RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4130
(314 letters)
>gnl|CDD|238112 cd00189, TPR, Tetratricopeptide repeat domain; typically contains
34 amino acids
[WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-
X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found
in a variety of organisms including bacteria,
cyanobacteria, yeast, fungi, plants, and humans in
various subcellular locations; involved in a variety of
functions including protein-protein interactions, but
common features in the interaction partners have not
been defined; involved in chaperone, cell-cycle,
transciption, and protein transport complexes; the
number of TPR motifs varies among proteins (1,3-11,13
15,16,19); 5-6 tandem repeats generate a right-handed
helical structure with an amphipathic channel that is
thought to accomodate an alpha-helix of a target
protein; it has been proposed that TPR proteins
preferably interact with WD-40 repeat proteins, but in
many instances several TPR-proteins seem to aggregate to
multi-protein complexes; examples of TPR-proteins
include, Cdc16p, Cdc23p and Cdc27p components of the
cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal
targeting signals, the Tom70p co-receptor for
mitochondrial targeting signals, Ser/Thr phosphatase 5C
and the p110 subunit of O-GlcNAc transferase; three
copies of the repeat are present here.
Length = 100
Score = 91.7 bits (228), Expect = 2e-23
Identities = 45/100 (45%), Positives = 61/100 (61%)
Query: 90 EKYKNLGNTAMQQDKPEQAVIEYSKAIDCDNSNPVYYCNRAASNNKLKNYKLALRDCQIA 149
E NLGN + ++A+ Y KA++ D N Y N AA+ KL Y+ AL D + A
Sbjct: 1 EALLNLGNLYYKLGDYDEALEYYEKALELDPDNADAYYNLAAAYYKLGKYEEALEDYEKA 60
Query: 150 IKIDPHYAKAYGRMGLAYTQMNDYKAALEAYTKAAELDPN 189
+++DP AKAY +GLAY ++ Y+ ALEAY KA ELDPN
Sbjct: 61 LELDPDNAKAYYNLGLAYYKLGKYEEALEAYEKALELDPN 100
Score = 63.6 bits (155), Expect = 6e-13
Identities = 28/81 (34%), Positives = 40/81 (49%)
Query: 126 YCNRAASNNKLKNYKLALRDCQIAIKIDPHYAKAYGRMGLAYTQMNDYKAALEAYTKAAE 185
N KL +Y AL + A+++DP A AY + AY ++ Y+ ALE Y KA E
Sbjct: 3 LLNLGNLYYKLGDYDEALEYYEKALELDPDNADAYYNLAAAYYKLGKYEEALEDYEKALE 62
Query: 186 LDPNDPLYANNMQAAMSNLNN 206
LDP++ N+ A L
Sbjct: 63 LDPDNAKAYYNLGLAYYKLGK 83
Score = 40.1 bits (94), Expect = 1e-04
Identities = 20/53 (37%), Positives = 27/53 (50%)
Query: 158 KAYGRMGLAYTQMNDYKAALEAYTKAAELDPNDPLYANNMQAAMSNLNNSSSA 210
+A +G Y ++ DY ALE Y KA ELDP++ N+ AA L A
Sbjct: 1 EALLNLGNLYYKLGDYDEALEYYEKALELDPDNADAYYNLAAAYYKLGKYEEA 53
>gnl|CDD|222112 pfam13414, TPR_11, TPR repeat.
Length = 69
Score = 65.8 bits (161), Expect = 5e-14
Identities = 26/68 (38%), Positives = 39/68 (57%), Gaps = 1/68 (1%)
Query: 88 EAEKYKNLGNTAMQQDKPEQAVIEYSKAIDCDNSNPVYYCNRAASNNKL-KNYKLALRDC 146
AE KNLGN + ++A+ Y KA++ D N Y N A + KL K+Y+ AL D
Sbjct: 2 NAEALKNLGNALFKLGDYDEAIEAYEKALELDPDNAEAYYNLALAYLKLGKDYEEALEDL 61
Query: 147 QIAIKIDP 154
+ A+++DP
Sbjct: 62 EKALELDP 69
Score = 60.4 bits (147), Expect = 4e-12
Identities = 26/68 (38%), Positives = 38/68 (55%), Gaps = 1/68 (1%)
Query: 122 NPVYYCNRAASNNKLKNYKLALRDCQIAIKIDPHYAKAYGRMGLAYTQMN-DYKAALEAY 180
N N + KL +Y A+ + A+++DP A+AY + LAY ++ DY+ ALE
Sbjct: 2 NAEALKNLGNALFKLGDYDEAIEAYEKALELDPDNAEAYYNLALAYLKLGKDYEEALEDL 61
Query: 181 TKAAELDP 188
KA ELDP
Sbjct: 62 EKALELDP 69
Score = 44.6 bits (106), Expect = 2e-06
Identities = 17/43 (39%), Positives = 25/43 (58%)
Query: 155 HYAKAYGRMGLAYTQMNDYKAALEAYTKAAELDPNDPLYANNM 197
A+A +G A ++ DY A+EAY KA ELDP++ N+
Sbjct: 1 DNAEALKNLGNALFKLGDYDEAIEAYEKALELDPDNAEAYYNL 43
>gnl|CDD|233223 TIGR00990, 3a0801s09, mitochondrial precursor proteins import
receptor (72 kDa mitochondrial outermembrane protein)
(mitochondrial import receptor for the ADP/ATP carrier)
(translocase of outermembrane tom70). [Transport and
binding proteins, Amino acids, peptides and amines].
Length = 615
Score = 70.4 bits (172), Expect = 2e-13
Identities = 42/103 (40%), Positives = 57/103 (55%), Gaps = 2/103 (1%)
Query: 75 SNINFSPTEEVKIEAEKYKNLGNTAMQQDKPEQAVIEYSKAIDCDNSNPVYYCNRAASNN 134
S N S EE K A K K GN A + +A+ YSKAI+C +PVYY NRAA +N
Sbjct: 114 SVANLS-EEERKKYAAKLKEKGNKAYRNKDFNKAIKLYSKAIEC-KPDPVYYSNRAACHN 171
Query: 135 KLKNYKLALRDCQIAIKIDPHYAKAYGRMGLAYTQMNDYKAAL 177
L +++ + D A+++DP Y+KA R AY + Y AL
Sbjct: 172 ALGDWEKVVEDTTAALELDPDYSKALNRRANAYDGLGKYADAL 214
Score = 36.1 bits (83), Expect = 0.020
Identities = 17/87 (19%), Positives = 44/87 (50%)
Query: 105 PEQAVIEYSKAIDCDNSNPVYYCNRAASNNKLKNYKLALRDCQIAIKIDPHYAKAYGRMG 164
P++A ++ KA+ ++ +P Y +RA + + A +D Q +I +DP + ++ ++G
Sbjct: 381 PDKAEEDFDKALKLNSEDPDIYYHRAQLHFIKGEFAQAGKDYQKSIDLDPDFIFSHIQLG 440
Query: 165 LAYTQMNDYKAALEAYTKAAELDPNDP 191
+ + +++ + + + P P
Sbjct: 441 VTQYKEGSIASSMATFRRCKKNFPEAP 467
Score = 35.0 bits (80), Expect = 0.047
Identities = 25/102 (24%), Positives = 44/102 (43%)
Query: 88 EAEKYKNLGNTAMQQDKPEQAVIEYSKAIDCDNSNPVYYCNRAASNNKLKNYKLALRDCQ 147
EA G + K +A+ + SK+I+ D Y RA+ N +L + A D
Sbjct: 330 EAIALNLRGTFKCLKGKHLEALADLSKSIELDPRVTQSYIKRASMNLELGDPDKAEEDFD 389
Query: 148 IAIKIDPHYAKAYGRMGLAYTQMNDYKAALEAYTKAAELDPN 189
A+K++ Y + ++ A + Y K+ +LDP+
Sbjct: 390 KALKLNSEDPDIYYHRAQLHFIKGEFAQAGKDYQKSIDLDPD 431
Score = 34.2 bits (78), Expect = 0.080
Identities = 15/50 (30%), Positives = 26/50 (52%)
Query: 142 ALRDCQIAIKIDPHYAKAYGRMGLAYTQMNDYKAALEAYTKAAELDPNDP 191
AL D +I++DP ++Y + ++ D A E + KA +L+ DP
Sbjct: 350 ALADLSKSIELDPRVTQSYIKRASMNLELGDPDKAEEDFDKALKLNSEDP 399
Score = 31.9 bits (72), Expect = 0.41
Identities = 30/116 (25%), Positives = 48/116 (41%), Gaps = 13/116 (11%)
Query: 78 NFSPTEEVKIEAEKYKNLGNTAMQQDKPEQAVIEYSKAIDCDNSNPVYYCNRAASNNK-- 135
NF +V Y G + Q+K ++A+ ++ AI+ + Y N NK
Sbjct: 462 NFPEAPDV------YNYYGELLLDQNKFDEAIEKFDTAIELEKETKPMYMNVLPLINKAL 515
Query: 136 -----LKNYKLALRDCQIAIKIDPHYAKAYGRMGLAYTQMNDYKAALEAYTKAAEL 186
+++ A C+ A+ IDP A M Q D AL+ + +AAEL
Sbjct: 516 ALFQWKQDFIEAENLCEKALIIDPECDIAVATMAQLLLQQGDVDEALKLFERAAEL 571
Score = 28.4 bits (63), Expect = 5.8
Identities = 13/60 (21%), Positives = 19/60 (31%)
Query: 151 KIDPHYAKAYGRMGLAYTQMNDYKAALEAYTKAAELDPNDPLYANNMQAAMSNLNNSSSA 210
K+ A A G + AL +K+ ELDP + L + A
Sbjct: 325 KLGEKEAIALNLRGTFKCLKGKHLEALADLSKSIELDPRVTQSYIKRASMNLELGDPDKA 384
>gnl|CDD|215568 PLN03088, PLN03088, SGT1, suppressor of G2 allele of SKP1;
Provisional.
Length = 356
Score = 69.0 bits (169), Expect = 3e-13
Identities = 38/100 (38%), Positives = 54/100 (54%)
Query: 99 AMQQDKPEQAVIEYSKAIDCDNSNPVYYCNRAASNNKLKNYKLALRDCQIAIKIDPHYAK 158
A D AV Y++AID D +N Y +RA +N KL N+ A+ D AI++DP AK
Sbjct: 12 AFVDDDFALAVDLYTQAIDLDPNNAELYADRAQANIKLGNFTEAVADANKAIELDPSLAK 71
Query: 159 AYGRMGLAYTQMNDYKAALEAYTKAAELDPNDPLYANNMQ 198
AY R G A ++ +Y+ A A K A L P D + ++
Sbjct: 72 AYLRKGTACMKLEEYQTAKAALEKGASLAPGDSRFTKLIK 111
>gnl|CDD|201277 pfam00515, TPR_1, Tetratricopeptide repeat.
Length = 34
Score = 48.2 bits (116), Expect = 4e-08
Identities = 17/34 (50%), Positives = 22/34 (64%)
Query: 157 AKAYGRMGLAYTQMNDYKAALEAYTKAAELDPND 190
AKA +G AY ++ Y ALE Y KA EL+PN+
Sbjct: 1 AKALYNLGNAYLKLGKYDEALEYYEKALELNPNN 34
Score = 35.9 bits (84), Expect = 0.001
Identities = 8/31 (25%), Positives = 15/31 (48%)
Query: 126 YCNRAASNNKLKNYKLALRDCQIAIKIDPHY 156
N + KL Y AL + A++++P+
Sbjct: 4 LYNLGNAYLKLGKYDEALEYYEKALELNPNN 34
Score = 29.3 bits (67), Expect = 0.22
Identities = 11/34 (32%), Positives = 21/34 (61%)
Query: 89 AEKYKNLGNTAMQQDKPEQAVIEYSKAIDCDNSN 122
A+ NLGN ++ K ++A+ Y KA++ + +N
Sbjct: 1 AKALYNLGNAYLKLGKYDEALEYYEKALELNPNN 34
>gnl|CDD|222123 pfam13432, TPR_16, Tetratricopeptide repeat.
Length = 65
Score = 48.4 bits (116), Expect = 7e-08
Identities = 15/57 (26%), Positives = 23/57 (40%)
Query: 135 KLKNYKLALRDCQIAIKIDPHYAKAYGRMGLAYTQMNDYKAALEAYTKAAELDPNDP 191
+ +Y AL + A+ P A+A +G A + A A DP+DP
Sbjct: 9 RAGDYDEALAALEAALARYPLAAEALLLLGEALLRQGRLAEAAALLRAALAADPDDP 65
>gnl|CDD|223533 COG0457, NrfG, FOG: TPR repeat [General function prediction only].
Length = 291
Score = 52.5 bits (124), Expect = 7e-08
Identities = 50/177 (28%), Positives = 81/177 (45%), Gaps = 3/177 (1%)
Query: 15 FLRKELLRDTLNAESKEGIEVAVECLCKAYDI-PDNIDPASNVDIESLFQLYYKDEVLQW 73
L + LL L E+ E A+E L KA + PD + + + +L++L +E L+
Sbjct: 93 NLAEALLNLGLLLEALGKYEEALELLEKALALDPDPDLAEALLALGALYELGDYEEALEL 152
Query: 74 YSNINFSPTEEVKIEAEKYKNLGNTAMQQDKPEQAVIEYSKAIDCD-NSNPVYYCNRAAS 132
Y E+ AE LG + E+A+ KA+ + + + N
Sbjct: 153 YEKA-LELDPELNELAEALLALGALLEALGRYEEALELLEKALKLNPDDDAEALLNLGLL 211
Query: 133 NNKLKNYKLALRDCQIAIKIDPHYAKAYGRMGLAYTQMNDYKAALEAYTKAAELDPN 189
KL Y+ AL + A+++DP A+A + L ++ Y+ ALEA KA ELDP+
Sbjct: 212 YLKLGKYEEALEYYEKALELDPDNAEALYNLALLLLELGRYEEALEALEKALELDPD 268
Score = 50.6 bits (119), Expect = 3e-07
Identities = 38/127 (29%), Positives = 57/127 (44%), Gaps = 5/127 (3%)
Query: 88 EAEKYKNLGNTAMQQDKPEQAVIEYSKAIDCD---NSNPVYYCNRAASNNKLKNYKLALR 144
AE LG + E+A+ Y KA++ D N A L Y+ AL
Sbjct: 130 LAEALLALG-ALYELGDYEEALELYEKALELDPELNELAEALLALGALLEALGRYEEALE 188
Query: 145 DCQIAIKIDP-HYAKAYGRMGLAYTQMNDYKAALEAYTKAAELDPNDPLYANNMQAAMSN 203
+ A+K++P A+A +GL Y ++ Y+ ALE Y KA ELDP++ N+ +
Sbjct: 189 LLEKALKLNPDDDAEALLNLGLLYLKLGKYEEALEYYEKALELDPDNAEALYNLALLLLE 248
Query: 204 LNNSSSA 210
L A
Sbjct: 249 LGRYEEA 255
Score = 37.1 bits (84), Expect = 0.008
Identities = 28/98 (28%), Positives = 42/98 (42%), Gaps = 6/98 (6%)
Query: 86 KIEAEKYKNLGNTAMQQDKPEQAVIEYSKAIDCDNSNPVYYCNRAASNNKLKNYKLALRD 145
+AE NLG ++ K E+A+ Y KA++ D N N A +L Y+ AL
Sbjct: 199 DDDAEALLNLGLLYLKLGKYEEALEYYEKALELDPDNAEALYNLALLLLELGRYEEALEA 258
Query: 146 CQIAIKIDPHYAKAYGRMGLAYTQMNDYKAALEAYTKA 183
+ A+++DP L + ALE KA
Sbjct: 259 LEKALELDPDLY------NLGLALLLLLAEALELLEKA 290
Score = 36.4 bits (82), Expect = 0.014
Identities = 25/124 (20%), Positives = 47/124 (37%), Gaps = 5/124 (4%)
Query: 83 EEVKIEAEKYKNLGNTAMQQDKPEQAVIEYSKA---IDCDNSNPVYYCNRAASNNKLKNY 139
++ EA G ++ +E + + ++ A + KL
Sbjct: 16 AKLLAEALALLEAGLALLELLGELAEALELLEEALELLPNSDLAGLLLLLALALLKLGRL 75
Query: 140 KLALRDCQIAIK--IDPHYAKAYGRMGLAYTQMNDYKAALEAYTKAAELDPNDPLYANNM 197
+ AL + A++ + P+ A+A +GL + Y+ ALE KA LDP+ L +
Sbjct: 76 EEALELLEKALELELLPNLAEALLNLGLLLEALGKYEEALELLEKALALDPDPDLAEALL 135
Query: 198 QAAM 201
Sbjct: 136 ALGA 139
>gnl|CDD|197478 smart00028, TPR, Tetratricopeptide repeats. Repeats present in 4
or more copies in proteins. Contain a minimum of 34
amino acids each and self-associate via a "knobs and
holes" mechanism.
Length = 34
Score = 45.9 bits (110), Expect = 2e-07
Identities = 18/34 (52%), Positives = 23/34 (67%)
Query: 157 AKAYGRMGLAYTQMNDYKAALEAYTKAAELDPND 190
A+A +G AY ++ DY ALE Y KA ELDPN+
Sbjct: 1 AEALYNLGNAYLKLGDYDEALEYYEKALELDPNN 34
Score = 35.9 bits (84), Expect = 9e-04
Identities = 9/34 (26%), Positives = 16/34 (47%)
Query: 123 PVYYCNRAASNNKLKNYKLALRDCQIAIKIDPHY 156
N + KL +Y AL + A+++DP+
Sbjct: 1 AEALYNLGNAYLKLGDYDEALEYYEKALELDPNN 34
Score = 32.4 bits (75), Expect = 0.016
Identities = 12/34 (35%), Positives = 20/34 (58%)
Query: 89 AEKYKNLGNTAMQQDKPEQAVIEYSKAIDCDNSN 122
AE NLGN ++ ++A+ Y KA++ D +N
Sbjct: 1 AEALYNLGNAYLKLGDYDEALEYYEKALELDPNN 34
>gnl|CDD|205602 pfam13424, TPR_12, Tetratricopeptide repeat.
Length = 78
Score = 46.6 bits (111), Expect = 4e-07
Identities = 19/72 (26%), Positives = 28/72 (38%), Gaps = 7/72 (9%)
Query: 125 YYCNRAASNNKLKNYKLALRDCQIAIKI-------DPHYAKAYGRMGLAYTQMNDYKAAL 177
N A +L +Y AL + A+++ P A+A + Y + DY AL
Sbjct: 7 ALNNLALVLRRLGDYDEALELLEKALELARELGEDHPETARALNNLARLYLALGDYDEAL 66
Query: 178 EAYTKAAELDPN 189
E KA L
Sbjct: 67 EYLEKALALREA 78
Score = 35.4 bits (82), Expect = 0.004
Identities = 15/49 (30%), Positives = 20/49 (40%), Gaps = 4/49 (8%)
Query: 153 DPHYAKAYGRMGLAYTQMNDYKAALEAYTKAAE----LDPNDPLYANNM 197
P A A + L ++ DY ALE KA E L + P A +
Sbjct: 1 HPDLAAALNNLALVLRRLGDYDEALELLEKALELARELGEDHPETARAL 49
>gnl|CDD|227343 COG5010, TadD, Flp pilus assembly protein TadD, contains TPR
repeats [Intracellular trafficking and secretion].
Length = 257
Score = 47.0 bits (112), Expect = 4e-06
Identities = 23/67 (34%), Positives = 36/67 (53%), Gaps = 2/67 (2%)
Query: 138 NYKLALRDCQIAIKIDPHYAKAYGRMGLAYTQMNDYKAALEAYTKAAELDPNDPLYANNM 197
N+ A+ + A ++ P +A+ +G A Q+ + A AY +A EL PN+P ANN+
Sbjct: 115 NFGEAVSVLRKAARLAPTDWEAWNLLGAALDQLGRFDEARRAYRQALELAPNEPSIANNL 174
Query: 198 QAAMSNL 204
MS L
Sbjct: 175 --GMSLL 179
Score = 30.5 bits (69), Expect = 1.1
Identities = 17/104 (16%), Positives = 36/104 (34%)
Query: 93 KNLGNTAMQQDKPEQAVIEYSKAIDCDNSNPVYYCNRAASNNKLKNYKLALRDCQIAIKI 152
G ++ +AV KA ++ + A+ ++L + A R + A+++
Sbjct: 104 AAQGKNQIRNGNFGEAVSVLRKAARLAPTDWEAWNLLGAALDQLGRFDEARRAYRQALEL 163
Query: 153 DPHYAKAYGRMGLAYTQMNDYKAALEAYTKAAELDPNDPLYANN 196
P+ +G++ D + A A D N
Sbjct: 164 APNEPSIANNLGMSLLLRGDLEDAETLLLPAYLSPAADSRVRQN 207
>gnl|CDD|191825 pfam07719, TPR_2, Tetratricopeptide repeat. This Pfam entry
includes outlying Tetratricopeptide-like repeats (TPR)
that are not matched by pfam00515.
Length = 34
Score = 41.7 bits (99), Expect = 7e-06
Identities = 20/34 (58%), Positives = 26/34 (76%)
Query: 157 AKAYGRMGLAYTQMNDYKAALEAYTKAAELDPND 190
A+A +GLAY ++ DY+ ALEAY KA ELDPN+
Sbjct: 1 AEALYNLGLAYYKLGDYEEALEAYEKALELDPNN 34
Score = 29.0 bits (66), Expect = 0.26
Identities = 12/34 (35%), Positives = 18/34 (52%)
Query: 89 AEKYKNLGNTAMQQDKPEQAVIEYSKAIDCDNSN 122
AE NLG + E+A+ Y KA++ D +N
Sbjct: 1 AEALYNLGLAYYKLGDYEEALEAYEKALELDPNN 34
>gnl|CDD|236875 PRK11189, PRK11189, lipoprotein NlpI; Provisional.
Length = 296
Score = 45.3 bits (108), Expect = 2e-05
Identities = 16/41 (39%), Positives = 23/41 (56%)
Query: 149 AIKIDPHYAKAYGRMGLAYTQMNDYKAALEAYTKAAELDPN 189
A+ + P A AY +G+ TQ ++ AA EA+ ELDP
Sbjct: 90 ALALRPDMADAYNYLGIYLTQAGNFDAAYEAFDSVLELDPT 130
Score = 29.5 bits (67), Expect = 1.9
Identities = 19/65 (29%), Positives = 28/65 (43%), Gaps = 9/65 (13%)
Query: 149 AIKIDPHYAKAYGRMGLAYTQMNDYKAALEAYTKAAELDPNDP-----LYAN----NMQA 199
+++DP Y AY G+A Y+ A + + DPNDP LY + +
Sbjct: 124 VLELDPTYNYAYLNRGIALYYGGRYELAQDDLLAFYQDDPNDPYRALWLYLAESKLDPKQ 183
Query: 200 AMSNL 204
A NL
Sbjct: 184 AKENL 188
>gnl|CDD|131573 TIGR02521, type_IV_pilW, type IV pilus biogenesis/stability protein
PilW. Members of this family are designated PilF in ref
(PMID:8973346) and PilW in ref (PMID:15612916). This
outer membrane protein is required both for pilus
stability and for pilus function such as adherence to
human cells. Members of this family contain copies of
the TPR (tetratricopeptide repeat) domain.
Length = 234
Score = 43.5 bits (103), Expect = 4e-05
Identities = 16/59 (27%), Positives = 32/59 (54%)
Query: 138 NYKLALRDCQIAIKIDPHYAKAYGRMGLAYTQMNDYKAALEAYTKAAELDPNDPLYANN 196
+ ++A + A++ DP AY + L Y Q+ + + A +++ +A L+PN+ NN
Sbjct: 46 DLEVAKENLDKALEHDPDDYLAYLALALYYQQLGELEKAEDSFRRALTLNPNNGDVLNN 104
Score = 33.5 bits (77), Expect = 0.092
Identities = 16/43 (37%), Positives = 21/43 (48%), Gaps = 1/43 (2%)
Query: 157 AKAYGRMGLAYTQMNDYKAALEAYTKAAELDPNDPLYANNMQA 199
AK ++ L Y + D + A E KA E DP+D L A A
Sbjct: 31 AKIRVQLALGYLEQGDLEVAKENLDKALEHDPDDYL-AYLALA 72
Score = 33.5 bits (77), Expect = 0.11
Identities = 24/105 (22%), Positives = 43/105 (40%), Gaps = 4/105 (3%)
Query: 89 AEKYKNLGNTAMQQDKPEQAVIEYSKAIDCDNSNPVYYCNRAASNNKLKNYKLALRDCQI 148
A+ L ++Q E A KA++ D + + Y A +L + A +
Sbjct: 31 AKIRVQLALGYLEQGDLEVAKENLDKALEHDPDDYLAYLALALYYQQLGELEKAEDSFRR 90
Query: 149 AIKIDPHYAKAYGRMGLAYTQMNDYKAALEAYTKAAELDPNDPLY 193
A+ ++P+ G Q Y+ A++ + +A E DPLY
Sbjct: 91 ALTLNPNNGDVLNNYGTFLCQQGKYEQAMQQFEQAIE----DPLY 131
Score = 32.3 bits (74), Expect = 0.24
Identities = 23/101 (22%), Positives = 45/101 (44%), Gaps = 4/101 (3%)
Query: 100 MQQDKPEQAVIEYSKAIDCDNSNPVYYCNRAASNNKLKNYKLALRDCQIAIKIDPHY--- 156
Q + E+A + +A+ + +N N + Y+ A++ + AI+ DP Y
Sbjct: 76 QQLGELEKAEDSFRRALTLNPNNGDVLNNYGTFLCQQGKYEQAMQQFEQAIE-DPLYPQP 134
Query: 157 AKAYGRMGLAYTQMNDYKAALEAYTKAAELDPNDPLYANNM 197
A++ GL + D+ A + T+A ++DP P +
Sbjct: 135 ARSLENAGLCALKAGDFDKAEKYLTRALQIDPQRPESLLEL 175
>gnl|CDD|234059 TIGR02917, PEP_TPR_lipo, putative PEP-CTERM system TPR-repeat
lipoprotein. This protein family occurs in strictly
within a subset of Gram-negative bacterial species with
the proposed PEP-CTERM/exosortase system, analogous to
the LPXTG/sortase system common in Gram-positive
bacteria. This protein occurs in a species if and only
if a transmembrane histidine kinase (TIGR02916) and a
DNA-binding response regulator (TIGR02915) also occur.
The present of tetratricopeptide repeats (TPR) suggests
protein-protein interaction, possibly for the regulation
of PEP-CTERM protein expression, since many PEP-CTERM
proteins in these genomes are preceded by a proposed DNA
binding site for the response regulator.
Length = 899
Score = 43.9 bits (104), Expect = 8e-05
Identities = 40/227 (17%), Positives = 79/227 (34%), Gaps = 16/227 (7%)
Query: 50 IDPASNVDIESLFQLYYK----DEVLQWYSNINFSPTEEVKIEAEKYKNLGNTAMQQDKP 105
IDP + I +L LY + +E + W E E E L + + +
Sbjct: 528 IDPKNLRAILALAGLYLRTGNEEEAVAWLE----KAAELNPQEIEPALALAQYYLGKGQL 583
Query: 106 EQAVIEYSKAIDCDNSNPVYYCNRAASNNKLKNYKLALRDCQIAIKIDPHYAKAYGRMGL 165
++A+ ++A D +P + + + A+ + + + P A A +
Sbjct: 584 KKALAILNEAADAAPDSPEAWLMLGRAQLAAGDLNKAVSSFKKLLALQPDSALALLLLAD 643
Query: 166 AYTQMNDYKAALEAYTKAAELDPNDPLYANNMQAAMSNLNNSSSASGSGGVFPGLSEMST 225
AY M +Y A+ + +A EL P D A A + + ++ +
Sbjct: 644 AYAVMKNYAKAITSLKRALELKP-DNTEAQIGLAQLLLAAKRTESA-----KKIAKSLQK 697
Query: 226 KVLSDPSIQQVFGELFANPGQQATATDGSNTGIQALLNASQQIAAQL 272
+ ++ G+L+ A ++ S Q A +L
Sbjct: 698 QHPKAALGFELEGDLYLRQKDYPAAIQAYRKALK--RAPSSQNAIKL 742
Score = 41.2 bits (97), Expect = 6e-04
Identities = 20/95 (21%), Positives = 34/95 (35%)
Query: 95 LGNTAMQQDKPEQAVIEYSKAIDCDNSNPVYYCNRAASNNKLKNYKLALRDCQIAIKIDP 154
G+ + E A+ Y KAI +N A + ++ A + +K P
Sbjct: 199 KGDLLLSLGNIELALAAYRKAIALRPNNIAVLLALATILIEAGEFEEAEKHADALLKKAP 258
Query: 155 HYAKAYGRMGLAYTQMNDYKAALEAYTKAAELDPN 189
+ A+ L Q +Y+ A E A + P
Sbjct: 259 NSPLAHYLKALVDFQKKNYEDARETLQDALKSAPE 293
Score = 40.1 bits (94), Expect = 0.001
Identities = 28/110 (25%), Positives = 45/110 (40%), Gaps = 2/110 (1%)
Query: 95 LGNTAMQQDKPEQAVIEYSKAIDCDNSNPVYYCNRAASNNKLKNYKLALRDCQIAIKIDP 154
G + Q EQA ++ + ++ A+ +L A+ A+ +DP
Sbjct: 301 AGASEYQLGNLEQAYQYLNQILKYAPNSHQARRLLASIQLRLGRVDEAIATLSPALGLDP 360
Query: 155 HYAKAYGRMGLAYTQMNDYKAALEAYTKAAELDPNDPLYANNMQAAMSNL 204
A +G AY + D++ A E KA ELDP + A Q +S L
Sbjct: 361 DDPAALSLLGEAYLALGDFEKAAEYLAKATELDPENA--AARTQLGISKL 408
Score = 37.4 bits (87), Expect = 0.008
Identities = 23/111 (20%), Positives = 46/111 (41%), Gaps = 3/111 (2%)
Query: 88 EAEKYKNLGNTAMQQDKPEQAVIEYSKAIDCD-NSNPVYYCNRAASNNKLKNYKLALRDC 146
A ++ G+ ++Q A+ Y KA+ +S +RA + N A++
Sbjct: 702 AALGFELEGDLYLRQKDYPAAIQAYRKALKRAPSSQNAIKLHRALLASG--NTAEAVKTL 759
Query: 147 QIAIKIDPHYAKAYGRMGLAYTQMNDYKAALEAYTKAAELDPNDPLYANNM 197
+ +K P+ A + Y DY A++ Y + P++ + NN+
Sbjct: 760 EAWLKTHPNDAVLRTALAELYLAQKDYDKAIKHYQTVVKKAPDNAVVLNNL 810
Score = 36.2 bits (84), Expect = 0.021
Identities = 25/116 (21%), Positives = 45/116 (38%)
Query: 95 LGNTAMQQDKPEQAVIEYSKAIDCDNSNPVYYCNRAASNNKLKNYKLALRDCQIAIKIDP 154
LG + E+A +KA + D N S + A+ D + A ++DP
Sbjct: 369 LGEAYLALGDFEKAAEYLAKATELDPENAAARTQLGISKLSQGDPSEAIADLETAAQLDP 428
Query: 155 HYAKAYGRMGLAYTQMNDYKAALEAYTKAAELDPNDPLYANNMQAAMSNLNNSSSA 210
+A + L+Y + + AL A K + P++ N + A + + A
Sbjct: 429 ELGRADLLLILSYLRSGQFDKALAAAKKLEKKQPDNASLHNLLGAIYLGKGDLAKA 484
>gnl|CDD|205362 pfam13181, TPR_8, Tetratricopeptide repeat.
Length = 34
Score = 38.2 bits (90), Expect = 1e-04
Identities = 18/33 (54%), Positives = 22/33 (66%)
Query: 157 AKAYGRMGLAYTQMNDYKAALEAYTKAAELDPN 189
A+AY +G Y Q+ DY+ A E Y KA ELDPN
Sbjct: 1 ARAYYLLGQIYLQLGDYEEAKEYYEKALELDPN 33
Score = 24.7 bits (55), Expect = 8.5
Identities = 11/31 (35%), Positives = 16/31 (51%)
Query: 92 YKNLGNTAMQQDKPEQAVIEYSKAIDCDNSN 122
Y LG +Q E+A Y KA++ D +N
Sbjct: 4 YYLLGQIYLQLGDYEEAKEYYEKALELDPNN 34
>gnl|CDD|227122 COG4783, COG4783, Putative Zn-dependent protease, contains TPR
repeats [General function prediction only].
Length = 484
Score = 41.2 bits (97), Expect = 5e-04
Identities = 20/93 (21%), Positives = 41/93 (44%)
Query: 95 LGNTAMQQDKPEQAVIEYSKAIDCDNSNPVYYCNRAASNNKLKNYKLALRDCQIAIKIDP 154
G+ ++ +K ++A+ KA+ D ++P+ N A + K + A+R + DP
Sbjct: 346 AGDILLEANKAKEAIERLKKALALDPNSPLLQLNLAQALLKGGKPQEAIRILNRYLFNDP 405
Query: 155 HYAKAYGRMGLAYTQMNDYKAALEAYTKAAELD 187
+ + AY ++ + AL A + L
Sbjct: 406 EDPNGWDLLAQAYAELGNRAEALLARAEGYALA 438
Score = 27.8 bits (62), Expect = 9.5
Identities = 25/116 (21%), Positives = 35/116 (30%), Gaps = 8/116 (6%)
Query: 171 NDYKAALEAYTKAAELDPNDPLYANNMQAAMSNLNNSSSASGSGGVFPGLSEMSTKVLSD 230
N K A+E KA LDPN PL N+ A+ A L+ D
Sbjct: 354 NKAKEAIERLKKALALDPNSPLLQLNLAQALLKGGKPQEA------IRILNRYLFNDPED 407
Query: 231 PSIQQVFGELFANPGQQATATDGSNTGIQALLNASQQIAAQLEQRNPELVEQIFQQ 286
P+ + + A A L + A R + V+ F
Sbjct: 408 PNGWDLLAQ--AYAELGNRAEALLARAEGYALAGRLEQAIIFLMRASQQVKLGFPD 461
>gnl|CDD|205550 pfam13371, TPR_9, Tetratricopeptide repeat.
Length = 73
Score = 37.6 bits (88), Expect = 5e-04
Identities = 14/55 (25%), Positives = 25/55 (45%)
Query: 137 KNYKLALRDCQIAIKIDPHYAKAYGRMGLAYTQMNDYKAALEAYTKAAELDPNDP 191
++++ AL + + + P GL Y Q+ ++AAL EL P+ P
Sbjct: 9 EDFERALAVVERLLLLAPDDPYERRDRGLLYAQLGCFQAALADLEYFLELCPDAP 63
>gnl|CDD|227124 COG4785, NlpI, Lipoprotein NlpI, contains TPR repeats [General
function prediction only].
Length = 297
Score = 38.6 bits (90), Expect = 0.002
Identities = 17/48 (35%), Positives = 25/48 (52%)
Query: 141 LALRDCQIAIKIDPHYAKAYGRMGLAYTQMNDYKAALEAYTKAAELDP 188
LA D A+ I P + + +G+ TQ ++ AA EA+ ELDP
Sbjct: 83 LARNDFSQALAIRPDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLELDP 130
Score = 30.6 bits (69), Expect = 0.88
Identities = 22/76 (28%), Positives = 33/76 (43%), Gaps = 9/76 (11%)
Query: 138 NYKLALRDCQIAIKIDPHYAKAYGRMGLAYTQMNDYKAALEAYTKAAELDPNDP-----L 192
N+ A +++DP Y A+ G+A YK A + + DPNDP L
Sbjct: 114 NFDAAYEAFDSVLELDPTYNYAHLNRGIALYYGGRYKLAQDDLLAFYQDDPNDPFRSLWL 173
Query: 193 YAN----NMQAAMSNL 204
Y N + + A +NL
Sbjct: 174 YLNEQKLDPKQAKTNL 189
>gnl|CDD|225605 COG3063, PilF, Tfp pilus assembly protein PilF [Cell motility and
secretion / Intracellular trafficking and secretion].
Length = 250
Score = 38.2 bits (89), Expect = 0.003
Identities = 18/59 (30%), Positives = 30/59 (50%)
Query: 138 NYKLALRDCQIAIKIDPHYAKAYGRMGLAYTQMNDYKAALEAYTKAAELDPNDPLYANN 196
+Y A ++ + A++ DP Y A+ Y ++ + A E+Y KA L PN+ NN
Sbjct: 50 DYAQAKKNLEKALEHDPSYYLAHLVRAHYYQKLGENDLADESYRKALSLAPNNGDVLNN 108
Score = 33.6 bits (77), Expect = 0.096
Identities = 30/140 (21%), Positives = 44/140 (31%), Gaps = 36/140 (25%)
Query: 89 AEKYKNLGNTAMQQDKPEQAVIEYSKAIDCDNSNPVYYCNRAASNNKLKNYKLALRDCQI 148
A+ L +QQ QA KA++ D S + + RA KL LA +
Sbjct: 35 AKARLQLALGYLQQGDYAQAKKNLEKALEHDPSYYLAHLVRAHYYQKLGENDLADESYRK 94
Query: 149 AIKI---------------------------------DPHY---AKAYGRMGLAYTQMND 172
A+ + DP Y + +GL +
Sbjct: 95 ALSLAPNNGDVLNNYGAFLCAQGRPEEAMQQFERALADPAYGEPSDTLENLGLCALKAGQ 154
Query: 173 YKAALEAYTKAAELDPNDPL 192
+ A E +A ELDP P
Sbjct: 155 FDQAEEYLKRALELDPQFPP 174
Score = 28.2 bits (63), Expect = 4.7
Identities = 13/61 (21%), Positives = 26/61 (42%), Gaps = 3/61 (4%)
Query: 63 QLYYKDEVLQWYSNINFSPTEEVKIEAEKYKNLGNTAMQQDKPEQAVIEYSKAIDCDNSN 122
Q +E +Q + P ++ +NLG A++ + +QA +A++ D
Sbjct: 116 QGRP-EEAMQQFERALADPA--YGEPSDTLENLGLCALKAGQFDQAEEYLKRALELDPQF 172
Query: 123 P 123
P
Sbjct: 173 P 173
>gnl|CDD|236983 PRK11788, PRK11788, tetratricopeptide repeat protein; Provisional.
Length = 389
Score = 38.3 bits (90), Expect = 0.003
Identities = 18/64 (28%), Positives = 26/64 (40%)
Query: 125 YYCNRAASNNKLKNYKLALRDCQIAIKIDPHYAKAYGRMGLAYTQMNDYKAALEAYTKAA 184
+YC A + A + A+ DP +A +G DY AA+EA +
Sbjct: 182 FYCELAQQALARGDLDAARALLKKALAADPQCVRASILLGDLALAQGDYAAAIEALERVE 241
Query: 185 ELDP 188
E DP
Sbjct: 242 EQDP 245
>gnl|CDD|176974 CHL00033, ycf3, photosystem I assembly protein Ycf3.
Length = 168
Score = 36.1 bits (84), Expect = 0.009
Identities = 24/64 (37%), Positives = 36/64 (56%), Gaps = 8/64 (12%)
Query: 136 LKNYKLALRDCQIAIKIDPHYAKAY--GRMGLAYTQMNDYKAALEAYTKAAELDPNDPLY 193
L+NY A+R ++IDP Y ++Y +GL +T ++ ALE Y +A E +P P
Sbjct: 55 LQNYYEAMR-----LEIDP-YDRSYILYNIGLIHTSNGEHTKALEYYFQALERNPFLPQA 108
Query: 194 ANNM 197
NNM
Sbjct: 109 LNNM 112
>gnl|CDD|233924 TIGR02552, LcrH_SycD, type III secretion low calcium response
chaperone LcrH/SycD. Genes in this family are found in
type III secretion operons. LcrH, from Yersinia is
believed to have a regulatory function in the
low-calcium response of the secretion system. The same
protein is also known as SycD (SYC = Specific Yop
Chaperone) for its chaperone role. In Pseudomonas, where
the homolog is known as PcrH, the chaperone role has
been demonstrated and the regulatory role appears to be
absent. ScyD/LcrH contains three central
tetratricopeptide-like repeats that are predicted to
fold into an all-alpha-helical array.
Length = 135
Score = 34.6 bits (80), Expect = 0.018
Identities = 23/97 (23%), Positives = 42/97 (43%)
Query: 98 TAMQQDKPEQAVIEYSKAIDCDNSNPVYYCNRAASNNKLKNYKLALRDCQIAIKIDPHYA 157
QQ + ++A+ + D N Y+ AA LK Y+ A+ +A +DP
Sbjct: 26 NLYQQGRYDEALKLFQLLAAYDPYNSRYWLGLAACCQMLKEYEEAIDAYALAAALDPDDP 85
Query: 158 KAYGRMGLAYTQMNDYKAALEAYTKAAELDPNDPLYA 194
+ Y + + ++AL+A A E+ +P Y+
Sbjct: 86 RPYFHAAECLLALGEPESALKALDLAIEICGENPEYS 122
Score = 33.4 bits (77), Expect = 0.042
Identities = 17/67 (25%), Positives = 30/67 (44%), Gaps = 3/67 (4%)
Query: 95 LGNTAMQQDKPEQAVIEYSKAIDCDNSNPVYYCNRAASNNKLKNYKLALRDCQIAIKI-- 152
L + E+A+ Y+ A D +P Y + A L + AL+ +AI+I
Sbjct: 57 LAACCQMLKEYEEAIDAYALAAALDPDDPRPYFHAAECLLALGEPESALKALDLAIEICG 116
Query: 153 -DPHYAK 158
+P Y++
Sbjct: 117 ENPEYSE 123
>gnl|CDD|226687 COG4235, COG4235, Cytochrome c biogenesis factor [Posttranslational
modification, protein turnover, chaperones].
Length = 287
Score = 35.4 bits (82), Expect = 0.027
Identities = 15/63 (23%), Positives = 27/63 (42%), Gaps = 1/63 (1%)
Query: 129 RAASNNKLKNYKLALRDCQIAIKIDPHYAKAYGRMGLAYTQMNDYKAALEAYTKAAELDP 188
A + + L R + ++ +P A+ + +G AY + AL AY A L
Sbjct: 129 LAQPPAEQEMEALIAR-LETHLQQNPGDAEGWDLLGRAYMALGRASDALLAYRNALRLAG 187
Query: 189 NDP 191
++P
Sbjct: 188 DNP 190
Score = 34.7 bits (80), Expect = 0.049
Identities = 26/108 (24%), Positives = 39/108 (36%), Gaps = 9/108 (8%)
Query: 89 AEKYKNLGNTAMQQDKPEQAVIEYSKAIDCDNSNPVYYCNRA----ASNNKLKNYK--LA 142
AE + LG M + A++ Y A+ NP A + K
Sbjct: 156 AEGWDLLGRAYMALGRASDALLAYRNALRLAGDNPEILLGLAEALYYQAGQQMTAKARAL 215
Query: 143 LRDCQIAIKIDPHYAKAYGRMGLAYTQMNDYKAALEAYTKAAELDPND 190
LR A+ +DP +A + A + DY A A+ +L P D
Sbjct: 216 LRQ---ALALDPANIRALSLLAFAAFEQGDYAEAAAAWQMLLDLLPAD 260
>gnl|CDD|225464 COG2912, COG2912, Uncharacterized conserved protein [Function
unknown].
Length = 269
Score = 35.0 bits (81), Expect = 0.034
Identities = 17/55 (30%), Positives = 26/55 (47%)
Query: 137 KNYKLALRDCQIAIKIDPHYAKAYGRMGLAYTQMNDYKAALEAYTKAAELDPNDP 191
++LALR + + ++P GL Y Q+ Y ALE + E P+DP
Sbjct: 195 LQWELALRVAERLLDLNPEDPYEIRDRGLIYAQLGCYHVALEDLSYFVEHCPDDP 249
>gnl|CDD|205609 pfam13431, TPR_17, Tetratricopeptide repeat.
Length = 34
Score = 31.4 bits (72), Expect = 0.037
Identities = 10/33 (30%), Positives = 19/33 (57%)
Query: 146 CQIAIKIDPHYAKAYGRMGLAYTQMNDYKAALE 178
+ A+++DP+ A+AY + L + Y AL+
Sbjct: 2 YEKALELDPNNAEAYYNLALLLLNLGQYDEALQ 34
Score = 27.5 bits (62), Expect = 0.93
Identities = 12/34 (35%), Positives = 16/34 (47%)
Query: 111 EYSKAIDCDNSNPVYYCNRAASNNKLKNYKLALR 144
Y KA++ D +N Y N A L Y AL+
Sbjct: 1 LYEKALELDPNNAEAYYNLALLLLNLGQYDEALQ 34
>gnl|CDD|221958 pfam13176, TPR_7, Tetratricopeptide repeat.
Length = 36
Score = 31.4 bits (72), Expect = 0.041
Identities = 12/35 (34%), Positives = 18/35 (51%), Gaps = 2/35 (5%)
Query: 159 AYGRMGLAYTQMNDYKAALEAYTKAAEL--DPNDP 191
A +G Y ++ DY+ A+ Y +A L DP D
Sbjct: 1 ALSNLGRLYRKLGDYEKAISLYERALALAKDPEDR 35
>gnl|CDD|233999 TIGR02757, TIGR02757, TIGR02757 family protein. Members of this
uncharacterized protein family are found sporadically,
so far only among spirochetes, epsilon and delta
proteobacteria, and Bacteroides. The function is unknown
and its gene neighborhoods show little conservation
[Hypothetical proteins, Conserved].
Length = 229
Score = 34.4 bits (79), Expect = 0.045
Identities = 13/42 (30%), Positives = 21/42 (50%)
Query: 150 IKIDPHYAKAYGRMGLAYTQMNDYKAALEAYTKAAELDPNDP 191
+ +D H + ++ L + D KAA+E EL+P DP
Sbjct: 174 LPLDTHVFRIAKKLKLLKRKSYDLKAAIEITEALRELNPEDP 215
>gnl|CDD|222121 pfam13428, TPR_14, Tetratricopeptide repeat.
Length = 44
Score = 31.4 bits (71), Expect = 0.050
Identities = 11/35 (31%), Positives = 15/35 (42%)
Query: 157 AKAYGRMGLAYTQMNDYKAALEAYTKAAELDPNDP 191
A + A + D AL +A LDP+DP
Sbjct: 1 PAALLALARALLALGDLDEALALLRRALALDPDDP 35
>gnl|CDD|183140 PRK11447, PRK11447, cellulose synthase subunit BcsC; Provisional.
Length = 1157
Score = 34.7 bits (80), Expect = 0.063
Identities = 17/50 (34%), Positives = 29/50 (58%)
Query: 142 ALRDCQIAIKIDPHYAKAYGRMGLAYTQMNDYKAALEAYTKAAELDPNDP 191
A+ + Q A++ +P ++A G +G AY+Q D A+ + KA LDP+
Sbjct: 288 AIPELQQAVRANPKDSEALGALGQAYSQQGDRARAVAQFEKALALDPHSS 337
Score = 28.9 bits (65), Expect = 4.1
Identities = 30/110 (27%), Positives = 43/110 (39%), Gaps = 18/110 (16%)
Query: 95 LGNTAMQQDKPEQAVIEYSKAIDCDNSNP------------VYYCNRAASNNKLK--NYK 140
LG QQ +AV ++ KA+ D + Y+ + LK N
Sbjct: 309 LGQAYSQQGDRARAVAQFEKALALDPHSSNRDKWESLLKVNRYWLLIQQGDAALKANNLA 368
Query: 141 LALRDCQIAIKIDPHYAKAYGRMGLAYTQM--NDYKAALEAYTKAAELDP 188
A R Q A ++D +Y +GL M DY AA Y +A +DP
Sbjct: 369 QAERLYQQARQVDN--TDSYAVLGLGDVAMARKDYAAAERYYQQALRMDP 416
>gnl|CDD|198111 smart01043, BTAD, Bacterial transcriptional activator domain.
Found in the DNRI/REDD/AFSR family of regulators. This
region of AFSR along with the C terminal region is
capable of independently directing actinorhodin
production. This family contains TPR repeats.
Length = 145
Score = 33.0 bits (76), Expect = 0.066
Identities = 12/58 (20%), Positives = 23/58 (39%)
Query: 129 RAASNNKLKNYKLALRDCQIAIKIDPHYAKAYGRMGLAYTQMNDYKAALEAYTKAAEL 186
A + L ++ AL + + +DP + + + A + AL AY + L
Sbjct: 67 LAEALLALGRHEEALALLERLLALDPLRERLHRLLMRALYRAGRRAEALRAYRRLRRL 124
Score = 32.3 bits (74), Expect = 0.12
Identities = 10/46 (21%), Positives = 19/46 (41%), Gaps = 1/46 (2%)
Query: 155 HYAKAYGRMGLAYTQMNDYKAALEAYTKAAELDP-NDPLYANNMQA 199
+A + A + ++ AL + LDP + L+ M+A
Sbjct: 59 LRLEALEALAEALLALGRHEEALALLERLLALDPLRERLHRLLMRA 104
>gnl|CDD|220339 pfam09674, DUF2400, Protein of unknown function (DUF2400). Members
of this uncharacterized protein family are found
sporadically, so far only among spirochetes, epsilon and
delta proteobacteria, and Bacteroides. The function is
unknown and its gene neighborhoods show little
conservation.
Length = 230
Score = 33.3 bits (77), Expect = 0.12
Identities = 18/46 (39%), Positives = 25/46 (54%)
Query: 146 CQIAIKIDPHYAKAYGRMGLAYTQMNDYKAALEAYTKAAELDPNDP 191
Q+ I +D H + ++GL + D KAALE ELDP+DP
Sbjct: 171 SQLIIPLDTHTHRVARKLGLLKRKQYDLKAALEITAALRELDPDDP 216
>gnl|CDD|179448 PRK02603, PRK02603, photosystem I assembly protein Ycf3;
Provisional.
Length = 172
Score = 32.0 bits (73), Expect = 0.20
Identities = 14/35 (40%), Positives = 20/35 (57%)
Query: 163 MGLAYTQMNDYKAALEAYTKAAELDPNDPLYANNM 197
MG+ Y ++ ALE Y +A EL+P P NN+
Sbjct: 78 MGIIYASNGEHDKALEYYHQALELNPKQPSALNNI 112
Score = 27.7 bits (62), Expect = 6.1
Identities = 15/36 (41%), Positives = 20/36 (55%), Gaps = 2/36 (5%)
Query: 157 AKAYGRMGLAYTQMNDYKAALEAYTKAAEL--DPND 190
A Y R G++ +Y ALE Y +A +L DPND
Sbjct: 35 AFVYYRDGMSAQADGEYAEALENYEEALKLEEDPND 70
>gnl|CDD|221956 pfam13174, TPR_6, Tetratricopeptide repeat.
Length = 33
Score = 29.0 bits (66), Expect = 0.27
Identities = 8/29 (27%), Positives = 15/29 (51%)
Query: 162 RMGLAYTQMNDYKAALEAYTKAAELDPND 190
++ LAY ++ D A EA + + P+
Sbjct: 5 KLALAYLKLGDTDEAKEALERLLKRYPDS 33
>gnl|CDD|176790 cd08812, CARD_RIG-I_like, Caspase activation and recruitment
domains found in RIG-I-like DEAD box helicases.
Caspase activation and recruitment domains (CARDs)
found in Retinoic acid Inducible Gene I (RIG-I)-like
DEAD box helicases. These helicases, including MDA5 and
RIG-I, contain two N-terminal CARD domains and a
C-terminal DEAD box RNA helicase domain. They are
cytoplasmic RNA helicases that play an important role
in host antiviral response by sensing incoming viral
RNA. Upon activation, the signal is transferred to
downstream pathways via the adaptor molecule IPS-1
(MAVS, VISA, CARDIF), leading to the induction of type
I interferons. Although very similar in sequence, RIG-I
and MDA5 have been shown to recognize different sets of
viruses. MDA5 and RIG-I associate with IPS-1 through a
CARD-CARD interaction. In general, CARDs are death
domains (DDs) found associated with caspases. They are
known to be important in the signaling pathways for
apoptosis, inflammation, and host-defense mechanisms.
DDs are protein-protein interaction domains found in a
variety of domain architectures. Their common feature
is that they form homodimers by self-association or
heterodimers by associating with other members of the
DD superfamily including PYRIN and DED (Death Effector
Domain). They serve as adaptors in signaling pathways
and can recruit other proteins into signaling
complexes.
Length = 88
Score = 30.0 bits (68), Expect = 0.37
Identities = 12/44 (27%), Positives = 16/44 (36%), Gaps = 4/44 (9%)
Query: 3 IKPEDIITSVITFLRKELLRDTLNAESKEGIEVAVE----CLCK 42
I P DI+ + L E L E +G A E L +
Sbjct: 19 IIPRDILDHLPECLTDEDKEQILAEERNKGNIAAAEELLDRLER 62
>gnl|CDD|222122 pfam13429, TPR_15, Tetratricopeptide repeat.
Length = 279
Score = 31.1 bits (71), Expect = 0.58
Identities = 15/45 (33%), Positives = 23/45 (51%), Gaps = 4/45 (8%)
Query: 160 YGRMGLAYTQMNDYKAALEAYTKAAELDPNDPL----YANNMQAA 200
+G AY + K AL + A+ +PNDPL YA+ ++ A
Sbjct: 216 WGPFAAAYLLLGRPKKALPYLRRQAKSNPNDPLWLLAYADALEMA 260
>gnl|CDD|225504 COG2956, COG2956, Predicted N-acetylglucosaminyl transferase
[Carbohydrate transport and metabolism].
Length = 389
Score = 31.2 bits (71), Expect = 0.65
Identities = 23/94 (24%), Positives = 36/94 (38%), Gaps = 12/94 (12%)
Query: 107 QAVIEYSKAIDC--------DNSNPV----YYCNRAASNNKLKNYKLALRDCQIAIKIDP 154
QA E+ KAID + V +YC A + A + A++ D
Sbjct: 152 QATREWEKAIDVAERLVKLGGQTYRVEIAQFYCELAQQALASSDVDRARELLKKALQADK 211
Query: 155 HYAKAYGRMGLAYTQMNDYKAALEAYTKAAELDP 188
+A +G DY+ A+EA + E +P
Sbjct: 212 KCVRASIILGRVELAKGDYQKAVEALERVLEQNP 245
>gnl|CDD|182501 PRK10503, PRK10503, multidrug efflux system subunit MdtB;
Provisional.
Length = 1040
Score = 31.2 bits (71), Expect = 0.70
Identities = 30/112 (26%), Positives = 46/112 (41%), Gaps = 31/112 (27%)
Query: 167 YTQMNDYKAALEAYTKAAELDPNDPLYANNMQAAMSNLNNSSSASGSGGVFPGLSEMSTK 226
YTQ N Y+ LE T+ ++ L+ S GGV P LS ++T
Sbjct: 754 YTQANQYRVVLEHNTEN--------------TPGLAALDTIRLTSSDGGVVP-LSSIAT- 797
Query: 227 VLSDPSIQQVFGELFANPGQQATAT-------DGSNTG--IQALLNASQQIA 269
I+Q FG L N Q +T DG + G +QA+++ + +
Sbjct: 798 ------IEQRFGPLSINHLDQFPSTTISFNVPDGYSLGDAVQAIMDTEKTLN 843
>gnl|CDD|234406 TIGR03939, PGA_TPR_OMP, poly-beta-1,6 N-acetyl-D-glucosamine export
porin PgaA. Members of this protein family are the
poly-beta-1,6 N-acetyl-D-glucosamine (PGA) export porin
PgaA of Gram-negative bacteria. There is no counterpart
in the poly-beta-1,6 N-acetyl-D-glucosamine biosynthesis
systems of Gram-positive bacteria such as Staphylococcus
epidermidis. The PGA polysaccharide adhesin is a
critical determinant of biofilm formation. The conserved
C-terminal domain of this outer membrane protein is
preceded by a variable number of TPR repeats.
Length = 800
Score = 30.4 bits (69), Expect = 1.3
Identities = 18/73 (24%), Positives = 27/73 (36%), Gaps = 9/73 (12%)
Query: 129 RAASNNKLKNYKLALRDCQIAIKIDPHYAKAYGRMGLAYTQ--MNDYKAALEAYTKAAEL 186
+A N K + AL + ++ DP+ G +GLA T AL+ E
Sbjct: 94 KAYRN--EKQWDKALELYRKLLQRDPNNPD--GLLGLALTLADAGKDAEALKY---LKEY 146
Query: 187 DPNDPLYANNMQA 199
P A +A
Sbjct: 147 VARFPTDAARYEA 159
>gnl|CDD|173852 cd01163, DszC, Dibenzothiophene (DBT) desulfurization enzyme C.
DszC is a flavin reductase dependent enzyme, which
catalyzes the first two steps of DBT desulfurization in
mesophilic bacteria. DszC converts DBT to DBT-sulfoxide,
which is then converted to DBT-sulfone. Bacteria with
this enzyme are candidates for the removal of organic
sulfur compounds from fossil fuels, which pollute the
environment. An equivalent enzyme tdsC, is found in
thermophilic bacteria. This alignment also contains a
closely related uncharacterized subgroup.
Length = 377
Score = 30.0 bits (68), Expect = 1.7
Identities = 14/62 (22%), Positives = 21/62 (33%), Gaps = 5/62 (8%)
Query: 225 TKVLSDPSIQQVFGELFANPGQQATATDG-SNTGIQALLNASQQIAAQLEQRNPELVEQI 283
DP +QQV G+L A A + +AL A+ A + E +
Sbjct: 256 ESARDDPYVQQVVGDLAAR----LHAAEALVLQAARALDAAAAAGTALTAEARGEAALAV 311
Query: 284 FQ 285
Sbjct: 312 AA 313
>gnl|CDD|205553 pfam13374, TPR_10, Tetratricopeptide repeat.
Length = 42
Score = 26.8 bits (60), Expect = 2.1
Identities = 6/30 (20%), Positives = 11/30 (36%)
Query: 157 AKAYGRMGLAYTQMNDYKAALEAYTKAAEL 186
A + + A Y+ A E +A +
Sbjct: 2 AASLNNLARALRAQGRYEEAEELLEEALAI 31
>gnl|CDD|225093 COG2182, MalE, Maltose-binding periplasmic proteins/domains
[Carbohydrate transport and metabolism].
Length = 420
Score = 29.3 bits (66), Expect = 2.6
Identities = 24/115 (20%), Positives = 35/115 (30%), Gaps = 28/115 (24%)
Query: 165 LAYTQMNDYKAALEAYTKAAELDPNDPLYANN--MQAAMSNLNNSSSASGSGGVFPGLSE 222
Q Y A E A + NDP N+ A + P + E
Sbjct: 327 NPKNQKLLYDEAGE--IPANKAARNDPEVKNDPLAAAVIEQAEY-------AQPMPNIPE 377
Query: 223 MSTKVLSDPSIQQVFGELFANPGQQA--TATDGSNTGIQALLNASQQIAAQLEQR 275
M+ P + A G T +AL +A +QI AQ++
Sbjct: 378 MAA---------------VWTPFKNALQNVASGKKTPEEALDDAVKQIKAQIKLA 417
>gnl|CDD|223571 COG0497, RecN, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 557
Score = 29.5 bits (67), Expect = 2.7
Identities = 26/164 (15%), Positives = 55/164 (33%), Gaps = 40/164 (24%)
Query: 75 SNINFSPTEEVKIEAEKYKNLGNTAMQQDKPEQAVIEYSKAIDCDNSNPVYYCNRAASNN 134
+N P E+ ++E E K L N+ +K +A+ + + ++ +
Sbjct: 198 EELNLQPGEDEELEEE-RKRLSNS----EKLAEAIQNALELLSGEDDTV----------S 242
Query: 135 KLKNYKLALRDCQIAIKIDPHYAKAYGRMGLAYTQMNDYKAALEAYTKAAELDPND---- 190
L AL + + D ++ + A ++ + L AY E DPN
Sbjct: 243 ALSLLGRALEALEDLSEYDGKLSELAELLEEALYELEEASEELRAYLDELEFDPNRLEEV 302
Query: 191 ---------------------PLYANNMQAAMSNLNNSSSASGS 213
Y + ++ ++ L+NS + +
Sbjct: 303 EERLFALKSLARKYGVTIEDLLEYLDKIKEELAQLDNSEESLEA 346
>gnl|CDD|234384 TIGR03896, cyc_nuc_ocin, bacteriocin-type transport-associated
protein. Members of this protein family are
uncharacterized and contain two copies of the cyclic
nucleotide-binding domain pfam00027. Members are
restricted to select cyanobacteria but are found
regularly in association with a transport operon that,
in turn, is associated with the production of putative
bacteriocins. The models describing the transport operon
are TIGR03794, TIGR03796, and TIGR03797.
Length = 317
Score = 29.1 bits (65), Expect = 3.1
Identities = 14/52 (26%), Positives = 24/52 (46%), Gaps = 2/52 (3%)
Query: 235 QVFGEL-FANPGQQATATDGSNTGIQALLNASQQIAAQLEQRNPELVEQIFQ 285
++ GE F N TAT + L QQ+AA+L+Q + + ++
Sbjct: 210 EILGETPFLNGSLPGTATVKAIENSVLLAIDKQQLAAKLQQ-DVGFASRFYR 260
>gnl|CDD|218583 pfam05420, BCSC_C, Cellulose synthase operon protein C C-terminus
(BCSC_C). This family contains the C-terminal regions
of several bacterial cellulose synthase operon C (BCSC)
proteins. BCSC is involved in cellulose synthesis
although the exact function of this protein is unknown.
Length = 339
Score = 28.8 bits (65), Expect = 3.9
Identities = 14/46 (30%), Positives = 15/46 (32%), Gaps = 3/46 (6%)
Query: 180 YTKAAELDPNDPLYANNMQAAMSNLNN---SSSASGSGGVFPGLSE 222
AA P DPL AA + N S SG G E
Sbjct: 257 KEDAAPYFPTDPLLQAQANAAAGDGNAVYPGDSGSGLGYSLRAAVE 302
>gnl|CDD|219835 pfam08426, ICE2, ICE2. ICE2 is a fungal ER protein which has been
shown to play an important role in forming/maintaining
the cortical ER. It has also bee identified as a protein
which is necessary for nuclear inner membrane targeting.
Length = 406
Score = 28.9 bits (65), Expect = 3.9
Identities = 8/52 (15%), Positives = 18/52 (34%)
Query: 249 TATDGSNTGIQALLNASQQIAAQLEQRNPELVEQIFQQFGPALNNFKSNVPR 300
D S + + L ++ L+ P L I + + +++P
Sbjct: 223 IFPDLSESATEELAELFKETWQSLQPEFPPLPPIIMASYSTLIKFLSASLPS 274
>gnl|CDD|221837 pfam12895, Apc3, Anaphase-promoting complex, cyclosome, subunit 3.
Apc3, otherwise known as Cdc27, is one of the subunits
of the anaphase-promoting complex or cyclosome. The
anaphase-promoting complex is a multiprotein subunit E3
ubiquitin ligase complex that controls segregation of
chromosomes and exit from mitosis in eukaryotes. The
protein members of this family contain TPR repeats just
as those of Apc7 do, and it appears that these TPR units
bind the C-termini of the APC co-activators CDH1 and
CDC20.
Length = 80
Score = 26.8 bits (60), Expect = 4.2
Identities = 13/56 (23%), Positives = 21/56 (37%), Gaps = 1/56 (1%)
Query: 138 NYKLALRDCQIAIKIDPHYAKAYGRMGLAYTQMNDYKAALEAYTKAAELDPNDPLY 193
NY+ A+ + + + P AY + Y YK A E K + + Y
Sbjct: 4 NYENAIFLAEKLLALTPSNEDAY-LLAQCYFLQGQYKRAYELLRKLKLDNSSGCRY 58
>gnl|CDD|238517 cd01083, GAG_Lyase, Glycosaminoglycan (GAG) polysaccharide lyase
family. This family consists of a group of secreted
bacterial lyase enzymes capable of acting on
glycosaminoglycans, such as hyaluronan and chondroitin,
in the extracellular matrix of host tissues,
contributing to the invasive capacity of the pathogen.
These are broad-specificity glycosaminoglycan lyases
which recognize uronyl residues in polysaccharides and
cleave their glycosidic bonds via a beta-elimination
reaction to form a double bond between C-4 and C-5 of
the non-reducing terminal uronyl residues of released
products. Substrates include chondroitin, chondroitin
4-sulfate, chondroitin 6-sulfate, and hyaluronic acid.
Family members include chondroitin AC lyase, chondroitin
abc lyase, xanthan lyase, and hyalurate lyase.
Length = 693
Score = 28.5 bits (64), Expect = 5.1
Identities = 29/140 (20%), Positives = 40/140 (28%), Gaps = 18/140 (12%)
Query: 89 AEKYKNLGNTAMQQDKPEQAVIEYSKAIDC----DNSNPVYYCNRAASNNKLKNYKLALR 144
E +L A K A I D PV+ + + KL L
Sbjct: 300 VEILASLLLLADAAPKALAA--ALRSLIKRWITRDTYYPVFN-----NPKSYSDIKLLLA 352
Query: 145 DCQIAIKIDPHYAKAYGRMGLAYTQM--NDYKAALEAY---TKAAELDPNDPLYANNMQA 199
D IA +P K + M D+ L Y T E + L
Sbjct: 353 DASIAPAAEPQGHKQFNSM--DRAVHRRPDFAFGLSMYSTRTANYEAGNGENLKGWYTGD 410
Query: 200 AMSNLNNSSSASGSGGVFPG 219
M+ L N+ S +P
Sbjct: 411 GMTYLYNNDGDQYSDFYWPT 430
>gnl|CDD|220211 pfam09375, Peptidase_M75, Imelysin. The imelysin peptidase was
first identified in Pseudomonas aeruginosa. The active
site residues have not been identified. However, His201
and Glu204 are completely conserved in the family and
occur in an HXXE motif that is also found in family M14.
Length = 282
Score = 28.5 bits (64), Expect = 5.1
Identities = 7/31 (22%), Positives = 13/31 (41%)
Query: 257 GIQALLNASQQIAAQLEQRNPELVEQIFQQF 287
G++ + + L +P L +I QF
Sbjct: 211 GLRNVYLGGPGLRDLLAAADPALAARIDAQF 241
>gnl|CDD|227310 COG4976, COG4976, Predicted methyltransferase (contains TPR repeat)
[General function prediction only].
Length = 287
Score = 28.2 bits (63), Expect = 5.5
Identities = 14/42 (33%), Positives = 24/42 (57%)
Query: 149 AIKIDPHYAKAYGRMGLAYTQMNDYKAALEAYTKAAELDPND 190
A+++ P +A + R+G + ++ AA AY + ELDP D
Sbjct: 21 ALELAPEWAAGWFRLGEYTEKAGEFDAAAAAYEEVLELDPED 62
>gnl|CDD|227222 COG4885, COG4885, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 312
Score = 28.4 bits (63), Expect = 5.5
Identities = 13/76 (17%), Positives = 29/76 (38%), Gaps = 17/76 (22%)
Query: 49 NIDPASNVDIESLFQLYYKDEVLQ-------WYSNINFSPTEEVK---------IEAEKY 92
+ + ++ + K +V + W +N +PT+++ +AEK+
Sbjct: 208 TVVSNAEFEVPDDYNYVVKLDVWRNGKIVKSWADVLNLAPTKKLSKGTVEKEVDFQAEKF 267
Query: 93 KNLGNTAMQQDKPEQA 108
+ D PEQ+
Sbjct: 268 ETADEPEYVPD-PEQS 282
>gnl|CDD|233994 TIGR02746, TraC-F-type, type-IV secretion system protein TraC. The
protein family described here is common among the F, P
and I-like type IV secretion systems. Gene symbols
include TraC (F-type), TrbE/VirB4 (P-type) and TraU
(I-type). The protein conyains the Walker A and B motifs
and so is a putative nucleotide triphosphatase.
Length = 797
Score = 28.1 bits (63), Expect = 7.0
Identities = 18/67 (26%), Positives = 26/67 (38%), Gaps = 11/67 (16%)
Query: 222 EMSTKVLSDPSIQQVFGELFANPGQQATATDGSNTGIQALLNASQQIAAQLEQRNPELVE 281
E++ +D S+ + L +G T IQ LL S QI L++ E
Sbjct: 25 ELTPLSGADESLVESLSSLLRTD-----LPEG--TDIQVLLWGSPQIGPFLDRNE----E 73
Query: 282 QIFQQFG 288
Q Q G
Sbjct: 74 QFSQNGG 80
>gnl|CDD|206749 cd01856, YlqF, Circularly permuted YlqF GTPase. Proteins of the
YlqF family contain all sequence motifs typical of the
vast class of P-loop-containing GTPases, but show a
circular permutation, with a G4-G1-G3 pattern of motifs
as opposed to the regular G1-G3-G4 pattern seen in most
GTPases. The YlqF subfamily is represented in all
eukaryotes as well as a phylogenetically diverse array
of bacteria (including gram-positive bacteria,
proteobacteria, Synechocystis, Borrelia, and
Thermotoga).
Length = 171
Score = 27.5 bits (62), Expect = 7.1
Identities = 10/49 (20%), Positives = 26/49 (53%), Gaps = 1/49 (2%)
Query: 228 LSDPSIQQVFGELFANPGQQATATDGSN-TGIQALLNASQQIAAQLEQR 275
L+DP+ + + + F + G+ + N G++ LL ++++ + E+
Sbjct: 58 LADPAKTKKWLKYFKSQGEPVLFVNAKNGKGVKKLLKKAKKLLKENEKL 106
>gnl|CDD|183497 PRK12394, PRK12394, putative metallo-dependent hydrolase;
Provisional.
Length = 379
Score = 27.8 bits (62), Expect = 7.1
Identities = 23/112 (20%), Positives = 36/112 (32%), Gaps = 26/112 (23%)
Query: 216 VFPGLSEMSTKVLSDPSIQQVFGELFANPGQQATATDGSNTG------------------ 257
V PGL + V D + V +++ P T D + G
Sbjct: 54 VTPGLIDYHAHVFYDGTEGGVRPDMYMPPNGVTTVVDAGSAGTANFDAFYRTVICASKVR 113
Query: 258 IQALLNAS---QQIAAQLEQRNP-----ELVEQIFQQFGPALNNFKSNVPRN 301
I+A L S Q + E +P + +F+Q+ L K V
Sbjct: 114 IKAFLTVSPPGQTWSGYQENYDPDNIDENKIHALFRQYRNVLQGLKLRVQTE 165
>gnl|CDD|217188 pfam02689, Herpes_Helicase, Helicase. This family consists of
Helicases from the Herpes viruses. Helicases are
responsible for the unwinding of DNA and are essential
for replication and completion of the viral life cycle.
Length = 801
Score = 28.1 bits (63), Expect = 7.3
Identities = 21/61 (34%), Positives = 28/61 (45%), Gaps = 17/61 (27%)
Query: 249 TATDGSNTGIQAL---LN---------ASQQIAAQLEQRNPELVEQIFQQFGPALNNFKS 296
TA G +T IQ L L+ A+Q ++A+L + IFQ FG FKS
Sbjct: 67 TAGAGKSTSIQTLNENLDCLITGATRVAAQNLSAKLSRAYSAYCPTIFQAFG-----FKS 121
Query: 297 N 297
N
Sbjct: 122 N 122
>gnl|CDD|223683 COG0610, COG0610, Type I site-specific restriction-modification
system, R (restriction) subunit and related helicases
[Defense mechanisms].
Length = 962
Score = 28.1 bits (63), Expect = 7.8
Identities = 17/108 (15%), Positives = 37/108 (34%), Gaps = 13/108 (12%)
Query: 85 VKIEAEKYKNLGNTAMQQDKPEQAVIEYSKAIDCDNSNPVYYCNRAASNNKLKNYKLALR 144
+ + E L + + + E + I D + + + N LA+R
Sbjct: 445 LPVYYENRVELELIEESIKEEAEELDERIEEITEDILEKI----KKKTKNLEFLAMLAVR 500
Query: 145 DCQIAIKIDPHYAKAYGRMGLAYTQMNDYKAALEAYTKAAELDPNDPL 192
+ A I H+ K ++ D KA + A ++ ++ +
Sbjct: 501 LIRAAKDIYDHFKK---------EEVFDLKAMVVASSRKVAVELYEAE 539
>gnl|CDD|173594 PTZ00403, PTZ00403, phosphatidylserine decarboxylase; Provisional.
Length = 353
Score = 27.9 bits (62), Expect = 8.0
Identities = 19/69 (27%), Positives = 36/69 (52%), Gaps = 8/69 (11%)
Query: 55 NVDIESLFQLYYKDEVLQWYSNINFSPTEEVKIEAEKYKNLGN----TAMQQDKPEQAVI 110
N++I + ++L + +++ Y IN EE+K E YK++G+ ++ +P V
Sbjct: 74 NIEIPNTYRLPIYNFLIK-YMGIN---KEEIKYPIESYKSIGDFFSRYIREETRPIGDVS 129
Query: 111 EYSKAIDCD 119
+YS CD
Sbjct: 130 DYSIVSPCD 138
>gnl|CDD|240389 PTZ00374, PTZ00374, dihydroxyacetone phosphate acyltransferase;
Provisional.
Length = 1108
Score = 27.9 bits (62), Expect = 8.6
Identities = 12/29 (41%), Positives = 17/29 (58%), Gaps = 1/29 (3%)
Query: 218 PGLSEMS-TKVLSDPSIQQVFGELFANPG 245
PGL+ S T +L+ PSIQ++ L G
Sbjct: 538 PGLTPESLTSILAQPSIQRLMTALAKKEG 566
>gnl|CDD|233816 TIGR02302, aProt_lowcomp, TIGR02302 family protein. Members of
this family are long (~850 residue) bacterial proteins
from the alpha Proteobacteria. Each has 2-3 predicted
transmembrane helices near the N-terminus and a long
C-terminal region that includes stretches of
Gln/Gly-rich low complexity sequence, predicted by TMHMM
to be outside the membrane. In Bradyrhizobium japonicum,
two tandem reading frames are together homologous the
single members found in other species; the cutoffs
scores are set low enough that the longer scores above
the trusted cutoff and the shorter above the noise
cutoff for this model.
Length = 851
Score = 28.0 bits (62), Expect = 9.2
Identities = 23/85 (27%), Positives = 34/85 (40%), Gaps = 4/85 (4%)
Query: 233 IQQVFGELFANPGQQATATDGSNTGI---QALLNASQQIAAQLEQRNPELVEQIFQQFGP 289
++Q+ +L NP Q A D NT + Q L N QI + + +Q+ Q
Sbjct: 540 MRQLAQQLRNNPQQLARPLD-PNTKVLRQQDLQNMMDQIENLARSGDRDQAKQLLSQLQQ 598
Query: 290 ALNNFKSNVPRNPPGNGDGSSGSSQ 314
+NN + P GD S Q
Sbjct: 599 MMNNLQMGQPGQGQQMGDQSGDMEQ 623
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.311 0.128 0.360
Gapped
Lambda K H
0.267 0.0733 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,701,736
Number of extensions: 1474785
Number of successful extensions: 1578
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1549
Number of HSP's successfully gapped: 134
Length of query: 314
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 217
Effective length of database: 6,635,264
Effective search space: 1439852288
Effective search space used: 1439852288
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 59 (26.5 bits)