 (486)
T ss_pred eeeecCCCCHH----HHHHHHHcCCCHHHHHHHHHHHHHHHHHHHCCcHHHHHHHHHHHH
Confidence 34444567776 367999999999999988877776663 4889999887554
No 11
>PF13154 DUF3991: Protein of unknown function (DUF3991)
Probab=47.34 E-value=11 Score=26.52 Aligned_cols=18 Identities=22% Similarity=0.578 Sum_probs=14.8
Q ss_pred HHHHH-cCCChhHHHHHHH
Q 028429 162 SYIEE-RGVNESLFPFLQA 179 (209)
Q Consensus 162 ~YLee-RGId~~la~fl~~ 179 (209)
.||.+ |||+.++.+.++.
T Consensus 1 ~YL~~~RgI~~~~v~~~~~ 19 (77)
T PF13154_consen 1 AYLTEERGIDPEIVDAFIN 19 (77)
T ss_pred CchhhhcCcCHHHHHHHHH
Confidence 37776 9999999988865
No 12
>PF08275 Toprim_N: DNA primase catalytic core, N-terminal domain; InterPro: IPR013264 This is the N-terminal, catalytic core domain of DNA primases. DNA primase (2.7.7 from EC) is a nucleotidyltransferase which synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork. It can also prime the leading strand and has been implicated in cell division []. ; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A 2AU3_A.
Probab=39.21 E-value=25 Score=27.17 Aligned_cols=18 Identities=17% Similarity=0.494 Sum_probs=13.2
Q ss_pred HHHHHHHHHcCCChhHHH
Q 028429 158 DALHSYIEERGVNESLFP 175 (209)
Q Consensus 158 ~~~~~YLeeRGId~~la~ 175 (209)
..-.+||..|||++++++
T Consensus 12 ~~a~~YL~~Rgl~~e~i~ 29 (128)
T PF08275_consen 12 KEALEYLKKRGLSDETIK 29 (128)
T ss_dssp HHHHHHHHHTT--HHHHH
T ss_pred HHHHHHHHHcCCCHHHHH
Confidence 346899999999999874
No 13
>PHA01623 hypothetical protein
Probab=38.58 E-value=1.1e+02 Score=20.31 Aligned_cols=30 Identities=13% Similarity=0.292 Sum_probs=24.9
Q ss_pred CccHHHHHHHHHHHHHcCCChhHHHHHHHHHH
Q 028429 151 DLDERMRDALHSYIEERGVNESLFPFLQAWLY 182 (209)
Q Consensus 151 ~LDe~Lq~~~~~YLeeRGId~~la~fl~~y~~ 182 (209)
.||++|...|..|.+..|++ ..++|.+-+.
T Consensus 19 rldeel~~~Ld~y~~~~g~~--rSe~IreAI~ 48 (56)
T PHA01623 19 YMDKDLKTRLKVYCAKNNLQ--LTQAIEEAIK 48 (56)
T ss_pred EeCHHHHHHHHHHHHHcCCC--HHHHHHHHHH
Confidence 49999999999999999997 7777765543
No 14
>PHA02360 hypothetical protein
Probab=37.70 E-value=35 Score=23.75 Aligned_cols=17 Identities=24% Similarity=0.655 Sum_probs=15.7
Q ss_pred HHHHHHHHHHHHHcCCC
Q 028429 154 ERMRDALHSYIEERGVN 170 (209)
Q Consensus 154 e~Lq~~~~~YLeeRGId 170 (209)
+.|+..+++|-|++||+
T Consensus 29 PklY~~i~k~YEe~gid 45 (70)
T PHA02360 29 PKLYKKIRKYYEEEGID 45 (70)
T ss_pred HHHHHHHHHHHHHcCCc
Confidence 57999999999999997
No 15
>PF10929 DUF2811: Protein of unknown function (DUF2811); InterPro: IPR021231 This is a bacterial family of uncharacterised proteins.
Probab=37.26 E-value=30 Score=23.45 Aligned_cols=31 Identities=26% Similarity=0.421 Sum_probs=24.6
Q ss_pred CCccHHHHHHHHHHHHH-------cCCChhHHHHHHHH
Q 028429 150 QDLDERMRDALHSYIEE-------RGVNESLFPFLQAW 180 (209)
Q Consensus 150 ~~LDe~Lq~~~~~YLee-------RGId~~la~fl~~y 180 (209)
.++++.|++++.+||+. |=+..-|+.||.+-
T Consensus 4 aeiPe~L~~~m~~fie~hP~WDQ~Rl~~aALa~FL~Qn 41 (57)
T PF10929_consen 4 AEIPEDLHQAMKDFIETHPNWDQYRLFQAALAGFLLQN 41 (57)
T ss_pred ccccHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHc
Confidence 57899999999999985 55667777777653
No 16
>PF00070 Pyr_redox: Pyridine nucleotide-disulphide oxidoreductase; InterPro: IPR001327 FAD flavoproteins belonging to the family of pyridine nucleotide-disulphide oxidoreductases (glutathione reductase, trypanothione reductase, lipoamide dehydrogenase, mercuric reductase, thioredoxin reductase, alkyl hydroperoxide reductase) share sequence similarity with a number of other flavoprotein oxidoreductases, in particular with ferredoxin-NAD+ reductases involved in oxidative metabolism of a variety of hydrocarbons (rubredoxin reductase, putidaredoxin reductase, terpredoxin reductase, ferredoxin-NAD+ reductase components of benzene 1,2-dioxygenase, toluene 1,2-dioxygenase, chlorobenzene dioxygenase, biphenyl dioxygenase), NADH oxidase and NADH peroxidase [, , ]. Comparison of the crystal structures of human glutathione reductase and Escherichia coli thioredoxin reductase reveals different locations of their active sites, suggesting that the enzymes diverged from an ancestral FAD/NAD(P)H reductase and acquired their disulphide reductase activities independently []. Despite functional similarities, oxidoreductases of this family show no sequence similarity with adrenodoxin reductases [] and flavoprotein pyridine nucleotide cytochrome reductases (FPNCR) []. Assuming that disulphide reductase activity emerged later, during divergent evolution, the family can be referred to as FAD-dependent pyridine nucleotide reductases, FADPNR. To date, 3D structures of glutathione reductase [], thioredoxin reductase [], mercuric reductase [], lipoamide dehydrogenase [], trypanothione reductase [] and NADH peroxidase [] have been solved. The enzymes share similar tertiary structures based on a doubly-wound alpha/beta fold, but the relative orientations of their FAD- and NAD(P)H-binding domains may vary significantly. By contrast with the FPNCR family, the folds of the FAD- and NAD(P)H-binding domains are similar, suggesting that the domains evolved by gene duplication []. This entry describes a small NADH binding domain within a larger FAD binding domain described by IPR023753 from INTERPRO. It is found in both class I and class II oxidoreductases. ; GO: 0016491 oxidoreductase activity, 0050660 flavin adenine dinucleotide binding, 0055114 oxidation-reduction process; PDB: 1ZKQ_A 3DGZ_A 1ZDL_A 2R9Z_B 2RAB_A 2A87_B 1M6I_A 2YVG_A 2GR1_A 2GQW_A ....
Probab=37.15 E-value=35 Score=23.45 Aligned_cols=22 Identities=27% Similarity=0.527 Sum_probs=19.7
Q ss_pred CCccHHHHHHHHHHHHHcCCCh
Q 028429 150 QDLDERMRDALHSYIEERGVNE 171 (209)
Q Consensus 150 ~~LDe~Lq~~~~~YLeeRGId~ 171 (209)
..+|+++...+.++|+.+||+-
T Consensus 36 ~~~~~~~~~~~~~~l~~~gV~v 57 (80)
T PF00070_consen 36 PGFDPDAAKILEEYLRKRGVEV 57 (80)
T ss_dssp TTSSHHHHHHHHHHHHHTTEEE
T ss_pred hhcCHHHHHHHHHHHHHCCCEE
Confidence 4689999999999999999864
No 17
>PF13376 OmdA: Bacteriocin-protection, YdeI or OmpD-Associated
Probab=35.62 E-value=74 Score=21.29 Aligned_cols=40 Identities=18% Similarity=0.356 Sum_probs=27.0
Q ss_pred CCccHHHHHHHHHHHHHcCCChhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028429 150 QDLDERMRDALHSYIEERGVNESLFPFLQAWLYVKDNRNLMHWFRQVG 197 (209)
Q Consensus 150 ~~LDe~Lq~~~~~YLeeRGId~~la~fl~~y~~~KEq~eYi~WL~~v~ 197 (209)
-.++++|+.+|.. ++....|-..+.. -.|++|+.|+...|
T Consensus 4 ~~vP~dl~~aL~~-------~p~a~~~f~~l~~-~~rr~~i~wi~~AK 43 (63)
T PF13376_consen 4 VEVPEDLEAALEA-------NPEAKEFFESLTP-SYRREYIRWINSAK 43 (63)
T ss_pred CCCCHHHHHHHHC-------CHHHHHHHHHCCH-HHHHHHHHHHHHcC
Confidence 3577888887764 4555566555544 45799999997654
No 18
>KOG2635 consensus Medium subunit of clathrin adaptor complex [Intracellular trafficking, secretion, and vesicular transport]
Probab=35.51 E-value=1.6e+02 Score=28.05 Aligned_cols=29 Identities=34% Similarity=0.377 Sum_probs=21.0
Q ss_pred EEcCCCCceEEEEEee-eCCeEEEeEEEeec
Q 028429 101 MSKPGQKNSLLFLCGL-YPDALGIHSVSMRP 130 (209)
Q Consensus 101 ItK~~~~~~L~f~c~~-~~~e~~I~~v~~~~ 130 (209)
|.|+ ..++|+|.|.+ +++.|.--.|+|..
T Consensus 446 Ia~N-~SGslEFs~~~~~~~~fFPl~VsF~s 475 (512)
T KOG2635|consen 446 IAKN-FSGSLEFSCPASDPDGFFPLSVSFTS 475 (512)
T ss_pred eccC-CCCcEEEeecCCCCCceeeEEEEEEe
Confidence 4665 46899999999 46666666677654
No 19
>PF13495 Phage_int_SAM_4: Phage integrase, N-terminal SAM-like domain; PDB: 2A3V_A.
Probab=35.39 E-value=77 Score=21.60 Aligned_cols=34 Identities=12% Similarity=0.363 Sum_probs=22.1
Q ss_pred HHHHHHHHHHHcCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 028429 156 MRDALHSYIEERGVNESLFPFLQAWLYVKDNRNLMHWFRQVGQYIS 201 (209)
Q Consensus 156 Lq~~~~~YLeeRGId~~la~fl~~y~~~KEq~eYi~WL~~v~~Fv~ 201 (209)
|-+.|..||..+|..+.. .+.|..||+.+..|+.
T Consensus 1 Ll~~f~~~l~~~~~s~~T------------i~~Y~~~l~~f~~~~~ 34 (85)
T PF13495_consen 1 LLEEFLEYLRLKGLSEKT------------IKNYRYHLKRFLRFLG 34 (85)
T ss_dssp -HHHHHHHHHHTT--HHH------------HHHHHHHHHHHHTTSS
T ss_pred CHHHHHHHHHHcCCCHHH------------HHHHHHHHHHHHHHcc
Confidence 456788888888877544 3567777777777765
No 20
>PF07063 DUF1338: Domain of unknown function (DUF1338); InterPro: IPR009770 This domain is found in a variety of bacterial and fungal hypothetical proteins of unknown function. The structure of this domain has been solved by structural genomics. The structure implies a zinc-binding function, so it is a putative metal hydrolase (information derived from TOPSAN for PDB:3iuz).; PDB: 3LHO_A 3IUZ_A 2RJB_C.
Probab=30.43 E-value=1.1e+02 Score=27.40 Aligned_cols=46 Identities=11% Similarity=0.261 Sum_probs=31.2
Q ss_pred CCccHHHHHHHHHHHHHcCCChhHHHHH-----------------------------------HHHHHHHHHHHHHHHHH
Q 028429 150 QDLDERMRDALHSYIEERGVNESLFPFL-----------------------------------QAWLYVKDNRNLMHWFR 194 (209)
Q Consensus 150 ~~LDe~Lq~~~~~YLeeRGId~~la~fl-----------------------------------~~y~~~KEq~eYi~WL~ 194 (209)
+.|++.+|+.+.+||..|.+-...+.-+ .+|..-++..+|..|+-
T Consensus 100 e~ls~~~q~~i~~~l~~r~~~~~~~~~~l~~~~~~~~l~~~~a~~~v~~~~~~~~W~~~~ps~~~Y~~L~~eSe~aAWi~ 179 (302)
T PF07063_consen 100 EELSPELQEIIEKYLSRRDPFSPRPLELLDQAERQGGLSAEQADEFVAEALSGFPWQHRAPSLADYQTLLAESEYAAWIA 179 (302)
T ss_dssp GGSSHHHHHHHHHHHTTS-GCGHHHHHHHHHHHHHSCEBHHHHHHHHHHHGGGCSS-SB-SBHHHHHHHHHH-HHHHHHH
T ss_pred hhcCHHHHHHHHHHHhcccCCCHHHHHHHHHHHHcCCCCHHHHHHHHHHHHcccCCCCCCCCHHHHHHHHHHhHHHHhhc
Confidence 4588999999999997666654322222 25666778899999986
Q ss_pred H
Q 028429 195 Q 195 (209)
Q Consensus 195 ~ 195 (209)
-
T Consensus 180 ~ 180 (302)
T PF07063_consen 180 A 180 (302)
T ss_dssp H
T ss_pred c
Confidence 5
No 21
>smart00667 LisH Lissencephaly type-1-like homology motif. Alpha-helical motif present in Lis1, treacle, Nopp140, some katanin p60 subunits, muskelin, tonneau, LEUNIG and numerous WD40 repeat-containing proteins. It is suggested that LisH motifs contribute to the regulation of microtubule dynamics, either by mediating dimerisation, or else by binding cytoplasmic dynein heavy chain or microtubules directly.
Probab=29.78 E-value=72 Score=17.55 Aligned_cols=27 Identities=11% Similarity=0.247 Sum_probs=21.0
Q ss_pred cHHHHHHHHHHHHHcCCChhHHHHHHH
Q 028429 153 DERMRDALHSYIEERGVNESLFPFLQA 179 (209)
Q Consensus 153 De~Lq~~~~~YLeeRGId~~la~fl~~ 179 (209)
..+|...+.+||...|-......|..+
T Consensus 3 ~~~l~~lI~~yL~~~g~~~ta~~l~~e 29 (34)
T smart00667 3 RSELNRLILEYLLRNGYEETAETLQKE 29 (34)
T ss_pred HHHHHHHHHHHHHHcCHHHHHHHHHHH
Confidence 346788899999999988887766543
No 22
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=29.38 E-value=79 Score=24.33 Aligned_cols=58 Identities=14% Similarity=0.171 Sum_probs=39.6
Q ss_pred eeeCCeEEEeEEEeecCccccCcccCCCCcCCCCCCCccHHHHHHHHHHHHHcCCChhHHHHH
Q 028429 115 GLYPDALGIHSVSMRPNLESEGILVVPSQYTGPSFQDLDERMRDALHSYIEERGVNESLFPFL 177 (209)
Q Consensus 115 ~~~~~e~~I~~v~~~~~~~~~~~~~~~~~Y~GP~F~~LDe~Lq~~~~~YLeeRGId~~la~fl 177 (209)
=..++.+.|..+.--.-. + .-...|.-|.|..|+++-+.-+..|+..||==.+++..+
T Consensus 2 PvCg~~l~vt~l~C~~C~----t-~i~G~F~l~~~~~L~~E~~~Fi~~Fi~~rGnlKe~e~~l 59 (113)
T PF09862_consen 2 PVCGGELVVTRLKCPSCG----T-EIEGEFELPWFARLSPEQLEFIKLFIKNRGNLKEMEKEL 59 (113)
T ss_pred CCCCCceEEEEEEcCCCC----C-EEEeeeccchhhcCCHHHHHHHHHHHHhcCCHHHHHHHH
Confidence 344566777776653321 0 112456778999999999999999999999655555543
No 23
>PF08321 PPP5: PPP5 TPR repeat region; InterPro: IPR013235 This domain is specific to the PPP5 subfamily of serine/threonine phosphatases.; GO: 0004722 protein serine/threonine phosphatase activity, 0046872 metal ion binding; PDB: 3ICF_B 3H60_B 3H63_A 3H66_A 3H62_B 1A17_A 1S95_B 3H69_A 3H68_D 3H64_D ....
Probab=28.46 E-value=50 Score=24.44 Aligned_cols=24 Identities=17% Similarity=0.470 Sum_probs=8.7
Q ss_pred CCCcCCCCCC--CccHHHHHHHHHHH
Q 028429 141 PSQYTGPSFQ--DLDERMRDALHSYI 164 (209)
Q Consensus 141 ~~~Y~GP~F~--~LDe~Lq~~~~~YL 164 (209)
+..|.||.++ .|+.+....+.++.
T Consensus 39 e~sY~GP~l~~~~it~efv~~mie~F 64 (95)
T PF08321_consen 39 EDSYDGPRLEDEPITLEFVKAMIEWF 64 (95)
T ss_dssp -SS--SS--BTTB--HHHHHHHHHHH
T ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHH
Confidence 4679999976 33334333333333
No 24
>PF14265 DUF4355: Domain of unknown function (DUF4355)
Probab=28.41 E-value=1.2e+02 Score=22.94 Aligned_cols=40 Identities=15% Similarity=0.252 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHHcCCChhHHHHHHHHHHHHHHHHHHHHHHH
Q 028429 155 RMRDALHSYIEERGVNESLFPFLQAWLYVKDNRNLMHWFRQ 195 (209)
Q Consensus 155 ~Lq~~~~~YLeeRGId~~la~fl~~y~~~KEq~eYi~WL~~ 195 (209)
++.....+.|.+.|++.+|++||. ..+..+=...+..|..
T Consensus 69 e~~~~~~~~l~e~GLp~~l~~~l~-g~d~e~~~~~v~~l~~ 108 (125)
T PF14265_consen 69 ELRSEAKKVLAEKGLPAELADFLV-GDDEEETKANVKALKK 108 (125)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHh-CCCHHHHHHHHHHHHH
Confidence 455667889999999999999995 4444444444444443
No 25
>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda. Members of this protein family are Hda (Homologous to DnaA). These proteins are about half the length of DnaA and homologous over length of Hda. In the model species Escherichia coli, the initiation of DNA replication requires DnaA bound to ATP rather than ADP; Hda helps facilitate the conversion of DnaA-ATP to DnaA-ADP.
Probab=27.14 E-value=1.5e+02 Score=24.00 Aligned_cols=55 Identities=22% Similarity=0.299 Sum_probs=41.6
Q ss_pred CCCCCccHHHHHHHHHHHHHcC--CChhHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCC
Q 028429 147 PSFQDLDERMRDALHSYIEERG--VNESLFPFLQAWLYVKDNRNLMHWFRQVGQYISGKN 204 (209)
Q Consensus 147 P~F~~LDe~Lq~~~~~YLeeRG--Id~~la~fl~~y~~~KEq~eYi~WL~~v~~Fv~~~~ 204 (209)
|.++. +++...+..++..+| ++++..++|..+ +.---++-.++|+.+..+..+++
T Consensus 157 ~~l~~--~e~~~~l~~~~~~~~~~~~~~~l~~L~~~-~~gn~r~L~~~l~~~~~~~~~~~ 213 (226)
T TIGR03420 157 PPLSD--EEKIAALQSRAARRGLQLPDEVADYLLRH-GSRDMGSLMALLDALDRASLAAK 213 (226)
T ss_pred CCCCH--HHHHHHHHHHHHHcCCCCCHHHHHHHHHh-ccCCHHHHHHHHHHHHHHHHHhC
Confidence 44455 566667777877665 689999999996 66678999999999987654444
No 26
>PF12122 DUF3582: Protein of unknown function (DUF3582); InterPro: IPR022732 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. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This entry represents the N-terminal domain of membrane-bound serine endopeptidases belonging to MEROPS peptidase family S54 (rhomboid-1, clan ST). This domain contains a conserved ASW sequence motif and a single completely conserved residue F that may be functionally important. The tertiary structure of the GlpG protein from Escherichia coli has been determined []. The GlpG protein has six transmembrane domains (other members of the family are predicted to have seven), with the N- and C-terminal ends anchored in the cytoplasm. One transmembrane domain is shorter than the rest, creating an internal, aqueous cavity just below the membrane surface and it is here were proteolysis occurs. There is also a membrane-embedded loop between the first and second transmembrane domains which is postulated to act as a gate controlling substrate access to the active site. No other family of serine peptidases is known to have active site residues within transmembrane domains (although transmembrane active sites are known for aspartic peptidase and metallopeptidases), and the GlpG protein has the type structure for clan ST.; GO: 0004252 serine-type endopeptidase activity, 0016021 integral to membrane; PDB: 3UBB_A 3B45_A 3B44_A 2NRF_A 3TXT_A 2O7L_A 2XTU_A 2IRV_A 2XOW_A 2XTV_A ....
Probab=27.03 E-value=60 Score=24.31 Aligned_cols=22 Identities=18% Similarity=0.424 Sum_probs=16.8
Q ss_pred cHHHHHHHHHHHHHcCCChhHH
Q 028429 153 DERMRDALHSYIEERGVNESLF 174 (209)
Q Consensus 153 De~Lq~~~~~YLeeRGId~~la 174 (209)
++.+-.+|.+||..+||+-.+-
T Consensus 9 n~r~AqaF~DYl~sqgI~~~i~ 30 (101)
T PF12122_consen 9 NPRAAQAFIDYLASQGIELQIE 30 (101)
T ss_dssp SHHHHHHHHHHHHHTT--EEEE
T ss_pred CHHHHHHHHHHHHHCCCeEEEE
Confidence 4678889999999999987664
No 27
>smart00777 Mad3_BUB1_I Mad3/BUB1 hoMad3/BUB1 homology region 1. Proteins containing this domain are checkpoint proteins involved in cell division. This region has been shown to be essential for the binding of the binding of BUB1 and MAD3 to CDC20p.
Probab=25.53 E-value=1.1e+02 Score=23.76 Aligned_cols=30 Identities=17% Similarity=0.478 Sum_probs=25.9
Q ss_pred HHHHHHHHHcCCChhHHHHHHHHHHHHHHH
Q 028429 158 DALHSYIEERGVNESLFPFLQAWLYVKDNR 187 (209)
Q Consensus 158 ~~~~~YLeeRGId~~la~fl~~y~~~KEq~ 187 (209)
..+..||..+||-..+|.|=..|+..-|.+
T Consensus 83 ~~if~~L~~~~IG~~~AlfYe~~A~~lE~~ 112 (125)
T smart00777 83 RELFQFLYSKGIGTKLALFYEEWAQLLEAA 112 (125)
T ss_pred HHHHHHHHHCCcchhhHHHHHHHHHHHHHc
Confidence 457999999999999999999888776654
No 28
>PF13434 K_oxygenase: L-lysine 6-monooxygenase (NADPH-requiring); PDB: 3S61_B 3S5W_B.
Probab=25.51 E-value=42 Score=30.23 Aligned_cols=33 Identities=18% Similarity=0.576 Sum_probs=25.0
Q ss_pred HHHHHHHHcCCChhHHHHHH---HHHHHHHHHHHHHHHH
Q 028429 159 ALHSYIEERGVNESLFPFLQ---AWLYVKDNRNLMHWFR 194 (209)
Q Consensus 159 ~~~~YLeeRGId~~la~fl~---~y~~~KEq~eYi~WL~ 194 (209)
.|.+||.++| .|..|+. .+....|-.+|++|.-
T Consensus 70 sflnYL~~~~---rl~~f~~~~~~~p~R~ef~dYl~Wva 105 (341)
T PF13434_consen 70 SFLNYLHEHG---RLYEFYNRGYFFPSRREFNDYLRWVA 105 (341)
T ss_dssp SHHHHHHHTT----HHHHHHH--SS-BHHHHHHHHHHHH
T ss_pred cHHHHHHHcC---ChhhhhhcCCCCCCHHHHHHHHHHHH
Confidence 5799999997 7777773 4567888899999963
No 29
>PF13034 DUF3895: Protein of unknown function (DUF3895)
Probab=25.22 E-value=1.1e+02 Score=22.10 Aligned_cols=28 Identities=25% Similarity=0.459 Sum_probs=20.6
Q ss_pred ccHHHHHHHHHHHH-HcCCCh-hHHHHHHH
Q 028429 152 LDERMRDALHSYIE-ERGVNE-SLFPFLQA 179 (209)
Q Consensus 152 LDe~Lq~~~~~YLe-eRGId~-~la~fl~~ 179 (209)
|++..|+.+..|++ +.+|+. ++|+||..
T Consensus 1 L~~~e~~~i~~yi~n~~~Isa~elcE~LI~ 30 (78)
T PF13034_consen 1 LSELEKEFINWYIQNEEEISARELCEYLIE 30 (78)
T ss_pred CCHHHHHHHHHHHhccccccHHHHHHHHHH
Confidence 67788888888998 577875 46666653
No 30
>PF10915 DUF2709: Protein of unknown function (DUF2709); InterPro: IPR024484 Members of this family appear restricted to Chlamydiales. Their function is unknown.
Probab=24.89 E-value=1e+02 Score=26.27 Aligned_cols=39 Identities=15% Similarity=0.426 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHcCCChhHHHHHHHHHHHHHHHHHH-HHHH
Q 028429 156 MRDALHSYIEERGVNESLFPFLQAWLYVKDNRNLM-HWFR 194 (209)
Q Consensus 156 Lq~~~~~YLeeRGId~~la~fl~~y~~~KEq~eYi-~WL~ 194 (209)
+-++|..+|+..=+.+..|.|+..++..-+-.-|+ +|+.
T Consensus 196 iE~~FL~~iq~~L~edKIa~Fve~la~~~~F~~~v~~Wve 235 (238)
T PF10915_consen 196 IEDSFLSFIQDQLVEDKIAEFVESLAEDTEFHPYVEQWVE 235 (238)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHhhc
Confidence 45677777777777788899999888887776665 3553
No 31
>cd04739 DHOD_like Dihydroorotate dehydrogenase (DHOD) like proteins. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences and cellular location. Members of class 1 are cytosolic enzymes and multimers while class 2 enzymes are membrane associated and monomeric. The class 1 enzymes can be further divided into subtypes 1A and 1B which are homodimers and heterotetrameric proteins, respectively. This subgroup has the conserved FMN binding site, but lacks some catalytic residues and may therefore be inactive.
Probab=23.56 E-value=1.1e+02 Score=27.22 Aligned_cols=50 Identities=18% Similarity=0.220 Sum_probs=35.6
Q ss_pred CCCcCCCCCCCccHHHHHHHHHHHHHcCCChhHHHHHHHH-------HHHHHHHHHHHHHH
Q 028429 141 PSQYTGPSFQDLDERMRDALHSYIEERGVNESLFPFLQAW-------LYVKDNRNLMHWFR 194 (209)
Q Consensus 141 ~~~Y~GP~F~~LDe~Lq~~~~~YLeeRGId~~la~fl~~y-------~~~KEq~eYi~WL~ 194 (209)
...|.||. +-..+.+.|.+||++.|+ .++.+++-.. +...|+.+|+..|.
T Consensus 268 a~~~~gp~---~~~~i~~~L~~~l~~~g~-~~i~e~~G~~~~~~~~~~~~~~r~~~~~~~~ 324 (325)
T cd04739 268 ALLRHGPD---YIGTLLAGLEAWMEEHGY-ESVQQLRGSMSQKNVPDPAAFERAQYMKALS 324 (325)
T ss_pred hhhhcCch---HHHHHHHHHHHHHHHcCC-CCHHHHhcccccccCCChhHhHHHHHHHHhh
Confidence 34567885 777899999999999998 4566665432 23467788887653
No 32
>PRK10416 signal recognition particle-docking protein FtsY; Provisional
Probab=23.53 E-value=2.9e+02 Score=24.69 Aligned_cols=35 Identities=17% Similarity=0.171 Sum_probs=31.6
Q ss_pred CCccHHHHHHHHHHHHHcCCChhHHHHHHHHHHHH
Q 028429 150 QDLDERMRDALHSYIEERGVNESLFPFLQAWLYVK 184 (209)
Q Consensus 150 ~~LDe~Lq~~~~~YLeeRGId~~la~fl~~y~~~K 184 (209)
..+|+++.+.+..-|-+.||+.+++.-|.+-...+
T Consensus 42 ~~~~~~~~~~l~~~L~~~dv~~~~a~~i~~~~~~~ 76 (318)
T PRK10416 42 KKIDEDLLEELEELLIEADVGVETTEEIIEELRER 76 (318)
T ss_pred CCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHH
Confidence 57999999999999999999999999998887655
No 33
>TIGR01981 sufD FeS assembly protein SufD, group 1. This protein, SufD, forms a cytosolic complex SufBCD. This complex enhances the cysteine desulfurase of SufSE. The system, together with SufA, is believed to act in iron-sulfur cluster formation during oxidative stress. SufB and SufD are homologous. Note that SufC belongs to the family of ABC transporter ATP binding proteins, so this protein, encoded by an adjacent gene, has often been annotated as a transporter component.
Probab=23.18 E-value=84 Score=28.58 Aligned_cols=37 Identities=19% Similarity=0.357 Sum_probs=27.7
Q ss_pred CCCCCCCccHHHHHHHHHHHHHcCCChhHHHHHHHHHHHHH
Q 028429 145 TGPSFQDLDERMRDALHSYIEERGVNESLFPFLQAWLYVKD 185 (209)
Q Consensus 145 ~GP~F~~LDe~Lq~~~~~YLeeRGId~~la~fl~~y~~~KE 185 (209)
.|--...||++- .=||.+|||+.+-|.-|.-...-.|
T Consensus 316 HgATvG~ldee~----LFYL~SRGi~~~eA~~llv~gF~~~ 352 (366)
T TIGR01981 316 HGATVGQIDDEQ----LFYLRSRGIDEEEARRLLIRGFLGE 352 (366)
T ss_pred cceeecCCCHHH----HHHHHHcCCCHHHHHHHHHHHHHHH
Confidence 455556677763 6799999999999998877666444
No 34
>TIGR01446 DnaD_dom DnaD and phage-associated domain. This model represents the conserved domain of DnaD, part of Bacillus subtilis replication restart primosome, and of a number of phage-associated proteins. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria.
Probab=23.11 E-value=2e+02 Score=19.28 Aligned_cols=34 Identities=15% Similarity=0.048 Sum_probs=30.6
Q ss_pred CccHHHHHHHHHHHHHcCCChhHHHHHHHHHHHH
Q 028429 151 DLDERMRDALHSYIEERGVNESLFPFLQAWLYVK 184 (209)
Q Consensus 151 ~LDe~Lq~~~~~YLeeRGId~~la~fl~~y~~~K 184 (209)
.|...-.+.+..+++.-|.+.++......|+..+
T Consensus 12 ~ls~~e~~~i~~~~~~~~~~~evI~~ai~~a~~~ 45 (73)
T TIGR01446 12 MLSPFEMEDLKYWLDEFGNSPELIKEALKEAVSN 45 (73)
T ss_pred CCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHc
Confidence 4788889999999999999999999999998764
No 35
>PRK13031 preprotein translocase subunit SecB; Provisional
Probab=23.01 E-value=1.9e+02 Score=23.30 Aligned_cols=31 Identities=10% Similarity=0.187 Sum_probs=19.5
Q ss_pred eeEEEEEEcCCCCceEEEEEee-eCCeEEEeEE
Q 028429 95 LFLHVEMSKPGQKNSLLFLCGL-YPDALGIHSV 126 (209)
Q Consensus 95 ~~~~V~ItK~~~~~~L~f~c~~-~~~e~~I~~v 126 (209)
+.++|+|+-.. +....|.|.. +.|-|.|.++
T Consensus 57 V~L~vtvta~~-~~~t~FlvEv~qaGIF~i~ni 88 (149)
T PRK13031 57 TVLTLEVKVEN-DGMVAFEAEVKQAGIFTVANM 88 (149)
T ss_pred EEEEEEEEEEe-CCceEEEEEEeEeeEEEEcCC
Confidence 44444444322 2345688887 6888999877
No 36
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=22.74 E-value=68 Score=21.59 Aligned_cols=42 Identities=17% Similarity=0.324 Sum_probs=26.3
Q ss_pred CCCccHHHHHHHHHHHHHcCCChhHHHHHHHHHHHHHHHHHH
Q 028429 149 FQDLDERMRDALHSYIEERGVNESLFPFLQAWLYVKDNRNLM 190 (209)
Q Consensus 149 F~~LDe~Lq~~~~~YLeeRGId~~la~fl~~y~~~KEq~eYi 190 (209)
|..|+.=+...+.+...--||.+..|+-|.+|....++++-+
T Consensus 23 f~sl~~l~~a~~e~L~~i~gIG~~~A~si~~ff~~~~n~~~i 64 (64)
T PF12826_consen 23 FGSLEALMNASVEELSAIPGIGPKIAQSIYEFFQDPENRELI 64 (64)
T ss_dssp CSCHHHHCC--HHHHCTSTT--HHHHHHHHHHHH-HHHHHHH
T ss_pred cCCHHHHHHcCHHHHhccCCcCHHHHHHHHHHHCCHHhhhhC
Confidence 445543333344555566899999999999999999887743
No 37
>COG5559 Uncharacterized conserved small protein [Function unknown]
Probab=22.61 E-value=52 Score=22.57 Aligned_cols=29 Identities=31% Similarity=0.505 Sum_probs=21.0
Q ss_pred CCCccHHHHHHHHHHHHHcCCChhHHHHHHHHHHHHHHH
Q 028429 149 FQDLDERMRDALHSYIEERGVNESLFPFLQAWLYVKDNR 187 (209)
Q Consensus 149 F~~LDe~Lq~~~~~YLeeRGId~~la~fl~~y~~~KEq~ 187 (209)
|..|+++|...+..|.| ||.+-..++.|.
T Consensus 8 fqkLPDdLKrEvldY~E----------fLlek~~k~~~~ 36 (65)
T COG5559 8 FQKLPDDLKREVLDYIE----------FLLEKKAKKKQK 36 (65)
T ss_pred HHHCcHHHHHHHHHHHH----------HHHHHHhcCcCC
Confidence 67899999999988853 555555555543
No 38
>PF09701 Cas_Cmr5: CRISPR-associated protein (Cas_Cmr5); InterPro: IPR010160 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. This entry represents a family of Cas proteins as represented by TM1791.1 from Thermotoga maritima. This family of Cas proteins are found in both archaeal and bacterial species.; PDB: 2OEB_A 2ZOP_A.
Probab=22.60 E-value=2e+02 Score=21.78 Aligned_cols=42 Identities=12% Similarity=0.398 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHcCCCh-----hHHHHHHH-----HH-HHHHHHHHHHHHHHHH
Q 028429 156 MRDALHSYIEERGVNE-----SLFPFLQA-----WL-YVKDNRNLMHWFRQVG 197 (209)
Q Consensus 156 Lq~~~~~YLeeRGId~-----~la~fl~~-----y~-~~KEq~eYi~WL~~v~ 197 (209)
|.+.+..||..++... +|...|.. |+ ...|==++..||++..
T Consensus 66 l~~~l~~wl~~~~~~~~~~~~~l~~~i~~~d~~~Y~~~t~e~La~l~WlKRfA 118 (122)
T PF09701_consen 66 LLEHLAEWLCERFKIDPNENNDLLEAIIEADLSEYMRATREALAFLNWLKRFA 118 (122)
T ss_dssp HHHHHHHHCCHTTHCTSS---HHHHHHHHS-HHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhccccchhhHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 8888888988876543 44444432 21 2233334556777653
No 39
>PF10281 Ish1: Putative stress-responsive nuclear envelope protein; InterPro: IPR018803 This group of proteins, found primarily in fungi, consists of putative stress-responsive nuclear envelope protein Ish1 and homologues [].
Probab=21.80 E-value=74 Score=19.15 Aligned_cols=15 Identities=20% Similarity=0.516 Sum_probs=12.6
Q ss_pred HHHHHHHHHcCCChh
Q 028429 158 DALHSYIEERGVNES 172 (209)
Q Consensus 158 ~~~~~YLeeRGId~~ 172 (209)
+.|.+||++.||...
T Consensus 7 ~~L~~wL~~~gi~~~ 21 (38)
T PF10281_consen 7 SDLKSWLKSHGIPVP 21 (38)
T ss_pred HHHHHHHHHcCCCCC
Confidence 478999999999765
No 40
>TIGR02793 nikR nickel-responsive transcriptional regulator NikR. Three members of the seed for this model, from Escherichia coli, Pseudomonas putida, and Brucella melitensis, are found associated with a nickel ABC transporter operon that acts to import nickel for use as a cofactor in urease or hydrogenase. These proteins, with characterized nickel-binding and DNA-binding domains, act as nickel-responsive transcriptional regulators. In the larger family of full-length homologs, most others both lack proximity to the nickel ABC transporter operon and form a separate clade. Several of the homologs not within the scope of this model, but rather scoring between the trusted and noise cutoffs, have been shown to bind nickel, copper, or both, and to regulate genes in response to nickel.
Probab=21.79 E-value=2e+02 Score=22.41 Aligned_cols=20 Identities=30% Similarity=0.576 Sum_probs=18.2
Q ss_pred CccHHHHHHHHHHHHHcCCC
Q 028429 151 DLDERMRDALHSYIEERGVN 170 (209)
Q Consensus 151 ~LDe~Lq~~~~~YLeeRGId 170 (209)
.||++|.+.|.++.+++|.+
T Consensus 6 slp~~ll~~lD~~~~~~g~~ 25 (129)
T TIGR02793 6 TLDDDLLETLDRLIARRGYQ 25 (129)
T ss_pred EcCHHHHHHHHHHHHHcCCC
Confidence 48999999999999999986
No 41
>PF02268 TFIIA_gamma_N: Transcription initiation factor IIA, gamma subunit, helical domain; InterPro: IPR015872 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site. After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the alpha-helical domain found at the N-terminal of the gamma subunit of transcription factor TFIIA.; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_D 1RM1_B 1YTF_D 1NH2_D.
Probab=21.34 E-value=1.5e+02 Score=19.39 Aligned_cols=32 Identities=19% Similarity=0.205 Sum_probs=26.1
Q ss_pred CCccHHHHHHHHHHHHHcCCChhHHHHHHHHH
Q 028429 150 QDLDERMRDALHSYIEERGVNESLFPFLQAWL 181 (209)
Q Consensus 150 ~~LDe~Lq~~~~~YLeeRGId~~la~fl~~y~ 181 (209)
..|=-.|+++|.+.+.+.-|++.||..|..-.
T Consensus 9 stlG~aL~dtLDeli~~~~I~p~La~kVL~~F 40 (49)
T PF02268_consen 9 STLGIALTDTLDELIQEGKITPQLAMKVLEQF 40 (49)
T ss_dssp SHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHH
T ss_pred chHHHHHHHHHHHHHHcCCCCHHHHHHHHHHH
Confidence 34667899999999999999999999987643
No 42
>PF09373 PMBR: Pseudomurein-binding repeat; InterPro: IPR018975 Methanothermobacter thermautotrophicus (Methanobacterium thermoformicicum) is a methanogenic Gram-positive microorganism with a cell wall consisting of pseudomurein. This repeat specifically binds to pseudomurein. This repeat is found at the N terminus of PeiW and PeiP which are pseudomurein binding phage proteins.
Probab=21.21 E-value=1e+02 Score=18.12 Aligned_cols=21 Identities=5% Similarity=0.192 Sum_probs=18.2
Q ss_pred HHHHHHHHHHHHhhcCCCCCC
Q 028429 187 RNLMHWFRQVGQYISGKNHAK 207 (209)
Q Consensus 187 ~eYi~WL~~v~~Fv~~~~~~~ 207 (209)
.+|+.-.+++.+|+.+++.+.
T Consensus 8 ~~~~d~a~rv~~f~~~ngRlP 28 (33)
T PF09373_consen 8 EEYLDMASRVNNFYESNGRLP 28 (33)
T ss_pred HHHHHHHHHHHHHHHHcCCCC
Confidence 578999999999999988764
No 43
>PF07671 DUF1601: Protein of unknown function (DUF1601); InterPro: IPR011632 This repeat is found in a small number of proteins and is apparently limited to Coxiella burnetii.
Probab=20.76 E-value=1.2e+02 Score=18.66 Aligned_cols=17 Identities=24% Similarity=0.581 Sum_probs=14.4
Q ss_pred HHHHHcCCChhHHHHHH
Q 028429 162 SYIEERGVNESLFPFLQ 178 (209)
Q Consensus 162 ~YLeeRGId~~la~fl~ 178 (209)
.||+++|.++.|..-|.
T Consensus 6 ~~l~~q~L~~~L~~aV~ 22 (37)
T PF07671_consen 6 RYLEEQRLSDRLLDAVR 22 (37)
T ss_pred hhhhhccchHHHHHHHH
Confidence 58888899988888887
No 44
>PF12123 Amidase02_C: N-acetylmuramoyl-l-alanine amidase; InterPro: IPR021976 This domain is found in bacteria and viruses. This domain is about 50 amino acids in length. This domain is classified with the enzyme classification code 3.5.1.28 from EC. This domain is the C-terminal of the enzyme which hydrolyses the link between N-acetylmuramoyl residues and L-amino acid residues in certain cell-wall glycopeptides. ; PDB: 2L48_B.
Probab=20.61 E-value=1.1e+02 Score=19.71 Aligned_cols=18 Identities=28% Similarity=0.582 Sum_probs=13.9
Q ss_pred ccHHHHHHHHHHHHHcCC
Q 028429 152 LDERMRDALHSYIEERGV 169 (209)
Q Consensus 152 LDe~Lq~~~~~YLeeRGI 169 (209)
+++.--+.|..||++||.
T Consensus 24 ~s~~~L~k~~~wld~rgW 41 (45)
T PF12123_consen 24 LSDAELDKFTAWLDERGW 41 (45)
T ss_dssp --HHHHHHHHHHHHHTT-
T ss_pred CCHHHHHHHHHHHHhcCc
Confidence 777888999999999985
No 45
>PF04726 Microvir_J: Microvirus J protein; InterPro: IPR006815 This small protein is involved in DNA packaging, interacting with DNA via its hydrophobic C terminus. In bacteriophage phi-X174, J is present in 60 copies, and forms an S-shaped polypeptide chain without any secondary structure. It is thought to interact with DNA through simple charge interactions [].; GO: 0003677 DNA binding, 0019073 viral DNA genome packaging, 0019028 viral capsid; PDB: 1M06_J 1GFF_3 1RB8_J 2BPA_3.
Probab=20.60 E-value=50 Score=18.20 Aligned_cols=13 Identities=23% Similarity=0.194 Sum_probs=6.6
Q ss_pred ccccCCCCCCCch
Q 028429 2 IARRRSTTSGFAV 14 (209)
Q Consensus 2 ~~~~~~~~~~~~~ 14 (209)
-.+|||.++++++
T Consensus 2 k~~rrs~~~~kga 14 (24)
T PF04726_consen 2 KSKRRSGGKRKGA 14 (24)
T ss_dssp -GGGS---SSSSS
T ss_pred cccccCCCccCce
Confidence 4578888888764
No 46
>PF08311 Mad3_BUB1_I: Mad3/BUB1 homology region 1; InterPro: IPR013212 Proteins containing this domain are checkpoint proteins involved in cell division. This region has been shown to be essential for the binding of BUB1 and MAD3 to CDC20p [].; PDB: 3ESL_B 4AEZ_I 4A1G_B 2LAH_A 2WVI_A 3SI5_B.
Probab=20.41 E-value=1.3e+02 Score=22.98 Aligned_cols=30 Identities=17% Similarity=0.504 Sum_probs=26.5
Q ss_pred HHHHHHHHHcCCChhHHHHHHHHHHHHHHH
Q 028429 158 DALHSYIEERGVNESLFPFLQAWLYVKDNR 187 (209)
Q Consensus 158 ~~~~~YLeeRGId~~la~fl~~y~~~KEq~ 187 (209)
..+..||..+||-..+|.|=..|+..-|++
T Consensus 83 ~~if~~l~~~~IG~~~A~fY~~wA~~le~~ 112 (126)
T PF08311_consen 83 REIFKFLYSKGIGTKLALFYEEWAEFLEKR 112 (126)
T ss_dssp HHHHHHHHHHTTSTTBHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHcCccHHHHHHHHHHHHHHHHc
Confidence 467889999999999999999999887765
No 47
>PF01458 UPF0051: Uncharacterized protein family (UPF0051); InterPro: IPR000825 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] []. FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins [, ]. It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly []. The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA []. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA [], acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins []. Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen []. This entry represents SufB and SufD proteins that form part of the SufBCD complex in the SUF system. No specific functions have been assigned to these proteins.; GO: 0016226 iron-sulfur cluster assembly; PDB: 1VH4_B 2ZU0_A 4DN7_A.
Probab=20.30 E-value=57 Score=27.39 Aligned_cols=32 Identities=25% Similarity=0.313 Sum_probs=20.3
Q ss_pred CCCCCCCccHHHHHHHHHHHHHcCCChhHHHHHHHH
Q 028429 145 TGPSFQDLDERMRDALHSYIEERGVNESLFPFLQAW 180 (209)
Q Consensus 145 ~GP~F~~LDe~Lq~~~~~YLeeRGId~~la~fl~~y 180 (209)
.|--...||++- .=||..|||+.+-|..|.-.
T Consensus 196 H~AtvG~idee~----LFYL~SRGl~~~eA~~Liv~ 227 (229)
T PF01458_consen 196 HGATVGQIDEEQ----LFYLMSRGLSEEEARKLIVK 227 (229)
T ss_dssp EEEEEEES-HHH----HHHHHCTT--HHHHHHHHHH
T ss_pred EeeEeecCCHHH----HHHHHHcCCCHHHHHHHHHh
Confidence 333444577763 57999999999999877643
No 48
>PHA02115 hypothetical protein
Probab=20.10 E-value=1.1e+02 Score=22.49 Aligned_cols=43 Identities=14% Similarity=0.295 Sum_probs=28.1
Q ss_pred HHHHHHHHHhc-C-CCCCCCCCCCCEEEeCCCCCCceEEEEeeCC
Q 028429 23 LRDHYEEVAKM-T-PPPKVSPPSSFTIVKGALDTHGPVLKRMYGS 65 (209)
Q Consensus 23 L~~Ei~~~~~~-~-~~~~~~~~~~F~i~~~~gd~~~v~L~R~~~~ 65 (209)
++.||++.++. . ...+...|.-|+|..+||=.-+.+..|+|--
T Consensus 3 iqkeiqe~~k~~gveasefk~p~iwki~rkpgwsyg~~fe~eft~ 47 (105)
T PHA02115 3 IQKEIQEIEKRLGVEASEFKMPSVWKVARKPGWSYGAVFEQEFTA 47 (105)
T ss_pred HHHHHHHHHHHhCcchhhccCccHHhhhcCCCCccceEeeeeeee
Confidence 45566655442 2 1224667789999999875566788888753
No 49
>PRK13658 hypothetical protein; Provisional
Probab=20.09 E-value=1.4e+02 Score=20.18 Aligned_cols=27 Identities=26% Similarity=0.411 Sum_probs=14.3
Q ss_pred HHHHHHHHHHHHh-cCCCCCCCCCCCCEE
Q 028429 20 LRSLRDHYEEVAK-MTPPPKVSPPSSFTI 47 (209)
Q Consensus 20 l~~L~~Ei~~~~~-~~~~~~~~~~~~F~i 47 (209)
|+.|+.|+-...+ ...|. ..+..||+|
T Consensus 32 LEILKaELL~~~~~~~~~~-~~pkaPwei 59 (59)
T PRK13658 32 LEILKAELLRQVAESTSPP-DIPKAPWEI 59 (59)
T ss_pred HHHHHHHHHHHhhcccCcc-cCCCCCCCC
Confidence 5677777553333 22232 235578865
Done!