Query psy9801
Match_columns 132
No_of_seqs 154 out of 950
Neff 4.9
Searched_HMMs 46136
Date Fri Aug 16 20:04:11 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9801.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9801hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01302 CAP_GLY: CAP-Gly doma 100.0 1.2E-28 2.6E-33 165.9 8.8 66 23-88 1-69 (69)
2 KOG3206|consensus 99.9 3E-23 6.6E-28 166.2 7.2 74 20-93 148-225 (234)
3 KOG0971|consensus 99.9 6.1E-22 1.3E-26 182.6 8.2 77 18-94 3-80 (1243)
4 COG5244 NIP100 Dynactin comple 99.8 1.4E-20 3.1E-25 165.4 7.2 70 20-90 3-72 (669)
5 KOG4568|consensus 99.8 6.3E-19 1.4E-23 159.6 5.7 78 13-90 10-87 (664)
6 KOG3207|consensus 99.7 4.5E-18 9.7E-23 148.6 7.6 72 20-92 2-75 (505)
7 KOG4568|consensus 99.3 1.4E-13 3E-18 125.1 0.4 76 16-91 150-225 (664)
8 KOG0241|consensus 99.2 4E-12 8.6E-17 119.3 3.6 71 19-93 1629-1699(1714)
9 KOG3556|consensus 99.2 2.1E-11 4.5E-16 108.9 6.6 71 20-90 235-315 (724)
10 PTZ00243 ABC transporter; Prov 96.1 0.014 3E-07 58.1 6.7 57 20-76 124-198 (1560)
11 PRK10708 hypothetical protein; 93.1 0.39 8.5E-06 31.9 5.5 55 21-85 1-61 (62)
12 PF10781 DSRB: Dextransucrase 93.1 0.39 8.6E-06 31.9 5.5 55 21-85 1-61 (62)
13 PF09926 DUF2158: Uncharacteri 79.5 8.5 0.00018 24.7 5.4 46 21-66 1-47 (53)
14 TIGR00739 yajC preprotein tran 64.3 22 0.00047 24.6 5.0 33 18-56 35-67 (84)
15 PF00924 MS_channel: Mechanose 63.8 7 0.00015 29.6 2.7 26 18-44 58-83 (206)
16 PRK05886 yajC preprotein trans 62.2 22 0.00049 26.0 5.0 34 18-57 36-69 (109)
17 PRK05585 yajC preprotein trans 54.0 36 0.00078 24.6 4.8 34 18-57 50-83 (106)
18 cd00539 MCR_gamma Methyl-coenz 52.7 5.4 0.00012 33.0 0.4 45 9-61 155-201 (246)
19 TIGR03259 met_CoM_red_gam meth 50.9 5.9 0.00013 32.7 0.4 45 9-61 155-201 (244)
20 PF13403 Hint_2: Hint domain 50.4 22 0.00048 26.6 3.4 28 18-45 18-45 (147)
21 COG3350 Uncharacterized conser 49.4 7.1 0.00015 25.4 0.5 30 49-78 6-35 (53)
22 PF02470 MCE: mce related prot 45.5 84 0.0018 20.4 6.1 44 16-59 10-53 (81)
23 TIGR02266 gmx_TIGR02266 Myxoco 43.6 82 0.0018 20.7 5.1 41 18-58 34-83 (96)
24 PRK06531 yajC preprotein trans 43.2 32 0.00069 25.3 3.2 24 18-41 34-57 (113)
25 PF02240 MCR_gamma: Methyl-coe 43.2 7 0.00015 32.3 -0.3 43 9-59 156-198 (247)
26 PRK10334 mechanosensitive chan 41.8 33 0.00072 28.5 3.5 25 18-43 127-151 (286)
27 KOG1999|consensus 40.2 82 0.0018 31.2 6.2 36 5-40 566-605 (1024)
28 PF07238 PilZ: PilZ domain; I 38.2 92 0.002 19.8 4.6 36 20-57 44-87 (102)
29 PF07154 DUF1392: Protein of u 38.2 54 0.0012 25.5 3.9 44 16-59 83-128 (150)
30 PF13785 DUF4178: Domain of un 35.3 1.1E+02 0.0024 21.8 5.0 20 21-40 1-23 (140)
31 COG1862 YajC Preprotein transl 34.1 1E+02 0.0022 22.1 4.5 25 19-43 42-66 (97)
32 smart00739 KOW KOW (Kyprides, 33.9 70 0.0015 16.4 2.9 11 21-31 2-12 (28)
33 PF13437 HlyD_3: HlyD family s 33.9 98 0.0021 20.7 4.3 37 17-53 46-89 (105)
34 COG1463 Ttg2C ABC-type transpo 29.6 1.3E+02 0.0027 25.6 5.1 61 16-77 48-117 (359)
35 PF12700 HlyD_2: HlyD family s 29.4 2.5E+02 0.0054 22.2 6.6 73 16-90 205-285 (328)
36 PF02211 NHase_beta: Nitrile h 26.6 30 0.00066 28.1 0.9 22 10-31 124-145 (222)
37 PF02699 YajC: Preprotein tran 26.5 20 0.00043 24.5 -0.2 23 18-40 34-56 (82)
38 KOG4600|consensus 26.4 1.4E+02 0.003 23.1 4.4 9 45-53 72-80 (144)
39 PTZ00328 eukaryotic initiation 25.7 2.2E+02 0.0049 22.4 5.5 68 7-84 14-86 (166)
40 cd04451 S1_IF1 S1_IF1: Transla 24.6 85 0.0018 19.9 2.6 20 20-39 40-63 (64)
41 COG4097 Predicted ferric reduc 24.4 44 0.00095 30.0 1.5 27 9-39 285-311 (438)
42 PLN03148 Blue copper-like prot 24.2 87 0.0019 24.5 3.0 14 17-30 42-55 (167)
43 COG4057 McrG Methyl coenzyme M 23.7 26 0.00056 28.9 -0.0 45 9-61 160-206 (257)
44 PF02298 Cu_bind_like: Plastoc 23.6 43 0.00094 22.8 1.1 14 17-30 15-28 (85)
45 PRK00276 infA translation init 23.2 90 0.002 20.5 2.5 19 21-39 47-69 (72)
46 COG5466 Predicted small metal- 23.0 72 0.0016 21.2 2.0 19 68-86 2-23 (59)
47 PF15290 Syntaphilin: Golgi-lo 22.8 37 0.00081 29.1 0.7 13 69-81 40-52 (305)
48 CHL00010 infA translation init 22.8 93 0.002 21.0 2.6 21 20-40 46-70 (78)
49 COG0668 MscS Small-conductance 22.7 1.1E+02 0.0025 24.1 3.5 27 18-44 145-171 (316)
50 PRK11281 hypothetical protein; 22.1 97 0.0021 30.9 3.5 25 18-43 936-960 (1113)
51 COG4841 Uncharacterized protei 21.5 2.7E+02 0.0059 20.1 4.8 52 18-75 16-68 (95)
52 PF14001 YdfZ: YdfZ protein 21.1 1.1E+02 0.0024 20.6 2.6 23 18-40 7-30 (64)
53 smart00449 SPRY Domain in SPla 21.1 1.4E+02 0.0031 20.2 3.3 29 47-75 65-98 (122)
54 PRK11465 putative mechanosensi 21.0 1.1E+02 0.0023 29.3 3.4 25 18-43 571-595 (741)
55 CHL00141 rpl24 ribosomal prote 21.0 1.1E+02 0.0023 21.1 2.6 22 19-40 7-32 (83)
56 PRK12281 rplX 50S ribosomal pr 21.0 1.2E+02 0.0025 20.7 2.8 22 19-40 5-30 (76)
57 PF02559 CarD_CdnL_TRCF: CarD- 20.6 1.6E+02 0.0035 19.9 3.5 51 21-90 2-54 (98)
58 PRK10929 putative mechanosensi 20.5 1.1E+02 0.0023 30.7 3.4 25 18-43 933-957 (1109)
59 PF04945 YHS: YHS domain; Int 20.3 40 0.00086 20.2 0.3 14 64-77 18-31 (47)
No 1
>PF01302 CAP_GLY: CAP-Gly domain; InterPro: IPR000938 Cytoskeleton-associated proteins (CAP) are made of three distinct parts, an N-terminal section that is most probably globular and contains the CAP-Gly domain, a large central region predicted to be in an alpha-helical coiled-coil conformation and, finally, a short C-terminal globular domain. The CAP-Gly domain is a conserved, glycine-rich domain of about 42 residues found in some CAPs []. Proteins known to contain this domain include restin (also known as cytoplasmic linker protein-170 or CLIP-170), a 160 kDa protein associated with intermediate filaments and that links endocytic vesicles to microtubules; vertebrate dynactin (150 kDa dynein-associated polypeptide; DAP) and Drosophila glued, a major component of activator I; yeast protein BIK1, which seems to be required for the formation or stabilisation of microtubules during mitosis and for spindle pole body fusion during conjugation; yeast protein NIP100 (NIP80); human protein CKAP1/TFCB; Schizosaccharomyces pombe protein alp11 and Caenorhabditis elegans hypothetical protein F53F4.3. The latter proteins contain a N-terminal ubiquitin domain and a C-terminal CAP-Gly domain. The crystal structure of the CAP-Gly domain of C. elegans F53F4.3 protein, solved by single wavelength sulphur-anomalous phasing, revealed a novel protein fold containing three beta-sheets. The most conserved sequence, GKNDG, is located in two consecutive sharp turns on the surface, forming the entrance to a groove. Residues in the groove are highly conserved as measured from the information content of the aligned sequences. The C-terminal tail of another molecule in the crystal is bound in this groove []. ; PDB: 2CP6_A 2E4H_A 2E3H_A 3E2U_B 2HL3_B 3TQ7_Q 2HKQ_B 2HQH_A 2HKN_B 2HL5_C ....
Probab=99.96 E-value=1.2e-28 Score=165.94 Aligned_cols=66 Identities=48% Similarity=0.956 Sum_probs=59.5
Q ss_pred cccEEEE--CCCceEEEEEEeecC-CCCCcEEEEEEcCCCCCCCcEECCEEeeecCCCCeeEEecCCee
Q psy9801 23 IGDRVYV--GGTKSGRIAFIGETK-FAPGDWAGVVLDDPVGKNDGQVGQARYFQCEPRFGLFAPVHKVS 88 (132)
Q Consensus 23 vGdRV~V--~g~~~GtVRyiG~v~-~~~g~wvGVELDep~GknDGt~~G~rYF~C~p~~GiFv~~~kv~ 88 (132)
|||||.| .....|+|||+|+++ ...|+|+|||||++.|+|||+++|+|||+|+|+||+||++++|+
T Consensus 1 VG~rV~v~~~~~~~G~vryiG~~~~~~~g~~vGVEld~~~G~~dGt~~G~rYF~c~~~~G~Fv~~~~v~ 69 (69)
T PF01302_consen 1 VGDRVRVDDPGGRRGTVRYIGPVPGFKSGIWVGVELDEPRGKNDGTVKGKRYFECPPNHGIFVRPSKVE 69 (69)
T ss_dssp TTSEEEESSTTTEEEEEEEEEE-SSSSSSEEEEEEESSSTSSBSSEETTEESS-SSTTTEEEEEGGGE-
T ss_pred CCCEEEEeeCCCCEEEEEEEeeCCCCCCCEEEEEEEcCCCCCCCcEECCEEEeeeCCCCEEEecHHHCC
Confidence 7999999 346899999999999 67789999999999999999999999999999999999999985
No 2
>KOG3206|consensus
Probab=99.88 E-value=3e-23 Score=166.21 Aligned_cols=74 Identities=38% Similarity=0.861 Sum_probs=68.9
Q ss_pred CcccccEEEEC--CC--ceEEEEEEeecCCCCCcEEEEEEcCCCCCCCcEECCEEeeecCCCCeeEEecCCeeeCCCC
Q psy9801 20 SFIIGDRVYVG--GT--KSGRIAFIGETKFAPGDWAGVVLDDPVGKNDGQVGQARYFQCEPRFGLFAPVHKVSKSPMS 93 (132)
Q Consensus 20 ~l~vGdRV~V~--g~--~~GtVRyiG~v~~~~g~wvGVELDep~GknDGt~~G~rYF~C~p~~GiFv~~~kv~~~~~~ 93 (132)
.+.||+||+|. |+ ++|+|||+|++++.+|.|+|||.|||.|||||+++|+|||.|+|+||.||+|..|....-|
T Consensus 148 ~i~vG~rCeVtv~G~~~Rrg~vrYvG~~~~k~G~wiGVeydEplGKnDGsv~G~ryF~c~p~yGgfVrP~~V~Vgdfp 225 (234)
T KOG3206|consen 148 TIAVGRRCEVTVPGQAPRRGTVRYVGPLEFKPGYWIGVEYDEPLGKNDGSVNGKRYFECAPKYGGFVRPRAVTVGDFP 225 (234)
T ss_pred ccccCCeeEEecCCCCCcceEEEEecccCCCCceEEEEecCCccccCCCcccceEeeecCCccCCccccceeeecCCC
Confidence 38999999986 43 8999999999999999999999999999999999999999999999999999999987544
No 3
>KOG0971|consensus
Probab=99.86 E-value=6.1e-22 Score=182.60 Aligned_cols=77 Identities=40% Similarity=0.815 Sum_probs=72.5
Q ss_pred CCCcccccEEEECC-CceEEEEEEeecCCCCCcEEEEEEcCCCCCCCcEECCEEeeecCCCCeeEEecCCeeeCCCCC
Q psy9801 18 TDSFIIGDRVYVGG-TKSGRIAFIGETKFAPGDWAGVVLDDPVGKNDGQVGQARYFQCEPRFGLFAPVHKVSKSPMSG 94 (132)
Q Consensus 18 ~~~l~vGdRV~V~g-~~~GtVRyiG~v~~~~g~wvGVELDep~GknDGt~~G~rYF~C~p~~GiFv~~~kv~~~~~~~ 94 (132)
...|+||.||.|.| +..|+|.|+|.+.|+.|.|+||-||+|.|||||+++|++||+|++|||+||+.+.|..++|+.
T Consensus 3 ~r~lkvG~RVevtgknl~G~VayvG~T~FA~G~WvGVvLDep~GKNnGsVqg~qYF~Cd~ncG~FVr~sq~r~lEda~ 80 (1243)
T KOG0971|consen 3 PRSLKVGTRVEVTGKNLQGTVAYVGQTQFAEGKWVGVVLDEPKGKNNGSVQGVQYFECDENCGVFVRSSQVRELEDAS 80 (1243)
T ss_pred CccccccceEEeccCCccceEEEecccccccCceEEEEeccccCCCCCcccceeeEecCCCcceEeehhhhHHhhccc
Confidence 56799999999997 578999999999999999999999999999999999999999999999999999998888763
No 4
>COG5244 NIP100 Dynactin complex subunit involved in mitotic spindle partitioning in anaphase B [Cell division and chromosome partitioning]
Probab=99.82 E-value=1.4e-20 Score=165.42 Aligned_cols=70 Identities=49% Similarity=0.876 Sum_probs=64.2
Q ss_pred CcccccEEEECCCceEEEEEEeecCCCCCcEEEEEEcCCCCCCCcEECCEEeeecCCCCeeEEecCCeeeC
Q psy9801 20 SFIIGDRVYVGGTKSGRIAFIGETKFAPGDWAGVVLDDPVGKNDGQVGQARYFQCEPRFGLFAPVHKVSKS 90 (132)
Q Consensus 20 ~l~vGdRV~V~g~~~GtVRyiG~v~~~~g~wvGVELDep~GknDGt~~G~rYF~C~p~~GiFv~~~kv~~~ 90 (132)
-+.|||+|.+.+ ..|+|||||.+.|+.|+|+|||||+|.|||||+++|+|||.|..+||+|+++..=..+
T Consensus 3 ~lSv~D~Vll~~-~~g~VrfiG~t~f~~GiW~GlELd~p~GkNDGSvnGvRYF~Ckk~~giFir~~~~~ll 72 (669)
T COG5244 3 LLSVNDRVLLGD-KFGTVRFIGKTKFKDGIWIGLELDDPVGKNDGSVNGVRYFHCKKRHGIFIRPDDDSLL 72 (669)
T ss_pred eeecCCEEEecc-ccceEEEeeecccccceEEEEEecCCCCCCCCccCceEEEEecCCcceEEecCchhhh
Confidence 467999999998 5899999999999999999999999999999999999999999999999997654333
No 5
>KOG4568|consensus
Probab=99.76 E-value=6.3e-19 Score=159.64 Aligned_cols=78 Identities=49% Similarity=0.833 Sum_probs=71.2
Q ss_pred EeccCCCCcccccEEEECCCceEEEEEEeecCCCCCcEEEEEEcCCCCCCCcEECCEEeeecCCCCeeEEecCCeeeC
Q psy9801 13 VLTEDTDSFIIGDRVYVGGTKSGRIAFIGETKFAPGDWAGVVLDDPVGKNDGQVGQARYFQCEPRFGLFAPVHKVSKS 90 (132)
Q Consensus 13 ~l~~~~~~l~vGdRV~V~g~~~GtVRyiG~v~~~~g~wvGVELDep~GknDGt~~G~rYF~C~p~~GiFv~~~kv~~~ 90 (132)
+......++.||++|.|.+...|.|||+|++.+..|+|+|||||+|.|||||+|+|+|||.|.+.+|+|++.-+....
T Consensus 10 ~q~~~~~~~~ig~~v~v~~~~~G~v~y~G~t~f~~G~w~GveL~~p~GKNdGsv~G~rYF~ce~~kgif~~~~~~t~~ 87 (664)
T KOG4568|consen 10 VQLDDLGQFIIGRRVWVNNVELGFVRYAGETDFAKGIWAGVELLEPKGKNDGSVHGKRYFQCEPKKGIFFRQGRGTAS 87 (664)
T ss_pred chhhhhhhhhhcceEEecCCcceeeeeccCcccccceeeceeeccccCCCCcccchhhhhccccccceeecccccccc
Confidence 344567789999999999989999999999999999999999999999999999999999999999999987665554
No 6
>KOG3207|consensus
Probab=99.73 E-value=4.5e-18 Score=148.65 Aligned_cols=72 Identities=42% Similarity=0.679 Sum_probs=68.0
Q ss_pred CcccccEEEECCCceEEEEEEeecCCCCCcEEEEEEcCCC-CCCCcEECCEEeeecC-CCCeeEEecCCeeeCCC
Q psy9801 20 SFIIGDRVYVGGTKSGRIAFIGETKFAPGDWAGVVLDDPV-GKNDGQVGQARYFQCE-PRFGLFAPVHKVSKSPM 92 (132)
Q Consensus 20 ~l~vGdRV~V~g~~~GtVRyiG~v~~~~g~wvGVELDep~-GknDGt~~G~rYF~C~-p~~GiFv~~~kv~~~~~ 92 (132)
.++||+||.|.+ ..+||||+|.+++..+.|+|||||+|. |||||.++|++||.|. |+.|+|+++.+|....|
T Consensus 2 ~~~IG~RvkI~~-~~~Tvr~iG~V~g~~~~w~GvEWDd~~RGKH~G~vdgk~YF~~q~P~GGSFik~~kV~~p~d 75 (505)
T KOG3207|consen 2 TMEIGTRVKIGG-EIATVRYIGEVEGNNSKWYGVEWDDPVRGKHDGIVDGKRYFQTQHPNGGSFIKPGKVKFPTD 75 (505)
T ss_pred ceeccceEEEcC-EEEEEEEEEEEcCCCCcceeeEecCCCccccCceecceeeeeeecCCCccccCCccCCCCcc
Confidence 478999999998 599999999999999999999999996 9999999999999998 99999999999988765
No 7
>KOG4568|consensus
Probab=99.35 E-value=1.4e-13 Score=125.14 Aligned_cols=76 Identities=58% Similarity=1.065 Sum_probs=72.4
Q ss_pred cCCCCcccccEEEECCCceEEEEEEeecCCCCCcEEEEEEcCCCCCCCcEECCEEeeecCCCCeeEEecCCeeeCC
Q psy9801 16 EDTDSFIIGDRVYVGGTKSGRIAFIGETKFAPGDWAGVVLDDPVGKNDGQVGQARYFQCEPRFGLFAPVHKVSKSP 91 (132)
Q Consensus 16 ~~~~~l~vGdRV~V~g~~~GtVRyiG~v~~~~g~wvGVELDep~GknDGt~~G~rYF~C~p~~GiFv~~~kv~~~~ 91 (132)
.....+.+||||.+.+...|++||+|...++.|-|+|||||+|.|++||++.+++||.|++.+|.|.+..++....
T Consensus 150 ~~~~~l~v~dr~l~~gq~~~~~r~~~~t~fa~g~w~~~elde~~~~~d~sv~k~~~~~~k~ky~~f~~v~kv~~~~ 225 (664)
T KOG4568|consen 150 TSMLGLRVGDRVLVGGQKSGTLRYSGHTKFASGSWLGVELDEPVGKNDGSVGKVRYFQCKPKYGKFAPVQKVFKIE 225 (664)
T ss_pred cCccccccccceeecCcccchhhhhccccccCCcccchhcccccccccccccccccccCcchhcchhHHHHHhhcc
Confidence 4577899999999999999999999999999999999999999999999999999999999999999999998873
No 8
>KOG0241|consensus
Probab=99.24 E-value=4e-12 Score=119.33 Aligned_cols=71 Identities=35% Similarity=0.495 Sum_probs=64.1
Q ss_pred CCcccccEEEECCCceEEEEEEeecCCCCCcEEEEEEcCCCCCCCcEECCEEeeecCCCCeeEEecCCeeeCCCC
Q psy9801 19 DSFIIGDRVYVGGTKSGRIAFIGETKFAPGDWAGVVLDDPVGKNDGQVGQARYFQCEPRFGLFAPVHKVSKSPMS 93 (132)
Q Consensus 19 ~~l~vGdRV~V~g~~~GtVRyiG~v~~~~g~wvGVELDep~GknDGt~~G~rYF~C~p~~GiFv~~~kv~~~~~~ 93 (132)
..+-.|.+|.+.....++|||+|+..|.+ |||||.|.|||||++.|+|||+|.|+||+||+++++..-+.+
T Consensus 1629 ew~~~ge~v~~~~h~t~v~r~vg~tefq~----gveld~p~gkndgs~gg~qyfrc~p~~g~~vr~s~~~~~~~~ 1699 (1714)
T KOG0241|consen 1629 EWRGFGERVVTVEHTTNVLRDVGFTEFQG----GVELDDPDGKNDGSAGGLQYFRCLPNKGGGVRVSDGLHHPSQ 1699 (1714)
T ss_pred hhhhcCceeEEeecccceeeecchhhccC----cccccCCCCCcCccccceeEEeecCCCCCcccchhhccCcHh
Confidence 34778999998876788999999999877 999999999999999999999999999999999999876643
No 9
>KOG3556|consensus
Probab=99.21 E-value=2.1e-11 Score=108.94 Aligned_cols=71 Identities=28% Similarity=0.369 Sum_probs=64.7
Q ss_pred CcccccEEEECC-----CceEEEEEEeecCCCCCcEEEEEEcCCC-----CCCCcEECCEEeeecCCCCeeEEecCCeee
Q psy9801 20 SFIIGDRVYVGG-----TKSGRIAFIGETKFAPGDWAGVVLDDPV-----GKNDGQVGQARYFQCEPRFGLFAPVHKVSK 89 (132)
Q Consensus 20 ~l~vGdRV~V~g-----~~~GtVRyiG~v~~~~g~wvGVELDep~-----GknDGt~~G~rYF~C~p~~GiFv~~~kv~~ 89 (132)
.|+||+.|+|.. ..+|+|||||.-|...|+|+|||+++.. +..||++.|.|||+|-.+..+||+...+..
T Consensus 235 ~L~IGslveV~np~~~~~~ygvVrWIG~pP~~~~Vl~gve~edet~~~~~~~~dgs~~g~Rlftc~d~~a~Fv~~~scs~ 314 (724)
T KOG3556|consen 235 NLKIGSLVEVENPETMRRVYGVVRWIGEPPEASGVLYGVEFEDETSQWPSSNQDGSSSGDRLFTCFDTNANFVMSGSCSV 314 (724)
T ss_pred cceecceEEecCCccccccceeeEecccCCcccCceEeeeecCccccCccccccCcccCceeeeeccccceeeEcCCCCc
Confidence 489999999974 3799999999999999999999999874 779999999999999999999999988776
Q ss_pred C
Q psy9801 90 S 90 (132)
Q Consensus 90 ~ 90 (132)
-
T Consensus 315 d 315 (724)
T KOG3556|consen 315 D 315 (724)
T ss_pred C
Confidence 4
No 10
>PTZ00243 ABC transporter; Provisional
Probab=96.11 E-value=0.014 Score=58.13 Aligned_cols=57 Identities=19% Similarity=0.212 Sum_probs=46.4
Q ss_pred CcccccEEEECC--CceEEEEEEeecC--CCCCcEEEEEEcCC-----------C---CCCCcEECCEEeeecCC
Q psy9801 20 SFIIGDRVYVGG--TKSGRIAFIGETK--FAPGDWAGVVLDDP-----------V---GKNDGQVGQARYFQCEP 76 (132)
Q Consensus 20 ~l~vGdRV~V~g--~~~GtVRyiG~v~--~~~g~wvGVELDep-----------~---GknDGt~~G~rYF~C~p 76 (132)
+-.||.+|-+.. .-.|++||+|.+. +.++.++||||.-| . +-|||.++|.+.|....
T Consensus 124 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 198 (1560)
T PTZ00243 124 NCMVGAEVVSTLDASSRGVLRWVGVPQQGGYTRMMAGVEWSVPPALRTAARSDDSGASPFFNGVAHGEHLFTPEQ 198 (1560)
T ss_pred ccccccEEEeeccccccceEEeecccccCCCcceeeeeeeccCchhhhcccCCCCCCccccccccccccccCccc
Confidence 345899998874 4799999999996 46789999999976 1 24999999999998753
No 11
>PRK10708 hypothetical protein; Provisional
Probab=93.09 E-value=0.39 Score=31.94 Aligned_cols=55 Identities=29% Similarity=0.525 Sum_probs=41.8
Q ss_pred cccccEEEEC--C--CceEEEEEEeecCCCCCcEEEEEEcC-CCCCCCcEECCEEeeec-CCCCeeEEecC
Q psy9801 21 FIIGDRVYVG--G--TKSGRIAFIGETKFAPGDWAGVVLDD-PVGKNDGQVGQARYFQC-EPRFGLFAPVH 85 (132)
Q Consensus 21 l~vGdRV~V~--g--~~~GtVRyiG~v~~~~g~wvGVELDe-p~GknDGt~~G~rYF~C-~p~~GiFv~~~ 85 (132)
+++.|||.|. | .+.|+|.-+ =+|..|+.+=|.|++ |.| +-||.= ...-|+||.+.
T Consensus 1 MkvnD~VtVKTDG~~rR~G~iLav--E~F~EG~MyLvaL~dYP~G--------iWFFNE~~~~~G~FVep~ 61 (62)
T PRK10708 1 MKVNDRVTVKTDGGPRRPGVVLAV--EEFSEGTMYLVSLEDYPLG--------IWFFNEAGHQDGIFVEKA 61 (62)
T ss_pred CccccEEEEecCCCccccceEEEE--eeccCcEEEEEEcCcCCCc--------eEEEeccCCCCceEeccc
Confidence 4789999997 2 378999887 467889999999987 433 447775 47889999663
No 12
>PF10781 DSRB: Dextransucrase DSRB; InterPro: IPR019717 DSRB is a novel dextransucrase which produces a dextran different from the typical dextran, as it contains (1-6) and (1-2) linkages, when this strain is grown in the presence of sucrose [].
Probab=93.05 E-value=0.39 Score=31.92 Aligned_cols=55 Identities=31% Similarity=0.505 Sum_probs=41.8
Q ss_pred cccccEEEEC--C--CceEEEEEEeecCCCCCcEEEEEEcC-CCCCCCcEECCEEeeec-CCCCeeEEecC
Q psy9801 21 FIIGDRVYVG--G--TKSGRIAFIGETKFAPGDWAGVVLDD-PVGKNDGQVGQARYFQC-EPRFGLFAPVH 85 (132)
Q Consensus 21 l~vGdRV~V~--g--~~~GtVRyiG~v~~~~g~wvGVELDe-p~GknDGt~~G~rYF~C-~p~~GiFv~~~ 85 (132)
+++.|||.|. | .+.|+|.-+ =+|..|+.+=|.|++ |.| +-||.= ...-|+||.+.
T Consensus 1 MkvnD~VtVKTDG~~rR~G~ilav--E~F~EG~MYLvaL~dYP~G--------iWFFNE~~~~dG~FVep~ 61 (62)
T PF10781_consen 1 MKVNDRVTVKTDGGPRREGVILAV--EPFNEGTMYLVALEDYPAG--------IWFFNEKDSPDGTFVEPR 61 (62)
T ss_pred CccccEEEEecCCcccccceEEEE--eeccCcEEEEEEcCcCCcc--------eEEEecCCCCCcEEeeec
Confidence 4789999997 2 378999887 467889999999987 433 447765 47889999764
No 13
>PF09926 DUF2158: Uncharacterized small protein (DUF2158); InterPro: IPR019226 This entry represents a family of predominantly prokaryotic proteins with no known function.
Probab=79.52 E-value=8.5 Score=24.72 Aligned_cols=46 Identities=26% Similarity=0.367 Sum_probs=36.5
Q ss_pred cccccEEEEC-CCceEEEEEEeecCCCCCcEEEEEEcCCCCCCCcEE
Q psy9801 21 FIIGDRVYVG-GTKSGRIAFIGETKFAPGDWAGVVLDDPVGKNDGQV 66 (132)
Q Consensus 21 l~vGdRV~V~-g~~~GtVRyiG~v~~~~g~wvGVELDep~GknDGt~ 66 (132)
|++||.|++. |...=||.++|+..+..+.|+=-.|-+..+...+.|
T Consensus 1 f~~GDvV~LKSGGp~MTV~~v~~~~~~~~~~v~C~WFd~~~~~~~~F 47 (53)
T PF09926_consen 1 FKIGDVVQLKSGGPRMTVTEVGPNAGASGGWVECQWFDGHGEQRETF 47 (53)
T ss_pred CCCCCEEEEccCCCCeEEEEccccccCCCCeEEEEeCCCCCcccccc
Confidence 5799999987 456779999999988888888888888766654443
No 14
>TIGR00739 yajC preprotein translocase, YajC subunit. While this protein is part of the preprotein translocase in Escherichia coli, it is not essential for viability or protein secretion. The N-terminus region contains a predicted membrane-spanning region followed by a region consisting almost entirely of residues with charged (acidic, basic, or zwitterionic) side chains. This small protein is about 100 residues in length, and is restricted to bacteria; however, this protein is absent from some lineages, including spirochetes and Mycoplasmas.
Probab=64.35 E-value=22 Score=24.59 Aligned_cols=33 Identities=27% Similarity=0.340 Sum_probs=26.0
Q ss_pred CCCcccccEEEECCCceEEEEEEeecCCCCCcEEEEEEc
Q psy9801 18 TDSFIIGDRVYVGGTKSGRIAFIGETKFAPGDWAGVVLD 56 (132)
Q Consensus 18 ~~~l~vGdRV~V~g~~~GtVRyiG~v~~~~g~wvGVELD 56 (132)
...|++||+|...+..+|+|.-++. .++-||..
T Consensus 35 ~~~L~~Gd~VvT~gGi~G~V~~i~d------~~v~vei~ 67 (84)
T TIGR00739 35 IESLKKGDKVLTIGGIIGTVTKIAE------NTIVIELN 67 (84)
T ss_pred HHhCCCCCEEEECCCeEEEEEEEeC------CEEEEEEC
Confidence 4579999999999889999998863 35556654
No 15
>PF00924 MS_channel: Mechanosensitive ion channel; InterPro: IPR006685 Mechanosensitive (MS) channels provide protection against hypo-osmotic shock, responding both to stretching of the cell membrane and to membrane depolarisation. They are present in the membranes of organisms from the three domains of life: bacteria, archaea, and eukarya []. There are two families of MS channels: large-conductance MS channels (MscL) and small-conductance MS channels (MscS or YGGB). The pressure threshold for MscS opening is 50% that of MscL []. The MscS family is much larger and more variable in size and sequence than the MscL family. Much of the diversity in MscS proteins occurs in the size of the transmembrane regions, which ranges from three to eleven transmembrane helices, although the three C-terminal helices are conserved. This family contains sequences form the MscS family of proteins. MscS folds as a homo-heptamer with a cylindrical shape, and can be divided into transmembrane and extramembrane regions: an N-terminal periplasmic region, a transmembrane region, and a C-terminal cytoplasmic region (middle and C-terminal domains). The transmembrane region forms a channel through the membrane that opens into a chamber enclosed by the extramembrane portion, the latter connecting to the cytoplasm through distinct portals [].; GO: 0055085 transmembrane transport, 0016020 membrane; PDB: 2OAU_E 2VV5_F.
Probab=63.83 E-value=7 Score=29.56 Aligned_cols=26 Identities=38% Similarity=0.736 Sum_probs=18.3
Q ss_pred CCCcccccEEEECCCceEEEEEEeecC
Q psy9801 18 TDSFIIGDRVYVGGTKSGRIAFIGETK 44 (132)
Q Consensus 18 ~~~l~vGdRV~V~g~~~GtVRyiG~v~ 44 (132)
...+++||+|++.+ ..|.|..+|-..
T Consensus 58 ~~pf~vGD~I~i~~-~~G~V~~I~l~~ 83 (206)
T PF00924_consen 58 ERPFKVGDRIEIGG-VEGRVEEIGLRS 83 (206)
T ss_dssp C-SS-TT-EEESSS--EEEEEEE-SSE
T ss_pred cCCccCCCEEEEEE-eehHHHhcCcce
Confidence 45799999999997 699999998763
No 16
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=62.17 E-value=22 Score=25.99 Aligned_cols=34 Identities=24% Similarity=0.207 Sum_probs=27.1
Q ss_pred CCCcccccEEEECCCceEEEEEEeecCCCCCcEEEEEEcC
Q psy9801 18 TDSFIIGDRVYVGGTKSGRIAFIGETKFAPGDWAGVVLDD 57 (132)
Q Consensus 18 ~~~l~vGdRV~V~g~~~GtVRyiG~v~~~~g~wvGVELDe 57 (132)
...|++||+|.-.+..+|+|.-++ +.++-||+.+
T Consensus 36 ~~~Lk~GD~VvT~gGi~G~V~~I~------d~~v~leia~ 69 (109)
T PRK05886 36 HESLQPGDRVHTTSGLQATIVGIT------DDTVDLEIAP 69 (109)
T ss_pred HHhcCCCCEEEECCCeEEEEEEEe------CCEEEEEECC
Confidence 357999999999988999999886 2467777653
No 17
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=53.95 E-value=36 Score=24.55 Aligned_cols=34 Identities=29% Similarity=0.484 Sum_probs=26.2
Q ss_pred CCCcccccEEEECCCceEEEEEEeecCCCCCcEEEEEEcC
Q psy9801 18 TDSFIIGDRVYVGGTKSGRIAFIGETKFAPGDWAGVVLDD 57 (132)
Q Consensus 18 ~~~l~vGdRV~V~g~~~GtVRyiG~v~~~~g~wvGVELDe 57 (132)
...|++||+|...+..+|+|.-+.. ..+=||..+
T Consensus 50 ~~~Lk~Gd~VvT~gGi~G~Vv~i~~------~~v~lei~~ 83 (106)
T PRK05585 50 LSSLAKGDEVVTNGGIIGKVTKVSE------DFVIIELND 83 (106)
T ss_pred HHhcCCCCEEEECCCeEEEEEEEeC------CEEEEEECC
Confidence 4579999999998889999998853 456666644
No 18
>cd00539 MCR_gamma Methyl-coenzyme M reductase (MCR) gamma subunit. MCR catalyzes the terminal step of methane formation in the energy metabolism of all methanogenic archaea, in which methyl-coenzyme M and coenzyme B are converted to methane and the heterodisulfide of coenzyme M and coenzyme B (CoM-S-S-CoB). MCR is a dimer of trimers, each of which consists of one alpha, one beta, and one gamma subunit, with two identical active sites containing nickel porphinoid factor 430 (F430).
Probab=52.70 E-value=5.4 Score=32.96 Aligned_cols=45 Identities=33% Similarity=0.497 Sum_probs=36.0
Q ss_pred CcceEeccCCCCcccccEEEECCCceEEEEEEeecCCCCCcEEEEEEcCCC--CC
Q psy9801 9 DSSQVLTEDTDSFIIGDRVYVGGTKSGRIAFIGETKFAPGDWAGVVLDDPV--GK 61 (132)
Q Consensus 9 ~~~~~l~~~~~~l~vGdRV~V~g~~~GtVRyiG~v~~~~g~wvGVELDep~--Gk 61 (132)
-|+++|.++..=|-.=+|+.+.. ..|.|.|+ ...+|+.||++. ||
T Consensus 155 GHslRLdEnGmMFD~L~R~~~d~-~~G~V~yv-------KDqvG~plD~~V~~Gk 201 (246)
T cd00539 155 GHSLRLDEDGLMFDALRRYRLDE-ETGEVEYV-------KDQVGIPLDEPVDLGK 201 (246)
T ss_pred cceeeecCCChhHHHHHHhhccc-CCCcEEEe-------hhhcCCcccCcccCCC
Confidence 47899999888787778887754 58999998 345899999986 76
No 19
>TIGR03259 met_CoM_red_gam methyl-coenzyme M reductase, gamma subunit. Members of this protein family are the gamma subunit of methyl coenzyme M reductase, also called coenzyme-B sulfoethylthiotransferase (EC 2.8.4.1). This enzyme, with alpha, beta, and gamma subunits, catalyzes the last step in methanogenesis. Several methanogens have encode two such enzymes, designated I and II; this model does not separate the isozymes.
Probab=50.95 E-value=5.9 Score=32.69 Aligned_cols=45 Identities=33% Similarity=0.450 Sum_probs=35.9
Q ss_pred CcceEeccCCCCcccccEEEECCCceEEEEEEeecCCCCCcEEEEEEcCCC--CC
Q psy9801 9 DSSQVLTEDTDSFIIGDRVYVGGTKSGRIAFIGETKFAPGDWAGVVLDDPV--GK 61 (132)
Q Consensus 9 ~~~~~l~~~~~~l~vGdRV~V~g~~~GtVRyiG~v~~~~g~wvGVELDep~--Gk 61 (132)
-|+++|.++..-|-.=+|+.+.. ..|.|.|+ ...+|+.||++. ||
T Consensus 155 GHslRLdEnGmMFD~LqR~~~d~-~~G~V~yv-------KDqvG~plD~~V~~Gk 201 (244)
T TIGR03259 155 GHSLRLDEDGVMFDMLQRYRFDE-ETGHIIMV-------KDQVGRPLDEPVDLGE 201 (244)
T ss_pred cceeeecCCChhHHHHHHhhccc-CCCcEEEe-------hhhcCCcccCcccCCC
Confidence 47899999888887778887754 58999998 345899999985 75
No 20
>PF13403 Hint_2: Hint domain
Probab=50.36 E-value=22 Score=26.63 Aligned_cols=28 Identities=21% Similarity=0.345 Sum_probs=23.7
Q ss_pred CCCcccccEEEECCCceEEEEEEeecCC
Q psy9801 18 TDSFIIGDRVYVGGTKSGRIAFIGETKF 45 (132)
Q Consensus 18 ~~~l~vGdRV~V~g~~~GtVRyiG~v~~ 45 (132)
..+|++||+|.-.....-.|+|||....
T Consensus 18 Ve~L~~GD~V~T~dgg~~~V~wig~~~~ 45 (147)
T PF13403_consen 18 VEDLRPGDRVLTRDGGFQPVRWIGRRTV 45 (147)
T ss_pred eeccCCCCEEEecCCCEEEEEEEEEEEe
Confidence 6789999999987667889999998754
No 21
>COG3350 Uncharacterized conserved protein [Function unknown]
Probab=49.40 E-value=7.1 Score=25.40 Aligned_cols=30 Identities=17% Similarity=0.402 Sum_probs=23.0
Q ss_pred cEEEEEEcCCCCCCCcEECCEEeeecCCCC
Q psy9801 49 DWAGVVLDDPVGKNDGQVGQARYFQCEPRF 78 (132)
Q Consensus 49 ~wvGVELDep~GknDGt~~G~rYF~C~p~~ 78 (132)
..+|-.+|...-..-=+++|+-||-|.+.+
T Consensus 6 PVcgm~v~~~~a~~k~~Y~GktYYFcse~~ 35 (53)
T COG3350 6 PVCGMKVDNENAEYKSSYGGKTYYFCSEEC 35 (53)
T ss_pred CCcCccccccccceeEEeCCEEEEEeCHHH
Confidence 456777777666677789999999997544
No 22
>PF02470 MCE: mce related protein; InterPro: IPR003399 This domain is found in all 24 mce genes associated with the four mammalian cell entry (mce) operons of Mycobacterium tuberculosis and their homologs in other Actinomycetales [, ]. The archetype (mce1A, Rv0169), was isolated as being necessary for colonisation of, and survival within, the macrophage []. The domain is also found in: Chloroplast Ycf22 and related cyanobacterial homologs, the majority of which have an N-terminal transmembrane domain and are putative ABC transporters. Proteobacterial homologs, which include YrbD, YebT, VpsC and Ttg2C, the latter being annotated as a toluene tolerance proteins, belong to the periplasmic substrate-binding ABC transporter superfamily.
Probab=45.50 E-value=84 Score=20.45 Aligned_cols=44 Identities=16% Similarity=0.212 Sum_probs=34.9
Q ss_pred cCCCCcccccEEEECCCceEEEEEEeecCCCCCcEEEEEEcCCC
Q psy9801 16 EDTDSFIIGDRVYVGGTKSGRIAFIGETKFAPGDWAGVVLDDPV 59 (132)
Q Consensus 16 ~~~~~l~vGdRV~V~g~~~GtVRyiG~v~~~~g~wvGVELDep~ 59 (132)
.+...|.+|+.|.+.|...|.|.=+.--+.....-+-+++++..
T Consensus 10 ~~~~GL~~gs~V~~~Gv~VG~V~~i~l~~~~~~v~v~~~i~~~~ 53 (81)
T PF02470_consen 10 DDAGGLSVGSPVRYRGVEVGKVTSIELDPDGNRVRVTLRIDPDY 53 (81)
T ss_pred CCcCCCCCcCEEEECCEEEEEEEEEEEcCCCCEEEEEEEEcCCc
Confidence 45688999999999998899999885424445678888888865
No 23
>TIGR02266 gmx_TIGR02266 Myxococcus xanthus paralogous domain TIGR02266. This domain is related to Type IV pilus assembly protein PilZ (Pfam model pfam07238). It is found in at least 12 copies in Myxococcus xanthus DK 1622.
Probab=43.63 E-value=82 Score=20.73 Aligned_cols=41 Identities=22% Similarity=0.328 Sum_probs=26.6
Q ss_pred CCCcccccEEEEC----C-----CceEEEEEEeecCCCCCcEEEEEEcCC
Q psy9801 18 TDSFIIGDRVYVG----G-----TKSGRIAFIGETKFAPGDWAGVVLDDP 58 (132)
Q Consensus 18 ~~~l~vGdRV~V~----g-----~~~GtVRyiG~v~~~~g~wvGVELDep 58 (132)
...+++|++|.+. + ...|.|+|+-+.......++||++.+.
T Consensus 34 ~~~~~~g~~v~l~l~l~~~~~~i~~~g~Vv~~~~~~~~~~~~~Gv~F~~~ 83 (96)
T TIGR02266 34 RKPLAVGTRVELKLTLPGGERPVELKGVVAWVRPAADGGPPGMGVRFEDL 83 (96)
T ss_pred CCCcCCCCEEEEEEEcCCCCeEEEEEEEEEEeCCCCCCCCCeeEEEeccC
Confidence 4568899988764 2 147888888433222125789998764
No 24
>PRK06531 yajC preprotein translocase subunit YajC; Validated
Probab=43.17 E-value=32 Score=25.32 Aligned_cols=24 Identities=21% Similarity=0.259 Sum_probs=20.8
Q ss_pred CCCcccccEEEECCCceEEEEEEe
Q psy9801 18 TDSFIIGDRVYVGGTKSGRIAFIG 41 (132)
Q Consensus 18 ~~~l~vGdRV~V~g~~~GtVRyiG 41 (132)
...|+.||+|.-.|..+|+|..++
T Consensus 34 ~~sLk~GD~VvT~GGi~G~V~~I~ 57 (113)
T PRK06531 34 LNAIQKGDEVVTIGGLYGTVDEVD 57 (113)
T ss_pred HHhcCCCCEEEECCCcEEEEEEEe
Confidence 346999999999988999998885
No 25
>PF02240 MCR_gamma: Methyl-coenzyme M reductase gamma subunit; InterPro: IPR003178 Methyl-coenzyme M reductase (MCR) catalyses the reduction of methyl-coenzyme M (CH3-SCoM) and coenzyme B (HS-CoB) to methane and the corresponding heterosulphide CoM-S-S-CoB (2.8.4.1 from EC), the final step in methane biosynthesis. This reaction proceeds under anaerobic conditions by methanogenic Archaea [], and requires a nickel-porphinoid prosthetic group, coenzyme F430, which is in the EPR-detectable Ni(I) oxidation state in the active enzyme. Studies on a catalytically inactive enzyme aerobically co-crystallized with coenzyme M displayed a fully occupied coenzyme M-binding site with no alternate conformations. The binding of coenzyme M appears to induce specific conformational changes that suggests a molecular mechanism by which the enzyme ensures that methyl-coenzyme M enters the substrate channel prior to coenzyme B, as required by the active-site geometry []. MCR is a hexamer composed of 2 alpha, 2 beta, and 2 gamma subunits with two identical nickel porphinoid active sites, which form two long active site channels with F430 embedded at the bottom [, ]. This entry represents the gamma subunit, which has a complex alpha-helical/beta-sheet topology.; GO: 0050524 coenzyme-B sulfoethylthiotransferase activity, 0015948 methanogenesis; PDB: 1MRO_C 3M32_C 3POT_F 1HBU_F 3M2U_C 3M2V_C 3M2R_F 1HBM_C 3M1V_C 1HBO_C ....
Probab=43.15 E-value=7 Score=32.31 Aligned_cols=43 Identities=26% Similarity=0.435 Sum_probs=27.7
Q ss_pred CcceEeccCCCCcccccEEEECCCceEEEEEEeecCCCCCcEEEEEEcCCC
Q psy9801 9 DSSQVLTEDTDSFIIGDRVYVGGTKSGRIAFIGETKFAPGDWAGVVLDDPV 59 (132)
Q Consensus 9 ~~~~~l~~~~~~l~vGdRV~V~g~~~GtVRyiG~v~~~~g~wvGVELDep~ 59 (132)
-|+++|.|+..-|-.=+|+.+.+ ..|.|.|+=.- +|+.||++.
T Consensus 156 GHSlRLdEnGmMFD~LqR~~~d~-~~G~V~yvKdq-------vG~plD~~V 198 (247)
T PF02240_consen 156 GHSLRLDENGMMFDMLQRYVLDE-ETGNVKYVKDQ-------VGRPLDEPV 198 (247)
T ss_dssp -TTS-BETTS-B--TT--EEEET-TTTEEEEEE-T-------TS-EEEEEE
T ss_pred cceeeecCCChhHHHHhheeecC-CCCcEEEeccc-------cCCcccCcc
Confidence 47899999988888889999876 48899998443 678888874
No 26
>PRK10334 mechanosensitive channel MscS; Provisional
Probab=41.80 E-value=33 Score=28.48 Aligned_cols=25 Identities=24% Similarity=0.360 Sum_probs=21.4
Q ss_pred CCCcccccEEEECCCceEEEEEEeec
Q psy9801 18 TDSFIIGDRVYVGGTKSGRIAFIGET 43 (132)
Q Consensus 18 ~~~l~vGdRV~V~g~~~GtVRyiG~v 43 (132)
...+++||.|++.+ ..|+|.-||-.
T Consensus 127 ~rpf~vGD~I~i~~-~~G~V~~I~~r 151 (286)
T PRK10334 127 FRPFRAGEYVDLGG-VAGTVLSVQIF 151 (286)
T ss_pred cCCCCCCCEEEECC-EEEEEEEEEeE
Confidence 45799999999986 69999999865
No 27
>KOG1999|consensus
Probab=40.19 E-value=82 Score=31.22 Aligned_cols=36 Identities=19% Similarity=0.288 Sum_probs=26.0
Q ss_pred eccCCcceEeccCCCCcccccEEEECC-C---ceEEEEEE
Q psy9801 5 WKAYDSSQVLTEDTDSFIIGDRVYVGG-T---KSGRIAFI 40 (132)
Q Consensus 5 ~~~s~~~~~l~~~~~~l~vGdRV~V~g-~---~~GtVRyi 40 (132)
.++..+++++......++++|.|.+.+ . ..|.|.||
T Consensus 566 kk~~r~~~~~D~~~n~I~~kD~Vkvi~Gp~~g~~G~v~~i 605 (1024)
T KOG1999|consen 566 KKDNRKAVAVDRNGNEIRVKDTVKVIGGPSKGREGEVLHI 605 (1024)
T ss_pred hhhhhhheeecccCCeecccceEEEecCCCCCccCcccee
Confidence 356777788888889999999998864 2 33555555
No 28
>PF07238 PilZ: PilZ domain; InterPro: IPR009875 The ubiquitous bacterial second messenger cyclic-di-GMP (c-di-GMP) is associated with the regulation of biofilm formation, the control of exopolysaccharide synthesis, flagellar- and pili-based motility, gene expression, interactions of bacteria with eukaryotic hosts and multicellular behaviour in diverse bacteria. With the exception of bacterial cellulose synthases, the identities of c-di-GMP receptors and end targets of the proteins having one or more PilZ domains are mostly uncharacterised. However it was suggested that the PilZ domains present in the BcsA subunits of bacterial cellulose synthases function in c-di-GMP binding []. More recently YcgR (see IPR023787 from INTERPRO) was found to bind c-di-GMP tightly and specifically; also isolated PilZ domains from YcgR and BcsA bound c-di-GMP indicating that the PilZ domain was sufficient for binding of c-di-GMP and significantly that site-directed mutagenesis performed on YcgR implicated the most conserved residues in the PilZ domain directly in c-di-GMP binding []. It was suggested that c-di-GMP binding to PilZ brings about conformational changes in the protein that stabilise the bound ligand and probability initiates the downstream signal transduction cascade. In the case of YcgR, c-di-GMP binding regulates flagellum-based motility in a c-di-GMP-dependent manner (see IPR023787 from INTERPRO) []. The association of the PilZ domain with a variety of other domains, including likely components of bacterial multidrug secretion system, could provide clues to multiple functions of the c-di-GMP in bacterial pathogenesis and cell development. Binding and mutagenesis studies of several PilZ domain proteins have confirmed this observation and demonstrated that c-di-GMP binding depends on residues in RxxxR and D/NxSxxG sequence motifs. The crystal structure, at 1.7 A, of a PilZ domain::c-di-GMP complex from Vibrio cholerae shows c-di-GMP contacting seven of nine strongly conserved residues. Binding of c-di-GMP causes a conformational switch whereby the C- and N-terminal domains are brought into close opposition forming a new allosteric interaction surface that spans these domains and the c-di-GMP at their interface []. ; GO: 0035438 cyclic-di-GMP binding; PDB: 2RDE_B 1YLN_A 3KYG_A 3DSG_B 2GJG_A 3KYF_A 1YWU_A 2L74_A 2L1T_A 3CNR_A ....
Probab=38.24 E-value=92 Score=19.84 Aligned_cols=36 Identities=33% Similarity=0.496 Sum_probs=25.4
Q ss_pred CcccccEEEEC-----C--C-ceEEEEEEeecCCCCCcEEEEEEcC
Q psy9801 20 SFIIGDRVYVG-----G--T-KSGRIAFIGETKFAPGDWAGVVLDD 57 (132)
Q Consensus 20 ~l~vGdRV~V~-----g--~-~~GtVRyiG~v~~~~g~wvGVELDe 57 (132)
.+.+|+.|.+. . . ..|.|+++-+. ..+.++|+++++
T Consensus 44 ~~~~~~~v~l~~~~~~~~~~~~~~~V~~~~~~--~~~~~~g~~f~~ 87 (102)
T PF07238_consen 44 PLEPGDRVRLSFSLPGGGFPIVTGRVVRIQKD--SDGYRVGVEFVD 87 (102)
T ss_dssp G--TTSEEEEEEECTTTSCEEEEEEEEEEEEE--SSEEEEEEEECH
T ss_pred CCCCCCEEEEEEEeCCCCeeEEEEEEEEEECC--CCceEEEEEEee
Confidence 78899977664 1 1 67888888666 667889999864
No 29
>PF07154 DUF1392: Protein of unknown function (DUF1392); InterPro: IPR009824 This family consists of several hypothetical cyanobacterial proteins of around 150 residues in length, which seem to be specific to Anabaena species. The function of this family is unknown.
Probab=38.21 E-value=54 Score=25.49 Aligned_cols=44 Identities=18% Similarity=0.175 Sum_probs=27.4
Q ss_pred cCCCCcccccEEEECC-CceEEEEEEeecCCCCC-cEEEEEEcCCC
Q psy9801 16 EDTDSFIIGDRVYVGG-TKSGRIAFIGETKFAPG-DWAGVVLDDPV 59 (132)
Q Consensus 16 ~~~~~l~vGdRV~V~g-~~~GtVRyiG~v~~~~g-~wvGVELDep~ 59 (132)
-..+.|.+||||.+.- ..--..|-|=-+-.-++ -++.|||-.|.
T Consensus 83 v~kp~F~LGd~V~~~f~~~~pkqRlIlGv~lv~~~W~Y~VE~~SPt 128 (150)
T PF07154_consen 83 VQKPAFRLGDRVEFRFYSDGPKQRLILGVFLVNNSWFYAVEWRSPT 128 (150)
T ss_pred ccCCceecCCEEEEEecCCCCceEEEEEEEEecCceEEEEEEeCCc
Confidence 3578899999998862 11223344433333344 45889999886
No 30
>PF13785 DUF4178: Domain of unknown function (DUF4178)
Probab=35.34 E-value=1.1e+02 Score=21.76 Aligned_cols=20 Identities=30% Similarity=0.493 Sum_probs=16.9
Q ss_pred cccccEEEECCC---ceEEEEEE
Q psy9801 21 FIIGDRVYVGGT---KSGRIAFI 40 (132)
Q Consensus 21 l~vGdRV~V~g~---~~GtVRyi 40 (132)
|++||.+.+.+. ..|.++|-
T Consensus 1 L~~G~~~~~~g~~~~ViG~~~~~ 23 (140)
T PF13785_consen 1 LQLGDIGRIDGKDYTVIGRIQYD 23 (140)
T ss_pred CCCCCEEEECCeEEEEEEEEEEE
Confidence 689999999983 68999984
No 31
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=34.08 E-value=1e+02 Score=22.09 Aligned_cols=25 Identities=28% Similarity=0.445 Sum_probs=21.5
Q ss_pred CCcccccEEEECCCceEEEEEEeec
Q psy9801 19 DSFIIGDRVYVGGTKSGRIAFIGET 43 (132)
Q Consensus 19 ~~l~vGdRV~V~g~~~GtVRyiG~v 43 (132)
..++.||+|.-.|...|+|.-++.-
T Consensus 42 ~sL~kGD~VvT~gGi~G~V~~v~d~ 66 (97)
T COG1862 42 NSLKKGDEVVTIGGIVGTVTKVGDD 66 (97)
T ss_pred HhccCCCEEEEcCCeEEEEEEEecC
Confidence 4689999999998899999998763
No 32
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=33.91 E-value=70 Score=16.41 Aligned_cols=11 Identities=45% Similarity=0.591 Sum_probs=9.1
Q ss_pred cccccEEEECC
Q psy9801 21 FIIGDRVYVGG 31 (132)
Q Consensus 21 l~vGdRV~V~g 31 (132)
+++||+|.|.+
T Consensus 2 ~~~G~~V~I~~ 12 (28)
T smart00739 2 FEVGDTVRVIA 12 (28)
T ss_pred CCCCCEEEEeE
Confidence 67899999873
No 33
>PF13437 HlyD_3: HlyD family secretion protein
Probab=33.88 E-value=98 Score=20.71 Aligned_cols=37 Identities=27% Similarity=0.323 Sum_probs=24.5
Q ss_pred CCCCcc-cccEEEEC---C---CceEEEEEEeecCCCCCcEEEE
Q psy9801 17 DTDSFI-IGDRVYVG---G---TKSGRIAFIGETKFAPGDWAGV 53 (132)
Q Consensus 17 ~~~~l~-vGdRV~V~---g---~~~GtVRyiG~v~~~~g~wvGV 53 (132)
....++ .|+.|.+. + ...|+|.+|.+.....+-.+-|
T Consensus 46 ~~~~i~~~g~~v~v~~~~~~~~~~~g~V~~I~~~~~~~~~~~~v 89 (105)
T PF13437_consen 46 DIARIKDPGQKVTVRLDPGPEKTIEGKVSSISPSPDPQGGTYRV 89 (105)
T ss_pred hhcceEeCCCEEEEEECCCCCcEEEEEEEEEeCcccCCCcEEEE
Confidence 456776 89988765 2 3689999998865444334443
No 34
>COG1463 Ttg2C ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=29.60 E-value=1.3e+02 Score=25.60 Aligned_cols=61 Identities=21% Similarity=0.362 Sum_probs=44.9
Q ss_pred cCCCCcccccEEEECCCceEEEEEEeecCCCCCcEEEEEEcCCC--CC-------CCcEECCEEeeecCCC
Q psy9801 16 EDTDSFIIGDRVYVGGTKSGRIAFIGETKFAPGDWAGVVLDDPV--GK-------NDGQVGQARYFQCEPR 77 (132)
Q Consensus 16 ~~~~~l~vGdRV~V~g~~~GtVRyiG~v~~~~g~wvGVELDep~--Gk-------nDGt~~G~rYF~C~p~ 77 (132)
.+...|..|+.|++.|...|.|+-|...+...+.-+=+++|... .+ ..| .-|.+|-+-.|+
T Consensus 48 ~~~~GL~~gs~V~~~GV~VG~V~~I~~~~~~~~~~v~~~id~~~~Ip~~s~A~I~~~g-L~G~~yIeL~~~ 117 (359)
T COG1463 48 DDAGGLYVGSPVRYRGVKVGKVASISLDPKPNGARVTLEIDSDYPIPADSTASIRTTG-LLGEKYIELTPG 117 (359)
T ss_pred cccccCCCCCceEEcCEEeEEEEEEEecCCCCceEEEEEecCCcccCCCceeeeeecc-ccceeEEEeccC
Confidence 46788999999999999999999998887555666777777532 32 222 238888887554
No 35
>PF12700 HlyD_2: HlyD family secretion protein; PDB: 3LNN_B 4DK0_A 4DK1_C 3FPP_B 2K32_A 2K33_A 3OW7_B 3OOC_A 3T53_B 4DNT_C ....
Probab=29.41 E-value=2.5e+02 Score=22.25 Aligned_cols=73 Identities=21% Similarity=0.338 Sum_probs=46.8
Q ss_pred cCCCCcccccEEE--EC----C-CceEEEEEEeecCCCCCcEEEEEEcCCCCC-CCcEECCEEeeecCCCCeeEEecCCe
Q psy9801 16 EDTDSFIIGDRVY--VG----G-TKSGRIAFIGETKFAPGDWAGVVLDDPVGK-NDGQVGQARYFQCEPRFGLFAPVHKV 87 (132)
Q Consensus 16 ~~~~~l~vGdRV~--V~----g-~~~GtVRyiG~v~~~~g~wvGVELDep~Gk-nDGt~~G~rYF~C~p~~GiFv~~~kv 87 (132)
.....+++|+.|. +. + ...|+|.+|.+.. ..-..+=|+++++.+. ..|.+-- -++......++.||.+-|
T Consensus 205 ~~~~~i~~g~~~~v~~~~~~~~~~~~g~v~~i~~~~-~~~~~v~~~~~~~~~~l~~g~~v~-v~i~~~~~~~~~VP~~Ai 282 (328)
T PF12700_consen 205 SDASKIKVGQKVEVTIDAPDNGKSFTGKVSSISPSA-SRTFKVRVSLDNPNGNLRPGMFVE-VSIILGSENGLVVPKSAI 282 (328)
T ss_dssp CGTTTHTTTGEEEEEETTSS-SSEEEEEEEEEESSE-TTEEEEEEEEE-SSS-S-TT-EEE-EEEESEESCEEEEEGGGE
T ss_pred HHHHhccCCcEEEEEEEeecCCCceeeEEeecCCcc-ceeeEEEEEeccccchhhhccccc-ceeccccccEEEEcChhh
Confidence 3567899999954 44 2 3789999998887 2223566888888543 4555422 334444488888888888
Q ss_pred eeC
Q psy9801 88 SKS 90 (132)
Q Consensus 88 ~~~ 90 (132)
...
T Consensus 283 ~~~ 285 (328)
T PF12700_consen 283 IEE 285 (328)
T ss_dssp EET
T ss_pred ccc
Confidence 754
No 36
>PF02211 NHase_beta: Nitrile hydratase beta subunit; InterPro: IPR024690 Nitrile hydratases (EC:4.2.1.84) are unusual metalloenzymes that catalyse the hydration of nitriles to their corresponding amides. They are used as biocatalysts in acrylamide production, one of the few commercial scale bioprocesses, as well as in environmental remediation for the removal of nitriles from waste streams. Nitrile hydratases are composed of two subunits, alpha and beta, and they contain one iron atom per alpha beta unit []. This entry represents the structural domain of nitrile hydratase beta subunit which contains irregular array of helices in the N-terminal extension.; GO: 0018822 nitrile hydratase activity; PDB: 2DXB_H 2DD5_K 2DD4_H 2ZZD_B 2DXC_H 1AHJ_F 2ZPE_B 2ZCF_B 2D0Q_B 2CZ7_B ....
Probab=26.64 E-value=30 Score=28.11 Aligned_cols=22 Identities=27% Similarity=0.447 Sum_probs=11.4
Q ss_pred cceEeccCCCCcccccEEEECC
Q psy9801 10 SSQVLTEDTDSFIIGDRVYVGG 31 (132)
Q Consensus 10 ~~~~l~~~~~~l~vGdRV~V~g 31 (132)
+..+-......|++||+|.|..
T Consensus 124 p~~r~~~~~~~F~vGd~Vrv~~ 145 (222)
T PF02211_consen 124 PADRPVDAPPRFAVGDRVRVRN 145 (222)
T ss_dssp --EETTSSS-SS-TT-EEEE--
T ss_pred CccCCCCCCCCCCCCCEEEECC
Confidence 3344445688999999999973
No 37
>PF02699 YajC: Preprotein translocase subunit; InterPro: IPR003849 Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component []. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins []. The translocase protein subunits are encoded on the bacterial chromosome. The translocase itself comprises 7 proteins, including a chaperone (SecB), ATPase (SecA), an integral membrane complex (SecY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) []. Other cytoplasmic/periplasmic proteins play a part in preprotein translocase activity, namely YidC and YajC []. The latter is bound in a complex to SecD and SecF, and plays a part in stabilising and regulating secretion through the SecYEG integral membrane component via SecA []. Homologues of the YajC gene have been found in a range of pathogenic and commensal microbes. Brucella abortis YajC- and SecD-like proteins were shown to stimulate a Th1 cell-mediated immune response in mice, and conferred protection when challenged with B.abortis []. Therefore, these proteins may have an antigenic role as well as a secretory one in virulent bacteria []. A number of previously uncharacterised "hypothetical" proteins also show similarity to E.coli YajC, suggesting that this family is wider than first thought []. More recently, the precise interactions between the E.coli SecYEG complex, SecD, SecF, YajC and YidC have been studied []. Rather than acting individually, the four proteins form a heterotetrameric complex and associate with the SecYEG heterotrimeric complex []. The SecF and YajC subunits link the complex to the integral membrane translocase. ; PDB: 2RDD_B.
Probab=26.46 E-value=20 Score=24.48 Aligned_cols=23 Identities=30% Similarity=0.271 Sum_probs=1.0
Q ss_pred CCCcccccEEEECCCceEEEEEE
Q psy9801 18 TDSFIIGDRVYVGGTKSGRIAFI 40 (132)
Q Consensus 18 ~~~l~vGdRV~V~g~~~GtVRyi 40 (132)
...|++||+|...+..+|+|.-+
T Consensus 34 ~~~Lk~Gd~VvT~gGi~G~V~~i 56 (82)
T PF02699_consen 34 LASLKPGDEVVTIGGIYGTVVEI 56 (82)
T ss_dssp GG---------------------
T ss_pred HHcCCCCCEEEECCcEEEEEEEE
Confidence 45799999999988789998877
No 38
>KOG4600|consensus
Probab=26.41 E-value=1.4e+02 Score=23.07 Aligned_cols=9 Identities=56% Similarity=1.158 Sum_probs=4.3
Q ss_pred CCCCcEEEE
Q psy9801 45 FAPGDWAGV 53 (132)
Q Consensus 45 ~~~g~wvGV 53 (132)
|.+|..+||
T Consensus 72 fHPG~nVGi 80 (144)
T KOG4600|consen 72 FHPGDNVGI 80 (144)
T ss_pred cCCCccccc
Confidence 444444444
No 39
>PTZ00328 eukaryotic initiation factor 5a; Provisional
Probab=25.67 E-value=2.2e+02 Score=22.39 Aligned_cols=68 Identities=13% Similarity=0.090 Sum_probs=44.4
Q ss_pred cCCcceEeccCCCCcccccEEEECCCceEEEEEEeecCCCCC----cEEEEEEcCCCCCCCcEECCEEee-ecCCCCeeE
Q psy9801 7 AYDSSQVLTEDTDSFIIGDRVYVGGTKSGRIAFIGETKFAPG----DWAGVVLDDPVGKNDGQVGQARYF-QCEPRFGLF 81 (132)
Q Consensus 7 ~s~~~~~l~~~~~~l~vGdRV~V~g~~~GtVRyiG~v~~~~g----~wvGVELDep~GknDGt~~G~rYF-~C~p~~GiF 81 (132)
|+..+.+.+-....|+.|..|.+.|.-+=+|+..=.=+++.| ..+||.+- .|++|= .|+-.|.+.
T Consensus 14 ~~gas~t~p~q~~~LkkG~yvvIkGrPCKIveistSKtGKHGhAK~~ivaidIF----------TgkK~edi~Ps~hnv~ 83 (166)
T PTZ00328 14 GDNASKTYPLPAGALKKGGYVCINGRPCKVIDLSVSKTGKHGHAKVSIVATDIF----------TGNRLEDQAPSTHNVE 83 (166)
T ss_pred CCCCCceecccccceeECCEEEECCeeeEEEEEecCCCCcCCceEEEEEEEecC----------CCCEEeeecCccceeE
Confidence 555677777788899999999999854445554211123333 36777553 344443 378888888
Q ss_pred Eec
Q psy9801 82 APV 84 (132)
Q Consensus 82 v~~ 84 (132)
||.
T Consensus 84 VP~ 86 (166)
T PTZ00328 84 VPF 86 (166)
T ss_pred eee
Confidence 876
No 40
>cd04451 S1_IF1 S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the formation of the first peptide bond. In Escherichia coli, the initiation mechanism requires, in addition to mRNA, fMet-tRNA, and ribosomal subunits, the presence of three additional proteins (initiation factors IF1, IF2, and IF3) and at least one GTP molecule. The three initiation factors influence both the kinetics and the stability of ternary complex formation. IF1 is the smallest of the three factors. IF1 enhances the rate of 70S ribosome subunit association and dissociation and the interaction of 30S ribosomal subunit with IF2 and IF3. It stimulates 30S complex formation. In addition, by binding to the A-site of the 30S ribosomal subunit, IF1 may contribute to the fidelity of the selection of the initiation site of th
Probab=24.60 E-value=85 Score=19.87 Aligned_cols=20 Identities=40% Similarity=0.674 Sum_probs=13.0
Q ss_pred CcccccEEEEC----CCceEEEEE
Q psy9801 20 SFIIGDRVYVG----GTKSGRIAF 39 (132)
Q Consensus 20 ~l~vGdRV~V~----g~~~GtVRy 39 (132)
.+.+||+|.+. ....|.|-|
T Consensus 40 ~~~vGD~V~~~~~~~~~~~g~I~~ 63 (64)
T cd04451 40 RILPGDRVKVELSPYDLTKGRIVY 63 (64)
T ss_pred ccCCCCEEEEEEeecCCCEEEEEE
Confidence 37789999876 233565544
No 41
>COG4097 Predicted ferric reductase [Inorganic ion transport and metabolism]
Probab=24.38 E-value=44 Score=29.98 Aligned_cols=27 Identities=26% Similarity=0.609 Sum_probs=18.7
Q ss_pred CcceEeccCCCCcccccEEEECCCceEEEEE
Q psy9801 9 DSSQVLTEDTDSFIIGDRVYVGGTKSGRIAF 39 (132)
Q Consensus 9 ~~~~~l~~~~~~l~vGdRV~V~g~~~GtVRy 39 (132)
|+|..+.+ .+++|++|+|+|. +|.--|
T Consensus 285 D~Tk~l~d---nLk~G~k~~vdGP-YG~F~~ 311 (438)
T COG4097 285 DFTKTLKD---NLKVGTKLEVDGP-YGKFDF 311 (438)
T ss_pred hhhHHHHH---hccCCceEEEecC-cceeec
Confidence 55665553 3999999999985 554443
No 42
>PLN03148 Blue copper-like protein; Provisional
Probab=24.24 E-value=87 Score=24.54 Aligned_cols=14 Identities=21% Similarity=0.570 Sum_probs=10.3
Q ss_pred CCCCcccccEEEEC
Q psy9801 17 DTDSFIIGDRVYVG 30 (132)
Q Consensus 17 ~~~~l~vGdRV~V~ 30 (132)
....|++||...+.
T Consensus 42 ~~k~F~VGD~LvF~ 55 (167)
T PLN03148 42 NNQTFYVGDLISFR 55 (167)
T ss_pred cCCCCccCCEEEEE
Confidence 35679999977664
No 43
>COG4057 McrG Methyl coenzyme M reductase, gamma subunit [Coenzyme metabolism]
Probab=23.72 E-value=26 Score=28.93 Aligned_cols=45 Identities=29% Similarity=0.415 Sum_probs=30.5
Q ss_pred CcceEeccCCCCcccccEEEECCCceEEEEEEeecCCCCCcEEEEEEcCCC--CC
Q psy9801 9 DSSQVLTEDTDSFIIGDRVYVGGTKSGRIAFIGETKFAPGDWAGVVLDDPV--GK 61 (132)
Q Consensus 9 ~~~~~l~~~~~~l~vGdRV~V~g~~~GtVRyiG~v~~~~g~wvGVELDep~--Gk 61 (132)
.|++.|.++..-|..=+|-...+ ..|.|-|+ ..-+|++||+|. |+
T Consensus 160 GHslRLdEnGlMfd~L~Ry~~~e-~tG~v~yv-------KdQvg~pLDepvd~G~ 206 (257)
T COG4057 160 GHSLRLDENGLMFDALQRYRYDE-ETGHVEYV-------KDQVGRPLDEPVDVGE 206 (257)
T ss_pred cceeeecCCchhHHHHHHHhhcc-cCceEEEe-------hhhcCCccCCCCcCCC
Confidence 36677777655555555554444 57889888 345899999996 65
No 44
>PF02298 Cu_bind_like: Plastocyanin-like domain; InterPro: IPR003245 Blue (type 1) copper proteins are small proteins which bind a single copper atom and which are characterised by an intense electronic absorption band near 600 nm [, ]. The most well known members of this class of proteins are the plant chloroplastic plastocyanins, which exchange electrons with cytochrome c6, and the distantly related bacterial azurins, which exchange electrons with cytochrome c551. This family of proteins also includes amicyanin from bacteria such as Methylobacterium extorquens or Paracoccus versutus (Thiobacillus versutus) that can grow on methylamine; auracyanins A and B from Chloroflexus aurantiacus []; blue copper protein from Alcaligenes faecalis; cupredoxin (CPC) from Cucumis sativus (Cucumber) peelings []; cusacyanin (basic blue protein; plantacyanin, CBP) from cucumber; halocyanin from Natronomonas pharaonis (Natronobacterium pharaonis) [], a membrane associated copper-binding protein; pseudoazurin from Pseudomonas; rusticyanin from Thiobacillus ferrooxidans []; stellacyanin from Rhus vernicifera (Japanese lacquer tree); umecyanin from the roots of Armoracia rusticana (Horseradish); and allergen Ra3 from ragweed. Although there is an appreciable amount of divergence in the sequences of all these proteins, the copper ligand sites are conserved. This domain is found in a variety of plant cyanins and pollern allergen. Some of the proteins in this family are allergens. Allergies are hypersensitivity reactions of the immune system to specific substances called allergens (such as pollen, stings, drugs, or food) that, in most people, result in no symptoms. A nomenclature system has been established for antigens (allergens) that cause IgE-mediated atopic allergies in humans [WHO/IUIS Allergen Nomenclature Subcommittee King T.P., Hoffmann D., Loewenstein H., Marsh D.G., Platts-Mills T.A.E., Thomas W. Bull. World Health Organ. 72:797-806(1994)]. This nomenclature system is defined by a designation that is composed of the first three letters of the genus; a space; the first letter of the species name; a space and an arabic number. In the event that two species names have identical designations, they are discriminated from one another by adding one or more letters (as necessary) to each species designation. The allergens in this family include allergens with the following designations: Amb a 3.; GO: 0005507 copper ion binding, 0009055 electron carrier activity; PDB: 1JER_A 1WS7_A 1WS8_D 1F56_B 1X9R_B 1X9U_A 2CBP_A.
Probab=23.63 E-value=43 Score=22.83 Aligned_cols=14 Identities=21% Similarity=0.510 Sum_probs=9.4
Q ss_pred CCCCcccccEEEEC
Q psy9801 17 DTDSFIIGDRVYVG 30 (132)
Q Consensus 17 ~~~~l~vGdRV~V~ 30 (132)
+...|.+||-+.+.
T Consensus 15 ~~~~F~vGD~LvF~ 28 (85)
T PF02298_consen 15 SGKTFRVGDTLVFN 28 (85)
T ss_dssp CTS-BETTEEEEEE
T ss_pred cCCcEeCCCEEEEE
Confidence 35578999987664
No 45
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=23.17 E-value=90 Score=20.54 Aligned_cols=19 Identities=37% Similarity=0.690 Sum_probs=12.5
Q ss_pred cccccEEEEC----CCceEEEEE
Q psy9801 21 FIIGDRVYVG----GTKSGRIAF 39 (132)
Q Consensus 21 l~vGdRV~V~----g~~~GtVRy 39 (132)
+.+||+|.+. ....|.|-|
T Consensus 47 i~vGD~V~ve~~~~~~~~g~Iv~ 69 (72)
T PRK00276 47 ILPGDKVTVELSPYDLTKGRITY 69 (72)
T ss_pred cCCCCEEEEEEcccCCCeEEEEE
Confidence 6788888876 234566655
No 46
>COG5466 Predicted small metal-binding protein [Function unknown]
Probab=22.97 E-value=72 Score=21.18 Aligned_cols=19 Identities=21% Similarity=0.336 Sum_probs=14.9
Q ss_pred CEEeeecC---CCCeeEEecCC
Q psy9801 68 QARYFQCE---PRFGLFAPVHK 86 (132)
Q Consensus 68 G~rYF~C~---p~~GiFv~~~k 86 (132)
+.+||.|. ++||.-++.+.
T Consensus 2 ~m~~f~C~slg~~C~f~~~a~~ 23 (59)
T COG5466 2 AMYLFKCGSLGMGCGFEARADS 23 (59)
T ss_pred CceEEEccccCCCCcceeccCc
Confidence 67899996 89988777543
No 47
>PF15290 Syntaphilin: Golgi-localised syntaxin-1-binding clamp
Probab=22.79 E-value=37 Score=29.11 Aligned_cols=13 Identities=31% Similarity=0.797 Sum_probs=11.3
Q ss_pred EEeeecCCCCeeE
Q psy9801 69 ARYFQCEPRFGLF 81 (132)
Q Consensus 69 ~rYF~C~p~~GiF 81 (132)
.||-.|.+||||=
T Consensus 40 ~rY~~C~dNHGik 52 (305)
T PF15290_consen 40 GRYMSCGDNHGIK 52 (305)
T ss_pred CceeecccCCCCC
Confidence 6899999999973
No 48
>CHL00010 infA translation initiation factor 1
Probab=22.77 E-value=93 Score=20.99 Aligned_cols=21 Identities=38% Similarity=0.589 Sum_probs=13.9
Q ss_pred CcccccEEEEC----CCceEEEEEE
Q psy9801 20 SFIIGDRVYVG----GTKSGRIAFI 40 (132)
Q Consensus 20 ~l~vGdRV~V~----g~~~GtVRyi 40 (132)
.+.+||+|.|. ....|.|-|-
T Consensus 46 ~~~vGD~V~ve~~~~~~~~g~Ii~r 70 (78)
T CHL00010 46 RILPGDRVKVELSPYDLTKGRIIYR 70 (78)
T ss_pred ccCCCCEEEEEEcccCCCeEEEEEE
Confidence 35689999886 2345776654
No 49
>COG0668 MscS Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]
Probab=22.66 E-value=1.1e+02 Score=24.12 Aligned_cols=27 Identities=26% Similarity=0.474 Sum_probs=21.1
Q ss_pred CCCcccccEEEECCCceEEEEEEeecC
Q psy9801 18 TDSFIIGDRVYVGGTKSGRIAFIGETK 44 (132)
Q Consensus 18 ~~~l~vGdRV~V~g~~~GtVRyiG~v~ 44 (132)
...+++||+|++.+...|+|.-++-..
T Consensus 145 ~~~f~vGD~I~i~~~~~G~V~~i~~~~ 171 (316)
T COG0668 145 ERPFKVGDWIEIGSGVEGTVEDIGLRS 171 (316)
T ss_pred ecCcCcCCEEEECCCceEEEEEEEEEE
Confidence 457999999999833688888887653
No 50
>PRK11281 hypothetical protein; Provisional
Probab=22.06 E-value=97 Score=30.94 Aligned_cols=25 Identities=32% Similarity=0.391 Sum_probs=21.2
Q ss_pred CCCcccccEEEECCCceEEEEEEeec
Q psy9801 18 TDSFIIGDRVYVGGTKSGRIAFIGET 43 (132)
Q Consensus 18 ~~~l~vGdRV~V~g~~~GtVRyiG~v 43 (132)
...++|||+|.|.+ ..|+|.-||-.
T Consensus 936 eRPfrIGD~I~I~~-~~G~V~~I~lR 960 (1113)
T PRK11281 936 ERPVRIGDTVTIGT-FSGTVSKIRIR 960 (1113)
T ss_pred cCCcCCCCEEEECC-EEEEEEEEEeE
Confidence 45799999999977 69999998765
No 51
>COG4841 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.53 E-value=2.7e+02 Score=20.07 Aligned_cols=52 Identities=17% Similarity=0.185 Sum_probs=36.7
Q ss_pred CCCcccccEEEECCCceEEEEEEeecCCCCCcEEEEEEcCCCCC-CCcEECCEEeeecC
Q psy9801 18 TDSFIIGDRVYVGGTKSGRIAFIGETKFAPGDWAGVVLDDPVGK-NDGQVGQARYFQCE 75 (132)
Q Consensus 18 ~~~l~vGdRV~V~g~~~GtVRyiG~v~~~~g~wvGVELDep~Gk-nDGt~~G~rYF~C~ 75 (132)
.-+|+-|+.|++ .|||=|.-...+|.-+||.-+.|.-. ---.++|.-+|--.
T Consensus 16 E~~l~~g~~vrf------fvRyGG~~~~~~GFS~gv~~e~PkE~g~~q~~Dgltffiee 68 (95)
T COG4841 16 ELDLEEGNKVRF------FVRYGGCSSLQQGFSLGVAKEVPKEIGYKQEYDGLTFFIEE 68 (95)
T ss_pred hcCCCCCCEEEE------EEEEcCcccccCCcceeeeccCchhhchheeecCeEEEEec
Confidence 345667777764 68999987788899999999987621 22356677777554
No 52
>PF14001 YdfZ: YdfZ protein
Probab=21.12 E-value=1.1e+02 Score=20.64 Aligned_cols=23 Identities=30% Similarity=0.551 Sum_probs=18.6
Q ss_pred CCCcccccEEEECC-CceEEEEEE
Q psy9801 18 TDSFIIGDRVYVGG-TKSGRIAFI 40 (132)
Q Consensus 18 ~~~l~vGdRV~V~g-~~~GtVRyi 40 (132)
-..|..|+||.+.+ ...|+|+-|
T Consensus 7 RN~i~~G~rVMiagtG~~gvikAi 30 (64)
T PF14001_consen 7 RNAITTGSRVMIAGTGATGVIKAI 30 (64)
T ss_pred cCcCCCCCEEEEcCCCcccEEeee
Confidence 44688999999986 468888877
No 53
>smart00449 SPRY Domain in SPla and the RYanodine Receptor. Domain of unknown function. Distant homologues are domains in butyrophilin/marenostrin/pyrin homologues.
Probab=21.09 E-value=1.4e+02 Score=20.17 Aligned_cols=29 Identities=31% Similarity=0.578 Sum_probs=18.8
Q ss_pred CCcEEEEEEcCCCCC----CCcEEC-CEEeeecC
Q psy9801 47 PGDWAGVVLDDPVGK----NDGQVG-QARYFQCE 75 (132)
Q Consensus 47 ~g~wvGVELDep~Gk----nDGt~~-G~rYF~C~ 75 (132)
.+..+||-||-..|. .+|... +..++.+.
T Consensus 65 ~gd~iGv~lD~~~g~l~F~~ng~~~~~~~f~~~~ 98 (122)
T smart00449 65 PGDVIGCFLDLEAGTISFYKNGKYLHGLAFFDVK 98 (122)
T ss_pred CCCEEEEEEECCCCEEEEEECCCEeeeEEEeccC
Confidence 388999999988764 455554 44444443
No 54
>PRK11465 putative mechanosensitive channel protein; Provisional
Probab=21.04 E-value=1.1e+02 Score=29.33 Aligned_cols=25 Identities=20% Similarity=0.336 Sum_probs=20.9
Q ss_pred CCCcccccEEEECCCceEEEEEEeec
Q psy9801 18 TDSFIIGDRVYVGGTKSGRIAFIGET 43 (132)
Q Consensus 18 ~~~l~vGdRV~V~g~~~GtVRyiG~v 43 (132)
...+++||.|++.+ ..|+|.-||--
T Consensus 571 e~pf~vGD~I~v~g-~~GtVe~I~lR 595 (741)
T PRK11465 571 ENGMNTGDLVTIGP-LTGTVERMSIR 595 (741)
T ss_pred cCCcCCCCEEEECC-eEEEEEEEeee
Confidence 45799999999987 68999988744
No 55
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=21.03 E-value=1.1e+02 Score=21.14 Aligned_cols=22 Identities=36% Similarity=0.400 Sum_probs=16.3
Q ss_pred CCcccccEEEEC-C---CceEEEEEE
Q psy9801 19 DSFIIGDRVYVG-G---TKSGRIAFI 40 (132)
Q Consensus 19 ~~l~vGdRV~V~-g---~~~GtVRyi 40 (132)
..+..||+|.|. | ...|+|..+
T Consensus 7 ~~I~~GD~V~Vi~G~dKGK~G~V~~V 32 (83)
T CHL00141 7 MHVKIGDTVKIISGSDKGKIGEVLKI 32 (83)
T ss_pred CcccCCCEEEEeEcCCCCcEEEEEEE
Confidence 368999999986 3 256777766
No 56
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=20.98 E-value=1.2e+02 Score=20.67 Aligned_cols=22 Identities=32% Similarity=0.365 Sum_probs=16.6
Q ss_pred CCcccccEEEEC-C---CceEEEEEE
Q psy9801 19 DSFIIGDRVYVG-G---TKSGRIAFI 40 (132)
Q Consensus 19 ~~l~vGdRV~V~-g---~~~GtVRyi 40 (132)
..+..||+|.|. | ...|+|..+
T Consensus 5 ~~I~kGD~V~Vi~G~dKGK~G~V~~V 30 (76)
T PRK12281 5 LKVKKGDMVKVIAGDDKGKTGKVLAV 30 (76)
T ss_pred ccccCCCEEEEeEcCCCCcEEEEEEE
Confidence 468999999986 3 256777777
No 57
>PF02559 CarD_CdnL_TRCF: CarD-like/TRCF domain; InterPro: IPR003711 The bacterium Myxococcus xanthus responds to blue light by producing carotenoids. It also responds to starvation conditions by developing fruiting bodies, where the cells differentiate into myxospores. Each response entails the transcriptional activation of a separate set of genes. A single gene, carD, is required for the activation of both light- and starvation-inducible genes []. The predicted protein contains four repeats of a DNA-binding domain present in mammalian high mobility group I(Y) proteins and other nuclear proteins from animals and plants. Other peptide stretches on CarD also resemble functional domains typical of eukaryotic transcription factors, including a very acidic region and a leucine zipper. High mobility group yI(Y) proteins are known to bind the minor groove of A+T-rich DNA [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3MLQ_H 2EYQ_A.
Probab=20.61 E-value=1.6e+02 Score=19.94 Aligned_cols=51 Identities=33% Similarity=0.495 Sum_probs=29.3
Q ss_pred cccccEEEECCCceEEEEEEeecCCCCCcEEEEEEcCCCCCCCcEECCEEeeecC--CCCeeEEecCCeeeC
Q psy9801 21 FIIGDRVYVGGTKSGRIAFIGETKFAPGDWAGVVLDDPVGKNDGQVGQARYFQCE--PRFGLFAPVHKVSKS 90 (132)
Q Consensus 21 l~vGdRV~V~g~~~GtVRyiG~v~~~~g~wvGVELDep~GknDGt~~G~rYF~C~--p~~GiFv~~~kv~~~ 90 (132)
|++||.|.......|.|.=|....+ .|.- +.|+.-. .+.-+|||.+++..+
T Consensus 2 f~~GD~VVh~~~Gv~~i~~i~~~~~-----------------~~~~--~~yy~L~~~~~~~i~vPv~~~~~i 54 (98)
T PF02559_consen 2 FKIGDYVVHPNHGVGRIEGIEEIEF-----------------GGEK--QEYYVLEYADDDTIYVPVDNADKI 54 (98)
T ss_dssp --TTSEEEETTTEEEEEEEEEEEEC-----------------TTEE--EEEEEEEECCCEEEEEECCCGGGE
T ss_pred CCCCCEEEECCCceEEEEEEEEEee-----------------CCee--EEEEEEEECCCCEEEEEcCChhhc
Confidence 7899999998744555544444322 1222 4566543 333699999986554
No 58
>PRK10929 putative mechanosensitive channel protein; Provisional
Probab=20.46 E-value=1.1e+02 Score=30.68 Aligned_cols=25 Identities=24% Similarity=0.381 Sum_probs=21.0
Q ss_pred CCCcccccEEEECCCceEEEEEEeec
Q psy9801 18 TDSFIIGDRVYVGGTKSGRIAFIGET 43 (132)
Q Consensus 18 ~~~l~vGdRV~V~g~~~GtVRyiG~v 43 (132)
...++|||.|.+.+ ..|+|.-||-.
T Consensus 933 erPfrVGD~I~I~~-~~GtV~~I~lR 957 (1109)
T PRK10929 933 EKPIRIGDTVTIRD-LTGSVTKINTR 957 (1109)
T ss_pred hCCCCCCCEEEECC-EEEEEEEEeee
Confidence 35799999999987 68999988864
No 59
>PF04945 YHS: YHS domain; InterPro: IPR007029 This short presumed domain is about 50 amino acid residues long. It often contains two cysteines that may be functionally important. This domain is found in copper transporting ATPases, some phenol hydroxylases and in a set of uncharacterised membrane proteins including Q9CNI0 from SWISSPROT. This domain is named after three of the most conserved amino acids it contains. The domain may be metal binding, possibly copper ions. This domain is duplicated in some copper transporting ATPases.; PDB: 3U52_B 2INN_A 2INP_B 1T0Q_A 2RDB_A 1T0R_A 2IND_A 1T0S_A 2INC_A 3DHI_A ....
Probab=20.34 E-value=40 Score=20.23 Aligned_cols=14 Identities=14% Similarity=0.392 Sum_probs=10.9
Q ss_pred cEECCEEeeecCCC
Q psy9801 64 GQVGQARYFQCEPR 77 (132)
Q Consensus 64 Gt~~G~rYF~C~p~ 77 (132)
-.++|+.|+-|.+.
T Consensus 18 ~~y~G~~Y~FCS~~ 31 (47)
T PF04945_consen 18 VEYNGRTYYFCSEG 31 (47)
T ss_dssp EEETTEEEEESSHH
T ss_pred EEECCEEEEEcCHH
Confidence 46899999999643
Done!