Query 030115
Match_columns 183
No_of_seqs 138 out of 585
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 08:45:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030115.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030115hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3225 Mitochondrial import i 100.0 3.9E-32 8.5E-37 215.4 4.6 148 17-181 17-166 (168)
2 TIGR00980 3a0801so1tim17 mitoc 99.9 5.4E-26 1.2E-30 183.8 13.2 124 38-179 5-128 (170)
3 PTZ00236 mitochondrial import 99.9 1.6E-24 3.5E-29 174.2 12.6 114 38-169 7-124 (164)
4 PF02466 Tim17: Tim17/Tim22/Ti 99.9 7.9E-24 1.7E-28 161.9 13.8 127 41-181 1-127 (128)
5 TIGR00983 3a0801s02tim23 mitoc 99.9 4.2E-22 9E-27 158.4 11.6 114 47-174 35-148 (149)
6 KOG1652 Mitochondrial import i 99.8 1.4E-21 3.1E-26 158.0 1.4 125 38-180 5-129 (183)
7 COG5596 TIM22 Mitochondrial im 99.7 4.8E-19 1E-23 144.1 -0.7 158 14-181 14-189 (191)
8 KOG3324 Mitochondrial import i 99.5 1.4E-14 2.9E-19 119.1 7.0 116 45-174 75-191 (206)
9 COG5596 TIM22 Mitochondrial im 97.7 2.3E-06 5.1E-11 70.2 -2.7 75 101-177 77-161 (191)
10 KOG4608 Uncharacterized conser 97.2 4.5E-05 9.7E-10 65.1 -1.9 54 98-151 127-180 (270)
11 TIGR00980 3a0801so1tim17 mitoc 90.9 3.6 7.7E-05 33.6 10.0 121 43-181 13-134 (170)
12 PTZ00236 mitochondrial import 90.3 4.1 8.9E-05 33.1 9.8 30 44-73 16-45 (164)
13 KOG1398 Uncharacterized conser 88.4 0.63 1.4E-05 42.8 4.1 49 100-148 297-345 (460)
14 PF10247 Romo1: Reactive mitoc 86.3 1.3 2.8E-05 31.0 3.8 66 41-121 2-67 (67)
15 KOG4096 Uncharacterized conser 84.9 0.84 1.8E-05 32.4 2.4 68 40-122 5-72 (75)
16 TIGR00983 3a0801s02tim23 mitoc 82.6 6.8 0.00015 31.2 7.1 119 34-168 28-146 (149)
17 KOG3225 Mitochondrial import i 57.2 5.1 0.00011 32.6 1.0 37 38-74 34-70 (168)
18 PF04418 DUF543: Domain of unk 52.5 20 0.00044 25.4 3.3 24 41-64 24-47 (75)
19 PF10439 Bacteriocin_IIc: Bact 47.6 68 0.0015 21.7 5.2 22 130-151 23-44 (65)
20 PF05957 DUF883: Bacterial pro 43.2 63 0.0014 23.1 4.8 15 50-64 77-91 (94)
21 PF12597 DUF3767: Protein of u 43.0 49 0.0011 25.3 4.4 51 125-175 33-83 (118)
22 COG4575 ElaB Uncharacterized c 42.3 1.1E+02 0.0023 23.2 6.0 32 6-37 25-57 (104)
23 PF02466 Tim17: Tim17/Tim22/Ti 41.5 1.4E+02 0.0031 22.0 7.1 114 46-173 10-123 (128)
24 COG5336 Uncharacterized protei 36.4 1.6E+02 0.0035 22.6 6.2 27 43-69 45-71 (116)
25 PTZ00478 Sec superfamily; Prov 30.1 1.9E+02 0.0042 20.9 5.4 63 6-68 7-70 (81)
26 KOG1398 Uncharacterized conser 29.3 90 0.002 29.1 4.4 43 105-147 81-123 (460)
27 COG4803 Predicted membrane pro 29.1 64 0.0014 26.2 3.1 56 12-68 11-76 (170)
28 PF05957 DUF883: Bacterial pro 27.0 2.3E+02 0.005 20.0 6.0 17 44-60 74-91 (94)
29 PF13940 Ldr_toxin: Toxin Ldr, 26.5 53 0.0011 20.0 1.7 21 129-149 11-31 (35)
30 KOG0682 Ammonia permease [Inor 24.7 3.6E+02 0.0077 25.8 7.6 63 117-181 272-334 (500)
31 PF14689 SPOB_a: Sensor_kinase 24.3 58 0.0013 21.7 1.8 24 118-141 8-34 (62)
32 PRK09400 secE preprotein trans 22.6 1.6E+02 0.0035 19.9 3.7 24 45-68 34-57 (61)
33 PF07080 DUF1348: Protein of u 22.2 39 0.00085 26.9 0.7 18 119-136 9-26 (143)
34 COG3558 Uncharacterized protei 22.1 45 0.00097 26.3 1.0 18 119-136 11-28 (154)
35 PF05818 TraT: Enterobacterial 21.2 81 0.0018 26.8 2.4 19 160-178 109-128 (215)
No 1
>KOG3225 consensus Mitochondrial import inner membrane translocase, subunit TIM22 [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.97 E-value=3.9e-32 Score=215.42 Aligned_cols=148 Identities=21% Similarity=0.233 Sum_probs=120.6
Q ss_pred hhhhHHHHHHHHhHHHHHHHH-hhCCChHHHHHHHHHHHHHHHHHHHHHHhhhcccCCCCCCCCCC-CCcchhhhhhhhh
Q 030115 17 KAIKDVQFKLKELENGYKSWL-AKQPLPVEAAIVTATTAINGAAIGAFLGVMTQDLTSSLPTPPPQ-SSLNPDAVAPFQQ 94 (183)
Q Consensus 17 ~~~~~~q~~~~~~~~~~k~~~-~~~~~~~e~~~~t~~g~~~G~~~G~f~g~v~~~~~~~~~~~~~~-~~~~~~~~~~~~~ 94 (183)
+++..+.|. |+-+.+.-+.+ -+++|++|++.++|+|+.+|+++|+|+++++..-.+ |+.. .++++|+ ++
T Consensus 17 ~~~~~l~pe-~~~~~~e~r~le~~n~c~~Ka~~sgV~GfglG~~~GlFlas~d~~~~d----P~i~~~~ar~q~---~k- 87 (168)
T KOG3225|consen 17 KQYSLLTPE-EVGDPTEMRYLEEENSCAVKAVKSGVTGFGLGGAFGLFLASLDTQPND----PTIYRMPARKQV---AK- 87 (168)
T ss_pred ccccccCcc-ccCChHHHHHHHHhcchhHHHHHhhccccchhhhHHhhhhhcccCCCC----CchhhhhhHHHH---HH-
Confidence 344444443 33333333444 678999999999999999999999999999965221 1111 2335555 45
Q ss_pred hHHhhcCchhhhhHHHHHHHHHHHHHHHHHHHhhccchhhHHHHHHHHhhhhhhccCCCCCCchHHHHHHHHHHHHHHHH
Q 030115 95 VQAVAGGPLVQARNFAVITGVNAGISCVMKRLRGKEDLQSSVVAAFGSGAAFSLVSGMGGANPAVNAFTSGLLFAIFQGC 174 (183)
Q Consensus 95 ~~~~~~~~~~~~~~fa~~g~~ysg~ec~~~~~Rgk~D~~N~~~aG~~tGa~l~~~~G~~~~~~~~~a~~gga~fa~fs~~ 174 (183)
+|+.+++++++||+++|++|+++||++|++|.|+||+|++++||+||+.++.+.| |++++.+|++|++||++
T Consensus 88 --dMg~r~~s~~knF~~iGlvfsg~Ec~iE~~RAK~D~~NgaiaG~vtGg~l~~raG------p~a~~~G~agfa~fS~~ 159 (168)
T KOG3225|consen 88 --DMGQRSGSYAKNFAIIGLVFSGVECLIESFRAKSDWYNGAIAGCVTGGSLGYRAG------PKAAAIGCAGFAAFSAA 159 (168)
T ss_pred --HHHhhhcchhhhhhhhhhhehhHHHHHHHHHhhhchhcceeeeeeeccchhhccc------chhhhhchhHHHHHHHH
Confidence 6999999999999999999999999999999999999999999999999999999 99999999999999999
Q ss_pred HHhhhcc
Q 030115 175 SFKNKRH 181 (183)
Q Consensus 175 ~~~~g~~ 181 (183)
|+|+=++
T Consensus 160 id~y~~~ 166 (168)
T KOG3225|consen 160 IDKYMRG 166 (168)
T ss_pred HHHhhhc
Confidence 9887543
No 2
>TIGR00980 3a0801so1tim17 mitochondrial import inner membrane translocase subunit tim17.
Probab=99.94 E-value=5.4e-26 Score=183.83 Aligned_cols=124 Identities=23% Similarity=0.261 Sum_probs=111.2
Q ss_pred hhCCChHHHHHHHHHHHHHHHHHHHHHHhhhcccCCCCCCCCCCCCcchhhhhhhhhhHHhhcCchhhhhHHHHHHHHHH
Q 030115 38 AKQPLPVEAAIVTATTAINGAAIGAFLGVMTQDLTSSLPTPPPQSSLNPDAVAPFQQVQAVAGGPLVQARNFAVITGVNA 117 (183)
Q Consensus 38 ~~~~~~~e~~~~t~~g~~~G~~~G~f~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fa~~g~~ys 117 (183)
..+||+++...+++.++.+|.++|.+++++++..+. | ..++++..++ +++.+.++++++||++|++|+
T Consensus 5 ~r~pcp~r~~d~~G~af~~G~~~G~~~g~~~G~rns-----p----~g~rl~g~l~---av~~rap~~g~~Fav~g~lys 72 (170)
T TIGR00980 5 TREPCPYRILDDFGGAFAMGTIGGSIFQAFKGFRNS-----P----KGEKLVGAMR---AIKTRAPVLGGNFAVWGGLFS 72 (170)
T ss_pred ccCCCcchhHHhhhHHHHHHHHHHHHHHHHHHhhcC-----C----ccchhhHHHH---HHHhhhhhHHHHHHHHHHHHH
Confidence 378999999999999999999999999999964322 1 1345667776 578888999999999999999
Q ss_pred HHHHHHHHHhhccchhhHHHHHHHHhhhhhhccCCCCCCchHHHHHHHHHHHHHHHHHHhhh
Q 030115 118 GISCVMKRLRGKEDLQSSVVAAFGSGAAFSLVSGMGGANPAVNAFTSGLLFAIFQGCSFKNK 179 (183)
Q Consensus 118 g~ec~~~~~Rgk~D~~N~~~aG~~tGa~l~~~~G~~~~~~~~~a~~gga~fa~fs~~~~~~g 179 (183)
++||+++++|+|||+||+++|||+||++|++++| +++++.+|+.+++|.++|+..|
T Consensus 73 ~~ec~i~~~R~KeD~~NsiiAG~~TGa~l~~r~G------~~a~~~~aa~gg~~la~ie~~g 128 (170)
T TIGR00980 73 TIDCAVVAIRKKEDPWNSIISGFLTGAALAVRGG------PRAMRGSAILGACILAVIEGVG 128 (170)
T ss_pred HHHHHHHHHhcccchHHHHHHHHHHHHHHHhccC------hHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999 9999999999999999998765
No 3
>PTZ00236 mitochondrial import inner membrane translocase subunit tim17; Provisional
Probab=99.92 E-value=1.6e-24 Score=174.21 Aligned_cols=114 Identities=21% Similarity=0.320 Sum_probs=96.4
Q ss_pred hhCCChHHHHHHHHHHHHHHHHHHHHHHhhhcccCCCCCCCCCCCCcchhhhhhhhhhHHhhcCchhhhhHHHHHHHHHH
Q 030115 38 AKQPLPVEAAIVTATTAINGAAIGAFLGVMTQDLTSSLPTPPPQSSLNPDAVAPFQQVQAVAGGPLVQARNFAVITGVNA 117 (183)
Q Consensus 38 ~~~~~~~e~~~~t~~g~~~G~~~G~f~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fa~~g~~ys 117 (183)
..|||+.++..++..++.+|.+.|.++..+.+..+. |. .+++...++ +++.+.++++++||++|++|+
T Consensus 7 ~r~pcp~ri~dd~G~af~~G~vgG~~~~~~~G~rns-----p~----g~rl~g~l~---~~~~rap~~g~~FAv~G~~ys 74 (164)
T PTZ00236 7 SREPCPDRIIEDMGGAFSMGCIGGFIWHFLKGMRNS-----PK----GERFSGGFY---LLRKRAPILGGNFAIWGGLFS 74 (164)
T ss_pred CcCCCchHHHHhccHHHHHHHHHHHHHHHHHHHHhC-----CC----cchHHHHHH---HHHhhhhhHHHHHHHHHHHHH
Confidence 589999999999999999999999998888874322 11 445666666 577889999999999999999
Q ss_pred HHHHHHHHHhhccchhhHHHHHHHHhhhhhhccCCCCCCchHH----HHHHHHHHH
Q 030115 118 GISCVMKRLRGKEDLQSSVVAAFGSGAAFSLVSGMGGANPAVN----AFTSGLLFA 169 (183)
Q Consensus 118 g~ec~~~~~Rgk~D~~N~~~aG~~tGa~l~~~~G~~~~~~~~~----a~~gga~fa 169 (183)
++||+++++|+|||+||+++|||+||++|++++| +++ ++.+|++++
T Consensus 75 ~~ec~~~~~R~K~D~~Nsi~AG~~TGa~l~~r~G------~~~~~~~a~~Gg~~~~ 124 (164)
T PTZ00236 75 TFDCTLQYLRGKEDHWNAIASGFFTGGVLAIRGG------WRSAVRNAIFGGILLG 124 (164)
T ss_pred HHHHHHHHHHccCchHHHHHHHHHHHHHHHHhcC------hHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999 774 455555533
No 4
>PF02466 Tim17: Tim17/Tim22/Tim23/Pmp24 family; InterPro: IPR003397 The membrane-embedded multi-protein complexes of mitochondria mediate the transport of nuclear-encoded proteins across and into the outer or inner mitochondrial membranes []. The TOM (translocase of the outer mitochondrial membrane) complex consists of cytosol-exposed receptors and a pore-forming core, and mediates the transport of proteins from the cytosol across and into the outer mitochondrial membrane. A novel protein complex in the outer membrane of mitochondria, called the SAM complex (sorting and assembly machinery), is involved in the biogenesis of beta-barrel proteins of the outer membrane. Two translocases of the inner mitochondrial membrane (TIM22 and TIM23 complexes) mediate protein transport at the inner membrane. The TIM23 complex (a presequence translocase) mediates the transport of presequence-containing proteins across and into the inner membrane. Tim23 and Tim17 form part of this complex. Tim23 forms a pore in the inner membrane. The role of Tim17 is not yet fully understood. The TIM22 complex (a twin-pore carrier translocase) catalyses the insertion of multi-spanning proteins that have internal targeting signals into the inner membrane. The TIM22 complex mediates the membrane insertion of multi-spanning inner-membrane proteins that have internal targeting signals, and it uses the membrane potential as an external driving force. The Tim22 subunit of the mitochondrial import inner membrane translocase is included in this family. This family also includes Pmp24, a peroxisomal membrane protein, and NADH ubiquinone dehydrogenase 1 alpha subunit 11. Pmp24 was previously known as Pmp27 [].
Probab=99.91 E-value=7.9e-24 Score=161.91 Aligned_cols=127 Identities=28% Similarity=0.386 Sum_probs=112.3
Q ss_pred CChHHHHHHHHHHHHHHHHHHHHHHhhhcccCCCCCCCCCCCCcchhhhhhhhhhHHhhcCchhhhhHHHHHHHHHHHHH
Q 030115 41 PLPVEAAIVTATTAINGAAIGAFLGVMTQDLTSSLPTPPPQSSLNPDAVAPFQQVQAVAGGPLVQARNFAVITGVNAGIS 120 (183)
Q Consensus 41 ~~~~e~~~~t~~g~~~G~~~G~f~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fa~~g~~ysg~e 120 (183)
||+-+.+.+++.+++.|.++|.+.++++..... +...+.+++++..++ .++++...++.+||.++++|+++|
T Consensus 1 ~c~~~~~~~~~~g~~~G~~~G~~~~~~~~~~~~-----~~~~~~~~~~~~~~~---~~~~~~~~~~~~~g~~~~~y~~~~ 72 (128)
T PF02466_consen 1 SCPERILDSTGKGFVAGAVFGGFIGAISAFTRP-----PRGSPLRPRLRSILN---AVGRRGPRHGARFGSFGGLYSGIE 72 (128)
T ss_pred CccHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc-----ccCCcHhHHHHHHHH---HHhccchHHHHHHHHHHHHHHHHH
Confidence 799999999999999999999999999652111 111233667888887 477788889999999999999999
Q ss_pred HHHHHHhhccchhhHHHHHHHHhhhhhhccCCCCCCchHHHHHHHHHHHHHHHHHHhhhcc
Q 030115 121 CVMKRLRGKEDLQSSVVAAFGSGAAFSLVSGMGGANPAVNAFTSGLLFAIFQGCSFKNKRH 181 (183)
Q Consensus 121 c~~~~~Rgk~D~~N~~~aG~~tGa~l~~~~G~~~~~~~~~a~~gga~fa~fs~~~~~~g~~ 181 (183)
|.++++|+|||+||++++|++||++++++.+ ++.++.+++++++++.+++.++||
T Consensus 73 ~~l~~~R~k~D~~N~~~aG~~aGa~~~~~~g------~~~~~~~~~~~a~~~~~~~~~~~~ 127 (128)
T PF02466_consen 73 CALERLRGKDDPWNSAIAGAAAGAVLGLRSG------PRGMASGAALGAAFAAAVEYYGRM 127 (128)
T ss_pred HHHHHhhcccccchhHHHHHHHHHHHHhccC------hHHHHHHHHHHHHHHHHHHHHhcc
Confidence 9999999999999999999999999999999 999999999999999999999987
No 5
>TIGR00983 3a0801s02tim23 mitochondrial import inner membrane translocase subunit tim23.
Probab=99.88 E-value=4.2e-22 Score=158.36 Aligned_cols=114 Identities=24% Similarity=0.217 Sum_probs=94.2
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhcccCCCCCCCCCCCCcchhhhhhhhhhHHhhcCchhhhhHHHHHHHHHHHHHHHHHHH
Q 030115 47 AIVTATTAINGAAIGAFLGVMTQDLTSSLPTPPPQSSLNPDAVAPFQQVQAVAGGPLVQARNFAVITGVNAGISCVMKRL 126 (183)
Q Consensus 47 ~~~t~~g~~~G~~~G~f~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fa~~g~~ysg~ec~~~~~ 126 (183)
+..+..++++|.++|.+++.+++....+ + ..+.++++...++ +++++.++++++||+++.+|+++||.++++
T Consensus 35 ~~~~G~ay~~G~~~Gg~~Gl~~G~~~~~----~-~~~~k~rln~~ln---~~~~~g~~~G~~~g~~g~lys~~e~~i~~~ 106 (149)
T TIGR00983 35 CFGTGTCYLTGLAIGALNGLRLGLKETQ----S-MPWTKLRLNQILN---MVTRRGPFWGNTLGILALVYNGINSIIEAT 106 (149)
T ss_pred hhhHhHHHHHHHHHHHHHHHHHHHhhCC----C-CCcHHHHHHHHHH---HHHhHhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3477777777777777777777654321 1 1123678888887 578899999999999999999999999999
Q ss_pred hhccchhhHHHHHHHHhhhhhhccCCCCCCchHHHHHHHHHHHHHHHH
Q 030115 127 RGKEDLQSSVVAAFGSGAAFSLVSGMGGANPAVNAFTSGLLFAIFQGC 174 (183)
Q Consensus 127 Rgk~D~~N~~~aG~~tGa~l~~~~G~~~~~~~~~a~~gga~fa~fs~~ 174 (183)
|+|||+||+++||++||++|+.++| +++++.+|+.-+++.++
T Consensus 107 R~k~D~~Nsv~AGa~TGal~~~~~G------~r~~~~g~~~G~~l~~~ 148 (149)
T TIGR00983 107 RGKHDDFNSVAAGALTGALYKSTRG------LRGMARSGALGATAAGV 148 (149)
T ss_pred hccchhhHhHHHHHHHHHHHHhccC------hHHHHHHhHHHHHHhhc
Confidence 9999999999999999999999999 99999998887776553
No 6
>KOG1652 consensus Mitochondrial import inner membrane translocase, subunit TIM17 [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.82 E-value=1.4e-21 Score=158.04 Aligned_cols=125 Identities=18% Similarity=0.231 Sum_probs=104.8
Q ss_pred hhCCChHHHHHHHHHHHHHHHHHHHHHHhhhcccCCCCCCCCCCCCcchhhhhhhhhhHHhhcCchhhhhHHHHHHHHHH
Q 030115 38 AKQPLPVEAAIVTATTAINGAAIGAFLGVMTQDLTSSLPTPPPQSSLNPDAVAPFQQVQAVAGGPLVQARNFAVITGVNA 117 (183)
Q Consensus 38 ~~~~~~~e~~~~t~~g~~~G~~~G~f~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fa~~g~~ys 117 (183)
..+||+.+.+..+...+.||.+-|..+..+..-.+. |. .......++ ..+.+.+.++++||+||++||
T Consensus 5 sr~pcp~riv~d~g~afamg~igG~~f~~ikG~~na-----p~----G~r~~gg~~---av~~~ap~~ggsFAvwgglfS 72 (183)
T KOG1652|consen 5 SREPCPIRIVDDCGGAFAMGTIGGSVFQLIKGFRNA-----PS----GARLVGGIS---AVKMRAPQSGGSFAVWGGLFS 72 (183)
T ss_pred cCCCCCceeeccccchhhhcccccceeeeeeeeecC-----Cc----ccccccchh---hhhccCcccccceeeeechhh
Confidence 468999999999999999999999988888874332 21 112233332 345677889999999999999
Q ss_pred HHHHHHHHHhhccchhhHHHHHHHHhhhhhhccCCCCCCchHHHHHHHHHHHHHHHHHHhhhc
Q 030115 118 GISCVMKRLRGKEDLQSSVVAAFGSGAAFSLVSGMGGANPAVNAFTSGLLFAIFQGCSFKNKR 180 (183)
Q Consensus 118 g~ec~~~~~Rgk~D~~N~~~aG~~tGa~l~~~~G~~~~~~~~~a~~gga~fa~fs~~~~~~g~ 180 (183)
.++|++..+|+|||.||++++|++||++|+.++| +++++.+++.|+++.+.|+-++.
T Consensus 73 t~dC~Lv~~R~KeDpwNsivsGa~TGg~La~r~g------~~a~~~sa~~~g~~lamieg~g~ 129 (183)
T KOG1652|consen 73 TVDCALVAIRKKEDPWNSIVSGAATGGLLAARGG------PKAMLTSAITGGLLLAMIEGLGI 129 (183)
T ss_pred HHHHHHHHHhcccchHHHHHHHhhccceeecccc------HHHHHHHHHHHHHHHHHHHhHHH
Confidence 9999999999999999999999999999999999 99999999999999999887653
No 7
>COG5596 TIM22 Mitochondrial import inner membrane translocase, subunit TIM22 [Posttranslational modification, protein turnover, chaperones]
Probab=99.72 E-value=4.8e-19 Score=144.08 Aligned_cols=158 Identities=15% Similarity=0.128 Sum_probs=126.7
Q ss_pred CCchhhhHHHHHHHHhHHHHHHHHhhC-----CChHHHHHHHHHHHHHHHHHHHHHHhhhcccCCC--CCC---------
Q 030115 14 LPQKAIKDVQFKLKELENGYKSWLAKQ-----PLPVEAAIVTATTAINGAAIGAFLGVMTQDLTSS--LPT--------- 77 (183)
Q Consensus 14 ~p~~~~~~~q~~~~~~~~~~k~~~~~~-----~~~~e~~~~t~~g~~~G~~~G~f~g~v~~~~~~~--~~~--------- 77 (183)
+.+++...+++. |+-..++....... .|.-|++++++.|+.+|..+|.|.+++....... ++.
T Consensus 14 ~s~~~~~~lS~~-e~d~~~~~~l~~~~~~~~~~~i~k~~~s~l~G~~~g~~~g~f~ssl~y~t~~~~~~g~nfg~vwGgl 92 (191)
T COG5596 14 PSPNAYNILSPE-ERDPCPLEKLADFMKAFSYSCIGKSALSGLKGFRLGGPSGGFSSSLAYGTGLVHLLGLNFGGVWGGL 92 (191)
T ss_pred CCCCcccccChh-hcCchhhhHHhhhccchhhcchhhhhhhcccccccccccccchhhcccccccccccCccccccccce
Confidence 335566666666 44444444444333 5999999999999999999999999998543321 110
Q ss_pred --CCCCCCcchhhhhhhhhhHHhhcCchhhhhHHHHHHHHHHHHHHHHHHHhhccchhhHHHHHHHHhhhhhhccCCCCC
Q 030115 78 --PPPQSSLNPDAVAPFQQVQAVAGGPLVQARNFAVITGVNAGISCVMKRLRGKEDLQSSVVAAFGSGAAFSLVSGMGGA 155 (183)
Q Consensus 78 --~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fa~~g~~ysg~ec~~~~~Rgk~D~~N~~~aG~~tGa~l~~~~G~~~~ 155 (183)
.....+.++|++.+++ ++..+....++||+++|..|++.+|+|+.+|+|||+.|++.+|++||+.+..+.|
T Consensus 93 ~~~i~~~~~r~q~~~~~~---n~~~rg~ftG~n~GvlGl~y~~~ns~I~~~r~k~d~~~~iaaG~~TGa~~~~~~g---- 165 (191)
T COG5596 93 FSTIDCTPFRLQLKEQLN---NAGKRGFFTGKNLGVLGLIYAGINSIITALRAKHDIANAIAAGAFTGAALASSAG---- 165 (191)
T ss_pred eeccccchHHHHHhhccc---cccccccccccccceeeeecccchhhhhhhhhccccchhhhhhhhhhHHHHhhcc----
Confidence 0111345788888888 5788999999999999999999999999999999999999999999999999999
Q ss_pred CchHHHHHHHHHHHHHHHHHHhhhcc
Q 030115 156 NPAVNAFTSGLLFAIFQGCSFKNKRH 181 (183)
Q Consensus 156 ~~~~~a~~gga~fa~fs~~~~~~g~~ 181 (183)
++++..++++|++|++++...-++
T Consensus 166 --~qa~~~~~a~~aa~s~~~~~~~~~ 189 (191)
T COG5596 166 --PQAMPMGGAGFAAFSAGITLAMKS 189 (191)
T ss_pred --ccccccCccchhhhhhhHHhhhhc
Confidence 999999999999999999877654
No 8
>KOG3324 consensus Mitochondrial import inner membrane translocase, subunit TIM23 [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.54 E-value=1.4e-14 Score=119.07 Aligned_cols=116 Identities=21% Similarity=0.178 Sum_probs=92.0
Q ss_pred HHHH-HHHHHHHHHHHHHHHHHhhhcccCCCCCCCCCCCCcchhhhhhhhhhHHhhcCchhhhhHHHHHHHHHHHHHHHH
Q 030115 45 EAAI-VTATTAINGAAIGAFLGVMTQDLTSSLPTPPPQSSLNPDAVAPFQQVQAVAGGPLVQARNFAVITGVNAGISCVM 123 (183)
Q Consensus 45 e~~~-~t~~g~~~G~~~G~f~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fa~~g~~ysg~ec~~ 123 (183)
|.+. .+...+..|.++|.|.|++......+ .....++++.++++ +..++...++++.++++.+|+.+|..+
T Consensus 75 E~l~f~tG~~yl~G~~iGa~~G~~~Glk~~e-----~~~~~Klr~nrILN---~~t~~G~~~gN~lG~laL~YsaiesgI 146 (206)
T KOG3324|consen 75 ENLTFGTGWAYLTGSAIGAFNGLILGLKNTE-----NGASGKLRLNRILN---SVTRRGRFWGNTLGSLALMYSAIESGI 146 (206)
T ss_pred hhhheeccchhccchhhhhHHHHHHhhhcCC-----CCCccchhHHHHhh---hccccccccccchhHHHHHHHHHHHHH
Confidence 6666 78888888999999999988754321 11233666666665 345566679999999999999999999
Q ss_pred HHHhhccchhhHHHHHHHHhhhhhhccCCCCCCchHHHHHHHHHHHHHHHH
Q 030115 124 KRLRGKEDLQSSVVAAFGSGAAFSLVSGMGGANPAVNAFTSGLLFAIFQGC 174 (183)
Q Consensus 124 ~~~Rgk~D~~N~~~aG~~tGa~l~~~~G~~~~~~~~~a~~gga~fa~fs~~ 174 (183)
+..|+|||++|++.||.+||+++....| ++++..+++..++..++
T Consensus 147 ~~~R~~dd~lnsv~AGalTGalyrs~~G------lr~~av~ga~g~~aa~a 191 (206)
T KOG3324|consen 147 EATRGKDDDLNSVAAGALTGALYRSTRG------LRAAAVAGAVGGTAAAA 191 (206)
T ss_pred HHhhccccchhhhhhhhhhhhhhhcCCC------chHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999 89988777665554443
No 9
>COG5596 TIM22 Mitochondrial import inner membrane translocase, subunit TIM22 [Posttranslational modification, protein turnover, chaperones]
Probab=97.73 E-value=2.3e-06 Score=70.19 Aligned_cols=75 Identities=21% Similarity=0.270 Sum_probs=59.3
Q ss_pred CchhhhhHHH-HHHHHHHHHHHHHHHHhhccchhhHHHHHHHHhhhhhhccCCCCCCchHHHHH---------HHHHHHH
Q 030115 101 GPLVQARNFA-VITGVNAGISCVMKRLRGKEDLQSSVVAAFGSGAAFSLVSGMGGANPAVNAFT---------SGLLFAI 170 (183)
Q Consensus 101 ~~~~~~~~fa-~~g~~ysg~ec~~~~~Rgk~D~~N~~~aG~~tGa~l~~~~G~~~~~~~~~a~~---------gga~fa~ 170 (183)
.....+.||+ ++|++++.+.|+.+++|.+.|.||....|+++|..++....+ .+...+.|. +.+++++
T Consensus 77 ~~~~~g~nfg~vwGgl~~~i~~~~~r~q~~~~~~n~~~rg~ftG~n~GvlGl~--y~~~ns~I~~~r~k~d~~~~iaaG~ 154 (191)
T COG5596 77 LVHLLGLNFGGVWGGLFSTIDCTPFRLQLKEQLNNAGKRGFFTGKNLGVLGLI--YAGINSIITALRAKHDIANAIAAGA 154 (191)
T ss_pred cccccCccccccccceeeccccchHHHHHhhccccccccccccccccceeeee--cccchhhhhhhhhccccchhhhhhh
Confidence 3355788898 899999999999999999999999999999999999887753 122444555 6666777
Q ss_pred HHHHHHh
Q 030115 171 FQGCSFK 177 (183)
Q Consensus 171 fs~~~~~ 177 (183)
|-++.++
T Consensus 155 ~TGa~~~ 161 (191)
T COG5596 155 FTGAALA 161 (191)
T ss_pred hhhHHHH
Confidence 7776644
No 10
>KOG4608 consensus Uncharacterized conserved protein [Function unknown]
Probab=97.17 E-value=4.5e-05 Score=65.09 Aligned_cols=54 Identities=24% Similarity=0.279 Sum_probs=48.8
Q ss_pred hhcCchhhhhHHHHHHHHHHHHHHHHHHHhhccchhhHHHHHHHHhhhhhhccC
Q 030115 98 VAGGPLVQARNFAVITGVNAGISCVMKRLRGKEDLQSSVVAAFGSGAAFSLVSG 151 (183)
Q Consensus 98 ~~~~~~~~~~~fa~~g~~ysg~ec~~~~~Rgk~D~~N~~~aG~~tGa~l~~~~G 151 (183)
+.++.+..|=..|.+.+.|-++...+..+|+|||+||=+++|.+||+++.+.-|
T Consensus 127 farGgf~~G~R~alfttSff~l~t~l~vyRgk~a~~~fvaaga~tgsvF~~~~g 180 (270)
T KOG4608|consen 127 FARGGFRWGWRTALFTTSFFTLNTSLNVYRGKDALSHFVAAGAVTGSVFRINVG 180 (270)
T ss_pred HhhccccceeEEeeehhhHHHHHHHHHHHcCchhhhhhhccccceeeeEEeehh
Confidence 456677777788999999999999999999999999999999999999988877
No 11
>TIGR00980 3a0801so1tim17 mitochondrial import inner membrane translocase subunit tim17.
Probab=90.94 E-value=3.6 Score=33.63 Aligned_cols=121 Identities=12% Similarity=0.023 Sum_probs=88.6
Q ss_pred hHHHHH-HHHHHHHHHHHHHHHHHhhhcccCCCCCCCCCCCCcchhhhhhhhhhHHhhcCchhhhhHHHHHHHHHHHHHH
Q 030115 43 PVEAAI-VTATTAINGAAIGAFLGVMTQDLTSSLPTPPPQSSLNPDAVAPFQQVQAVAGGPLVQARNFAVITGVNAGISC 121 (183)
Q Consensus 43 ~~e~~~-~t~~g~~~G~~~G~f~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fa~~g~~ysg~ec 121 (183)
+++++- ...+|.+.|++++++-+..+.....++ +..+..+.+++ ..-..+.+.--+++.++...++.
T Consensus 13 ~~d~~G~af~~G~~~G~~~g~~~G~rnsp~g~rl---------~g~l~av~~ra---p~~g~~Fav~g~lys~~ec~i~~ 80 (170)
T TIGR00980 13 ILDDFGGAFAMGTIGGSIFQAFKGFRNSPKGEKL---------VGAMRAIKTRA---PVLGGNFAVWGGLFSTIDCAVVA 80 (170)
T ss_pred hHHhhhHHHHHHHHHHHHHHHHHHhhcCCccchh---------hHHHHHHHhhh---hhHHHHHHHHHHHHHHHHHHHHH
Confidence 456666 778888888888888877776454431 33333355443 23334567777888888999988
Q ss_pred HHHHHhhccchhhHHHHHHHHhhhhhhccCCCCCCchHHHHHHHHHHHHHHHHHHhhhcc
Q 030115 122 VMKRLRGKEDLQSSVVAAFGSGAAFSLVSGMGGANPAVNAFTSGLLFAIFQGCSFKNKRH 181 (183)
Q Consensus 122 ~~~~~Rgk~D~~N~~~aG~~tGa~l~~~~G~~~~~~~~~a~~gga~fa~fs~~~~~~g~~ 181 (183)
.-+|-=-.+-++-..+.|.+-++-=+.+.= ...++.+++.+++|.++=-.+.|+
T Consensus 81 ~R~KeD~~NsiiAG~~TGa~l~~r~G~~a~------~~~aa~gg~~la~ie~~g~~~~~~ 134 (170)
T TIGR00980 81 IRKKEDPWNSIISGFLTGAALAVRGGPRAM------RGSAILGACILAVIEGVGLVLTRW 134 (170)
T ss_pred HhcccchHHHHHHHHHHHHHHHhccChHHH------HHHHHHHHHHHHHHHHHHHHHHHh
Confidence 877766688899999999998887777776 889999999999999876555443
No 12
>PTZ00236 mitochondrial import inner membrane translocase subunit tim17; Provisional
Probab=90.30 E-value=4.1 Score=33.13 Aligned_cols=30 Identities=20% Similarity=0.089 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhcccCC
Q 030115 44 VEAAIVTATTAINGAAIGAFLGVMTQDLTS 73 (183)
Q Consensus 44 ~e~~~~t~~g~~~G~~~G~f~g~v~~~~~~ 73 (183)
++++-.+...+..|+.++.|+..+.++...
T Consensus 16 ~dd~G~af~~G~vgG~~~~~~~G~rnsp~g 45 (164)
T PTZ00236 16 IEDMGGAFSMGCIGGFIWHFLKGMRNSPKG 45 (164)
T ss_pred HHhccHHHHHHHHHHHHHHHHHHHHhCCCc
Confidence 355664444444445555555555555444
No 13
>KOG1398 consensus Uncharacterized conserved protein [Function unknown]
Probab=88.36 E-value=0.63 Score=42.77 Aligned_cols=49 Identities=12% Similarity=0.158 Sum_probs=42.2
Q ss_pred cCchhhhhHHHHHHHHHHHHHHHHHHHhhccchhhHHHHHHHHhhhhhh
Q 030115 100 GGPLVQARNFAVITGVNAGISCVMKRLRGKEDLQSSVVAAFGSGAAFSL 148 (183)
Q Consensus 100 ~~~~~~~~~fa~~g~~ysg~ec~~~~~Rgk~D~~N~~~aG~~tGa~l~~ 148 (183)
+.....+.-.+.+-++|..+.|++.+++-+||..|.++||.+++..+..
T Consensus 297 renlqlg~FlgsfvfIfkatsC~lr~v~n~dd~l~aifAgglAs~Smmf 345 (460)
T KOG1398|consen 297 RENLQLGSFLGSFVFIFKATSCALRKVANKDDKLVAIFAGGLASLSMMF 345 (460)
T ss_pred cccchhhHHHHHHHHHHHhHHHHHHHhccCcHHHHHHHHhhhhhheeee
Confidence 3445667778899999999999999999999999999999998866543
No 14
>PF10247 Romo1: Reactive mitochondrial oxygen species modulator 1; InterPro: IPR018450 The majority of endogenous reactive oxygen species (ROS) in cells are produced by the mitochondrial respiratory chain. An increase or imbalance in ROS alters the intracellular redox homeostasis, triggers DNA damage, and may contribute to cancer development and progression. This entry contains the mitochondrial protein, reactive oxygen species modulator 1 (Romo1), that is responsible for increasing the level of ROS in cells. In various cancer cell lines with elevated levels of ROS there is also an increased abundance of Romo1 []. Increased Romo1 expression can have a number of other affects including: inducing premature senescence of cultured human fibroblasts [, ] and increased resistance to 5-fluorouracil [].
Probab=86.28 E-value=1.3 Score=30.97 Aligned_cols=66 Identities=14% Similarity=0.108 Sum_probs=36.7
Q ss_pred CChHHHHHHHHHHHHHHHHHHHHHHhhhcccCCCCCCCCCCCCcchhhhhhhhhhHHhhcCchhhhhHHHHHHHHHHHHH
Q 030115 41 PLPVEAAIVTATTAINGAAIGAFLGVMTQDLTSSLPTPPPQSSLNPDAVAPFQQVQAVAGGPLVQARNFAVITGVNAGIS 120 (183)
Q Consensus 41 ~~~~e~~~~t~~g~~~G~~~G~f~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fa~~g~~ysg~e 120 (183)
+|.-|.-.-..+|...|..+|.++|.++.-... .++ +.-++. +++-+..++..|+.+=++=+.++
T Consensus 2 sc~~kikmG~~MG~~VG~~~G~l~G~~~~~r~g---~~~-----~~~~~~-------lg~~~l~sg~tFG~Fm~iGs~IR 66 (67)
T PF10247_consen 2 SCFDKIKMGFMMGGAVGGAFGALFGTFSAFRYG---ARG-----RGLMRT-------LGKYMLGSGATFGFFMSIGSVIR 66 (67)
T ss_pred cHHHHHHHHHHHhhHHHhhhhhhhhhHHHhccC---CCC-----cchHhH-------HhHHHhcchhHHHHHHhhhcccc
Confidence 455555556666667777777777776653221 111 222322 34445567777887766655555
Q ss_pred H
Q 030115 121 C 121 (183)
Q Consensus 121 c 121 (183)
|
T Consensus 67 c 67 (67)
T PF10247_consen 67 C 67 (67)
T ss_pred C
Confidence 4
No 15
>KOG4096 consensus Uncharacterized conserved protein [Function unknown]
Probab=84.93 E-value=0.84 Score=32.37 Aligned_cols=68 Identities=19% Similarity=0.214 Sum_probs=44.3
Q ss_pred CCChHHHHHHHHHHHHHHHHHHHHHHhhhcccCCCCCCCCCCCCcchhhhhhhhhhHHhhcCchhhhhHHHHHHHHHHHH
Q 030115 40 QPLPVEAAIVTATTAINGAAIGAFLGVMTQDLTSSLPTPPPQSSLNPDAVAPFQQVQAVAGGPLVQARNFAVITGVNAGI 119 (183)
Q Consensus 40 ~~~~~e~~~~t~~g~~~G~~~G~f~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fa~~g~~ysg~ 119 (183)
.+|.-|.-...++|...|.+.|.++|.+...-.. ++ -+.-++. +++-+..++..|+.+=++=+++
T Consensus 5 pSc~dKikmG~~mG~avG~a~G~lfGgf~~lR~g----~~----g~~~vr~-------iGkt~~~SagtFG~FM~igs~I 69 (75)
T KOG4096|consen 5 PSCFDKIKMGLMMGGAVGGATGALFGGFAALRYG----PR----GRGLVRT-------IGKTMLQSAGTFGLFMGIGSGI 69 (75)
T ss_pred ccHHHHHHHHHHHHhhhhhhhhhhccchhheeec----CC----hhHHHHH-------HhHHHHhccchhhhhhhhhhhe
Confidence 4576676667777777788888888877763221 11 0222222 3455667888999988888888
Q ss_pred HHH
Q 030115 120 SCV 122 (183)
Q Consensus 120 ec~ 122 (183)
+|.
T Consensus 70 r~~ 72 (75)
T KOG4096|consen 70 RCG 72 (75)
T ss_pred ecC
Confidence 775
No 16
>TIGR00983 3a0801s02tim23 mitochondrial import inner membrane translocase subunit tim23.
Probab=82.65 E-value=6.8 Score=31.21 Aligned_cols=119 Identities=13% Similarity=0.013 Sum_probs=66.9
Q ss_pred HHHHhhCCChHHHHHHHHHHHHHHHHHHHHHHhhhcccCCCCCCCCCCCCcchhhhhhhhhhHHhhcCchhhhhHHHHHH
Q 030115 34 KSWLAKQPLPVEAAIVTATTAINGAAIGAFLGVMTQDLTSSLPTPPPQSSLNPDAVAPFQQVQAVAGGPLVQARNFAVIT 113 (183)
Q Consensus 34 k~~~~~~~~~~e~~~~t~~g~~~G~~~G~f~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fa~~g 113 (183)
+.|. |+.-.....+.++|.+.|+++|++.|..+.....+. +..++..+..+-++.-.++.....++..|..+
T Consensus 28 R~~~--e~~~~~~G~ay~~G~~~Gg~~Gl~~G~~~~~~~~~~-----k~rln~~ln~~~~~g~~~G~~~g~~g~lys~~- 99 (149)
T TIGR00983 28 RGWF--EDLCFGTGTCYLTGLAIGALNGLRLGLKETQSMPWT-----KLRLNQILNMVTRRGPFWGNTLGILALVYNGI- 99 (149)
T ss_pred CChh--hhhhhhHhHHHHHHHHHHHHHHHHHHHhhCCCCCcH-----HHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHH-
Confidence 4454 444578999999999999999999999985332210 12235555555554433444444444444443
Q ss_pred HHHHHHHHHHHHHhhccchhhHHHHHHHHhhhhhhccCCCCCCchHHHHHHHHHH
Q 030115 114 GVNAGISCVMKRLRGKEDLQSSVVAAFGSGAAFSLVSGMGGANPAVNAFTSGLLF 168 (183)
Q Consensus 114 ~~ysg~ec~~~~~Rgk~D~~N~~~aG~~tGa~l~~~~G~~~~~~~~~a~~gga~f 168 (183)
-+.++..-.+-=-.+-+.-..+.|.+--+--+++.- ...++.++++.
T Consensus 100 --e~~i~~~R~k~D~~Nsv~AGa~TGal~~~~~G~r~~------~~g~~~G~~l~ 146 (149)
T TIGR00983 100 --NSIIEATRGKHDDFNSVAAGALTGALYKSTRGLRGM------ARSGALGATAA 146 (149)
T ss_pred --HHHHHHHhccchhhHhHHHHHHHHHHHHhccChHHH------HHHhHHHHHHh
Confidence 334443333322355566666666665555555555 44555544443
No 17
>KOG3225 consensus Mitochondrial import inner membrane translocase, subunit TIM22 [Intracellular trafficking, secretion, and vesicular transport]
Probab=57.24 E-value=5.1 Score=32.56 Aligned_cols=37 Identities=14% Similarity=0.269 Sum_probs=29.8
Q ss_pred hhCCChHHHHHHHHHHHHHHHHHHHHHHhhhcccCCC
Q 030115 38 AKQPLPVEAAIVTATTAINGAAIGAFLGVMTQDLTSS 74 (183)
Q Consensus 38 ~~~~~~~e~~~~t~~g~~~G~~~G~f~g~v~~~~~~~ 74 (183)
+.....--.+++++.+.|+|+++|+.+|++..+++.+
T Consensus 34 r~le~~n~c~~Ka~~sgV~GfglG~~~GlFlas~d~~ 70 (168)
T KOG3225|consen 34 RYLEEENSCAVKAVKSGVTGFGLGGAFGLFLASLDTQ 70 (168)
T ss_pred HHHHHhcchhHHHHHhhccccchhhhHHhhhhhcccC
Confidence 5666444334499999999999999999999998764
No 18
>PF04418 DUF543: Domain of unknown function (DUF543); InterPro: IPR007512 This family of short eukaryotic proteins has no known function. Most of the members of this family are only 80 amino acid residues long. However the Arabidopsis homologue is over 300 residues long. These proteins contain a conserved N-terminal cysteine and a conserved motif GXGXGXG in the carboxy terminal half that may be functionally important.
Probab=52.45 E-value=20 Score=25.39 Aligned_cols=24 Identities=8% Similarity=-0.000 Sum_probs=16.3
Q ss_pred CChHHHHHHHHHHHHHHHHHHHHH
Q 030115 41 PLPVEAAIVTATTAINGAAIGAFL 64 (183)
Q Consensus 41 ~~~~e~~~~t~~g~~~G~~~G~f~ 64 (183)
.|.-..+++++.|++.|.++++++
T Consensus 24 ~cl~~~l~k~~~G~~~G~~~s~l~ 47 (75)
T PF04418_consen 24 RCLSDTLVKTGLGFGIGVVFSLLF 47 (75)
T ss_pred HHHHHHHHHHhhhhhHHHHHHHHH
Confidence 355555667887777777777765
No 19
>PF10439 Bacteriocin_IIc: Bacteriocin class II with double-glycine leader peptide; InterPro: IPR019493 Bacteriocins are proteinaceous toxins produced by bacteria to inhibit the growth of similar or closely related strains. The producer bacteria are protected from the effects of their own bacteriocins by production of a specific immunity protein which is co-transcribed with the genes encoding the bacteriocins, e.g. IPR015046 from INTERPRO. The bacteriocins are structurally more specific than their immunity-protein counterparts. Typically, production of the bacteriocin gene is from within an operon carrying up to 6 genes including a typical two-component regulatory system (R and H), a small peptide pheromone (C), and a dedicated ABC transporter (A and -B) as well as an immunity protein []. The ABC transporter is thought to recognise the N termini of both the pheromone and the bacteriocins and to transport these peptides across the cytoplasmic membrane, concurrent with cleavage at the conserved double-glycine motif. Cleaved extracellular C can then bind to the sensor kinase, H, resulting in activation of R and up-regulation of the entire gene cluster via binding to consensus sequences within each promoter []. It seems likely that the whole regulon is carried on a transmissible plasmid which is passed between closely related Firmicute species since many clinical isolates from different Firmicutes can produce at least two bacteriocins, and the same bacteriocins can be produced by different species. The proteins in this entry include amylovorin-L, lactacin-F and salivaricin CRL 1328, all of them class IIb two-peptide bacteriocins.
Probab=47.55 E-value=68 Score=21.68 Aligned_cols=22 Identities=23% Similarity=0.219 Sum_probs=17.6
Q ss_pred cchhhHHHHHHHHhhhhhhccC
Q 030115 130 EDLQSSVVAAFGSGAAFSLVSG 151 (183)
Q Consensus 130 ~D~~N~~~aG~~tGa~l~~~~G 151 (183)
.|.+..+.+++++|++.+...+
T Consensus 23 ~~~~~~~~~~~~~G~~~G~~~g 44 (65)
T PF10439_consen 23 GNCVGGVGGGAAGGAAAGAAGG 44 (65)
T ss_pred HHHHHHHHHHHHHHHHHhhhcc
Confidence 4566677888888988888888
No 20
>PF05957 DUF883: Bacterial protein of unknown function (DUF883); InterPro: IPR010279 This family consists of several bacterial proteins of unknown function that include the Escherichia coli genes for ElaB, YgaM and YqjD.
Probab=43.17 E-value=63 Score=23.07 Aligned_cols=15 Identities=27% Similarity=0.301 Sum_probs=7.7
Q ss_pred HHHHHHHHHHHHHHH
Q 030115 50 TATTAINGAAIGAFL 64 (183)
Q Consensus 50 t~~g~~~G~~~G~f~ 64 (183)
.+.++..|+++|+++
T Consensus 77 vgiAagvG~llG~Ll 91 (94)
T PF05957_consen 77 VGIAAGVGFLLGLLL 91 (94)
T ss_pred HHHHHHHHHHHHHHH
Confidence 344444555555554
No 21
>PF12597 DUF3767: Protein of unknown function (DUF3767); InterPro: IPR022533 This group of proteins includes mitochodrial cytochrome c oxidase proteins [], and some transmembrane domain-containing proteins of unknown function known as FAM36A. Proteins in this family are typically between 112 and 199 amino acids in length.
Probab=43.00 E-value=49 Score=25.29 Aligned_cols=51 Identities=14% Similarity=-0.031 Sum_probs=27.4
Q ss_pred HHhhccchhhHHHHHHHHhhhhhhccCCCCCCchHHHHHHHHHHHHHHHHH
Q 030115 125 RLRGKEDLQSSVVAAFGSGAAFSLVSGMGGANPAVNAFTSGLLFAIFQGCS 175 (183)
Q Consensus 125 ~~Rgk~D~~N~~~aG~~tGa~l~~~~G~~~~~~~~~a~~gga~fa~fs~~~ 175 (183)
++..---.-|+++-|+.+|.++|.-.-+...++.+++=.+-.+|.+.|.+.
T Consensus 33 ~~~~iPCfR~slL~Gi~~G~~vG~~~fl~~~~~~~A~nwavgsF~l~s~~~ 83 (118)
T PF12597_consen 33 NVHKIPCFRDSLLYGIAGGFGVGGLRFLFTSNPRKAANWAVGSFFLGSLGS 83 (118)
T ss_pred HHhcCCcHHHHHHHHHHHHHHHHhhhhcccCCCccchhhhhHHHHHHHHHH
Confidence 343434455667777777766665544333344555444555566555554
No 22
>COG4575 ElaB Uncharacterized conserved protein [Function unknown]
Probab=42.31 E-value=1.1e+02 Score=23.18 Aligned_cols=32 Identities=19% Similarity=0.192 Sum_probs=19.3
Q ss_pred cccc-cccCCCchhhhHHHHHHHHhHHHHHHHH
Q 030115 6 EKVM-SLVQLPQKAIKDVQFKLKELENGYKSWL 37 (183)
Q Consensus 6 ~~~~-~~~~~p~~~~~~~q~~~~~~~~~~k~~~ 37 (183)
|.|. |...++....++++...+.+.++.+.-+
T Consensus 25 EevL~ssg~~a~~e~~~lR~r~~~~Lk~~r~rl 57 (104)
T COG4575 25 EEVLKSSGSLAGDEAEELRSKAESALKEARDRL 57 (104)
T ss_pred HHHHHhcccchhhHHHHHHHHHHHHHHHHHHHH
Confidence 3455 4444456777777777666666665544
No 23
>PF02466 Tim17: Tim17/Tim22/Tim23/Pmp24 family; InterPro: IPR003397 The membrane-embedded multi-protein complexes of mitochondria mediate the transport of nuclear-encoded proteins across and into the outer or inner mitochondrial membranes []. The TOM (translocase of the outer mitochondrial membrane) complex consists of cytosol-exposed receptors and a pore-forming core, and mediates the transport of proteins from the cytosol across and into the outer mitochondrial membrane. A novel protein complex in the outer membrane of mitochondria, called the SAM complex (sorting and assembly machinery), is involved in the biogenesis of beta-barrel proteins of the outer membrane. Two translocases of the inner mitochondrial membrane (TIM22 and TIM23 complexes) mediate protein transport at the inner membrane. The TIM23 complex (a presequence translocase) mediates the transport of presequence-containing proteins across and into the inner membrane. Tim23 and Tim17 form part of this complex. Tim23 forms a pore in the inner membrane. The role of Tim17 is not yet fully understood. The TIM22 complex (a twin-pore carrier translocase) catalyses the insertion of multi-spanning proteins that have internal targeting signals into the inner membrane. The TIM22 complex mediates the membrane insertion of multi-spanning inner-membrane proteins that have internal targeting signals, and it uses the membrane potential as an external driving force. The Tim22 subunit of the mitochondrial import inner membrane translocase is included in this family. This family also includes Pmp24, a peroxisomal membrane protein, and NADH ubiquinone dehydrogenase 1 alpha subunit 11. Pmp24 was previously known as Pmp27 [].
Probab=41.50 E-value=1.4e+02 Score=21.99 Aligned_cols=114 Identities=13% Similarity=-0.038 Sum_probs=57.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhcccCCCCCCCCCCCCcchhhhhhhhhhHHhhcCchhhhhHHHHHHHHHHHHHHHHHH
Q 030115 46 AAIVTATTAINGAAIGAFLGVMTQDLTSSLPTPPPQSSLNPDAVAPFQQVQAVAGGPLVQARNFAVITGVNAGISCVMKR 125 (183)
Q Consensus 46 ~~~~t~~g~~~G~~~G~f~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fa~~g~~ysg~ec~~~~ 125 (183)
.....+.|++.|+..+..-+.-......+.. ...+..++..-++ ........+.--++..++-..++..-++
T Consensus 10 ~~~g~~~G~~~G~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~---~~~~~~~~g~~~~~y~~~~~~l~~~R~k 81 (128)
T PF02466_consen 10 TGKGFVAGAVFGGFIGAISAFTRPPRGSPLR-----PRLRSILNAVGRR---GPRHGARFGSFGGLYSGIECALERLRGK 81 (128)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhhcccCCcHh-----HHHHHHHHHHhcc---chHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 3336777777777777773321111111100 0113333333221 1112234455555666666666665544
Q ss_pred HhhccchhhHHHHHHHHhhhhhhccCCCCCCchHHHHHHHHHHHHHHH
Q 030115 126 LRGKEDLQSSVVAAFGSGAAFSLVSGMGGANPAVNAFTSGLLFAIFQG 173 (183)
Q Consensus 126 ~Rgk~D~~N~~~aG~~tGa~l~~~~G~~~~~~~~~a~~gga~fa~fs~ 173 (183)
--..|-..-..++|.+-+.--+++.- ...++.+++..+++..
T Consensus 82 ~D~~N~~~aG~~aGa~~~~~~g~~~~------~~~~~~~a~~~~~~~~ 123 (128)
T PF02466_consen 82 DDPWNSAIAGAAAGAVLGLRSGPRGM------ASGAALGAAFAAAVEY 123 (128)
T ss_pred cccchhHHHHHHHHHHHHhccChHHH------HHHHHHHHHHHHHHHH
Confidence 44466677777777776665555555 6666666666555544
No 24
>COG5336 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.41 E-value=1.6e+02 Score=22.59 Aligned_cols=27 Identities=19% Similarity=0.213 Sum_probs=16.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 030115 43 PVEAAIVTATTAINGAAIGAFLGVMTQ 69 (183)
Q Consensus 43 ~~e~~~~t~~g~~~G~~~G~f~g~v~~ 69 (183)
+++.....+.|.+.|.++|.|+==+.+
T Consensus 45 a~klssefIsGilVGa~iG~llD~~ag 71 (116)
T COG5336 45 AFKLSSEFISGILVGAGIGWLLDKFAG 71 (116)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 445555667777777777776544443
No 25
>PTZ00478 Sec superfamily; Provisional
Probab=30.12 E-value=1.9e+02 Score=20.88 Aligned_cols=63 Identities=10% Similarity=-0.069 Sum_probs=34.3
Q ss_pred cccccccCCCchhhhHHHHHHHHhHHHHHHHHhhCCC-hHHHHHHHHHHHHHHHHHHHHHHhhh
Q 030115 6 EKVMSLVQLPQKAIKDVQFKLKELENGYKSWLAKQPL-PVEAAIVTATTAINGAAIGAFLGVMT 68 (183)
Q Consensus 6 ~~~~~~~~~p~~~~~~~q~~~~~~~~~~k~~~~~~~~-~~e~~~~t~~g~~~G~~~G~f~g~v~ 68 (183)
|.+..++.+-+.-.+..++++++-..=++++.+.+-= -.+++..|+.|+++=+.+|++.=++.
T Consensus 7 ~~~~~~m~~~~~v~~~~~eF~kds~r~vkrctKPdrkEf~kiakat~iGf~imG~IGy~IKLIh 70 (81)
T PTZ00478 7 EFLTDKSNPVGYVVSGVQEFANDSRRLIRKCTKPDAKEYTNIAYACSVGFFIMGFIGYSIKLVF 70 (81)
T ss_pred hHhhcccchhHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHhhheeE
Confidence 3333333333444445555544444444444432221 12566688999888888888877665
No 26
>KOG1398 consensus Uncharacterized conserved protein [Function unknown]
Probab=29.32 E-value=90 Score=29.10 Aligned_cols=43 Identities=14% Similarity=0.159 Sum_probs=35.0
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHhhccchhhHHHHHHHHhhhhh
Q 030115 105 QARNFAVITGVNAGISCVMKRLRGKEDLQSSVVAAFGSGAAFS 147 (183)
Q Consensus 105 ~~~~fa~~g~~ysg~ec~~~~~Rgk~D~~N~~~aG~~tGa~l~ 147 (183)
++.-+.-..+.|-...|.+++++||...||+.+++++.+.-.+
T Consensus 81 s~lflvtn~~~f~al~C~lRkwlgkftp~t~glv~s~las~ia 123 (460)
T KOG1398|consen 81 SGLFLVTNTGSFHALRCCLRKWLGKFTPLTSGLVGSVLASSIA 123 (460)
T ss_pred hceeeeechHHHHHHHHHHHHHhcccCcccHHHHHHHHhhhhh
Confidence 4455556677888899999999999999999999998875444
No 27
>COG4803 Predicted membrane protein [Function unknown]
Probab=29.06 E-value=64 Score=26.24 Aligned_cols=56 Identities=23% Similarity=0.362 Sum_probs=33.1
Q ss_pred cCCCchhhhHHHHHHHHhHHHHHH---------HHhhCCChHHHHH-HHHHHHHHHHHHHHHHHhhh
Q 030115 12 VQLPQKAIKDVQFKLKELENGYKS---------WLAKQPLPVEAAI-VTATTAINGAAIGAFLGVMT 68 (183)
Q Consensus 12 ~~~p~~~~~~~q~~~~~~~~~~k~---------~~~~~~~~~e~~~-~t~~g~~~G~~~G~f~g~v~ 68 (183)
|+++... ++.+++++++.+++.- |...-....+-.+ .|..|++.|.+.|+++|.+.
T Consensus 11 f~~e~~A-eev~~~l~~LqkE~LI~L~DAvvvvk~~~gkvklkQ~~Nlt~aGa~sGafWG~LiGllF 76 (170)
T COG4803 11 FDDEDKA-EEVRERLNELQKEYLITLEDAVVVVKDEDGKVKLKQLMNLTGAGAVSGAFWGMLIGLLF 76 (170)
T ss_pred cCCcchH-HHHHHHHHHhhHHHheeccceEEEEeCCCCCeeHHHHhhhhhhccccccHHHHHHHHHH
Confidence 4444444 4555555777776632 1111223445555 67788888888888877766
No 28
>PF05957 DUF883: Bacterial protein of unknown function (DUF883); InterPro: IPR010279 This family consists of several bacterial proteins of unknown function that include the Escherichia coli genes for ElaB, YgaM and YqjD.
Probab=26.98 E-value=2.3e+02 Score=20.03 Aligned_cols=17 Identities=6% Similarity=0.010 Sum_probs=9.9
Q ss_pred HHHHH-HHHHHHHHHHHH
Q 030115 44 VEAAI-VTATTAINGAAI 60 (183)
Q Consensus 44 ~e~~~-~t~~g~~~G~~~ 60 (183)
++++- ..+.|+++|.++
T Consensus 74 ~~svgiAagvG~llG~Ll 91 (94)
T PF05957_consen 74 WQSVGIAAGVGFLLGLLL 91 (94)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 44444 666666666655
No 29
>PF13940 Ldr_toxin: Toxin Ldr, type I toxin-antitoxin system
Probab=26.47 E-value=53 Score=20.00 Aligned_cols=21 Identities=14% Similarity=0.218 Sum_probs=18.3
Q ss_pred ccchhhHHHHHHHHhhhhhhc
Q 030115 129 KEDLQSSVVAAFGSGAAFSLV 149 (183)
Q Consensus 129 k~D~~N~~~aG~~tGa~l~~~ 149 (183)
-||+--++++|.+++.+++.-
T Consensus 11 WhDLAAP~iagIi~s~iv~w~ 31 (35)
T PF13940_consen 11 WHDLAAPIIAGIIASLIVGWL 31 (35)
T ss_pred HHHhHhHHHHHHHHHHHHHHH
Confidence 489999999999999998753
No 30
>KOG0682 consensus Ammonia permease [Inorganic ion transport and metabolism]
Probab=24.72 E-value=3.6e+02 Score=25.84 Aligned_cols=63 Identities=14% Similarity=0.100 Sum_probs=39.9
Q ss_pred HHHHHHHHHHhhccchhhHHHHHHHHhhhhhhccCCCCCCchHHHHHHHHHHHHHHHHHHhhhcc
Q 030115 117 AGISCVMKRLRGKEDLQSSVVAAFGSGAAFSLVSGMGGANPAVNAFTSGLLFAIFQGCSFKNKRH 181 (183)
Q Consensus 117 sg~ec~~~~~Rgk~D~~N~~~aG~~tGa~l~~~~G~~~~~~~~~a~~gga~fa~fs~~~~~~g~~ 181 (183)
..+-|.+..+|.++=-.+-++.|+++|.+ +.+.| ...-.|.+++..|+.-+++.-+..|+.++
T Consensus 272 glt~~~~d~~~~~kwsv~~~cnG~laGlV-aiT~g-c~~v~pWaAiviG~va~~~~~~~~kL~~~ 334 (500)
T KOG0682|consen 272 GLTWLIIDYLRHGKWSVIGLCNGILAGLV-AITPG-CGVVEPWAAIVIGAVAGLVCNAANKLKER 334 (500)
T ss_pred hhhhhhhhhhhcCCcchhhhHHHHHHHHH-hhcCC-CcccCcHHHHHHhHHHHHHHHHHHHHHHH
Confidence 34556777777655334444455554433 55655 23335888999999988888877777654
No 31
>PF14689 SPOB_a: Sensor_kinase_SpoOB-type, alpha-helical domain; PDB: 1F51_C 2FTK_B 1IXM_B.
Probab=24.34 E-value=58 Score=21.71 Aligned_cols=24 Identities=13% Similarity=0.317 Sum_probs=17.7
Q ss_pred HHHHHHHHHhh-ccchhhHH--HHHHH
Q 030115 118 GISCVMKRLRG-KEDLQSSV--VAAFG 141 (183)
Q Consensus 118 g~ec~~~~~Rg-k~D~~N~~--~aG~~ 141 (183)
-++..++.+|. +||+.|-+ +.|.+
T Consensus 8 ~~~~~~~~lR~~RHD~~NhLqvI~gll 34 (62)
T PF14689_consen 8 ELEELIDSLRAQRHDFLNHLQVIYGLL 34 (62)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhHHHHHHHHHHHHHH
Confidence 45677888885 99999975 45554
No 32
>PRK09400 secE preprotein translocase subunit SecE; Reviewed
Probab=22.60 E-value=1.6e+02 Score=19.91 Aligned_cols=24 Identities=21% Similarity=0.102 Sum_probs=16.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhh
Q 030115 45 EAAIVTATTAINGAAIGAFLGVMT 68 (183)
Q Consensus 45 e~~~~t~~g~~~G~~~G~f~g~v~ 68 (183)
+.+..++.|.++=+++|++.-.+-
T Consensus 34 ~ia~~~~iG~~i~G~iGf~Ikli~ 57 (61)
T PRK09400 34 LVAKVTGLGILLIGLIGFIIYLIM 57 (61)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455578888887777888776543
No 33
>PF07080 DUF1348: Protein of unknown function (DUF1348); InterPro: IPR009783 This family consists of several highly conserved hypothetical proteins of around 150 residues in length. The function of this family is unknown.; PDB: 2IMJ_B.
Probab=22.24 E-value=39 Score=26.86 Aligned_cols=18 Identities=22% Similarity=0.302 Sum_probs=15.6
Q ss_pred HHHHHHHHhhccchhhHH
Q 030115 119 ISCVMKRLRGKEDLQSSV 136 (183)
Q Consensus 119 ~ec~~~~~Rgk~D~~N~~ 136 (183)
.|.+++|+|.-+|.||+=
T Consensus 9 ~etA~~KVr~AEdaWNsr 26 (143)
T PF07080_consen 9 RETAIQKVRAAEDAWNSR 26 (143)
T ss_dssp HHHHHHHHHHHHHHHTTT
T ss_pred HHHHHHHHHHHHhccccC
Confidence 378899999999999973
No 34
>COG3558 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.15 E-value=45 Score=26.25 Aligned_cols=18 Identities=22% Similarity=0.257 Sum_probs=15.5
Q ss_pred HHHHHHHHhhccchhhHH
Q 030115 119 ISCVMKRLRGKEDLQSSV 136 (183)
Q Consensus 119 ~ec~~~~~Rgk~D~~N~~ 136 (183)
.|.+++++|-.+|.||+=
T Consensus 11 ~eta~~kvr~aed~wnsr 28 (154)
T COG3558 11 AETAIQKVRMAEDAWNSR 28 (154)
T ss_pred HHHHHHHHHHhHhccccC
Confidence 377889999999999974
No 35
>PF05818 TraT: Enterobacterial TraT complement resistance protein; InterPro: IPR008874 The traT gene is one of the F factor transfer genes and encodes an outer membrane protein which is involved in interactions between Escherichia coli and its surroundings []. The protein plays a role in preventing unproductive conjugation between bacteria carrying like plasmids.; GO: 0046999 regulation of conjugation, 0019867 outer membrane
Probab=21.17 E-value=81 Score=26.77 Aligned_cols=19 Identities=21% Similarity=-0.013 Sum_probs=10.1
Q ss_pred HHHHH-HHHHHHHHHHHHhh
Q 030115 160 NAFTS-GLLFAIFQGCSFKN 178 (183)
Q Consensus 160 ~a~~g-ga~fa~fs~~~~~~ 178 (183)
.++.+ |+.-|+.+.+.+++
T Consensus 109 g~~~G~GlaGalig~~ada~ 128 (215)
T PF05818_consen 109 GAAIGAGLAGALIGMIADAM 128 (215)
T ss_pred chhhhhhHHHhHHHHHHhhh
Confidence 33333 66666666665443
Done!