RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1863
(425 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 = 60.5 bits (147), Expect = 1e-11
Identities = 28/86 (32%), Positives = 41/86 (47%)
Query: 202 AFVNLGNCAMAREDYVKGKELYVHALDNDATCIEALYNLGLAHKHLNEYSDSLECFHKLQ 261
A +NLGN DY + E Y AL+ D +A YNL A+ L +Y ++LE + K
Sbjct: 2 ALLNLGNLYYKLGDYDEALEYYEKALELDPDNADAYYNLAAAYYKLGKYEEALEDYEKAL 61
Query: 262 AIVPSMPEVLYQIASLYEITGDVEQA 287
+ P + Y + Y G E+A
Sbjct: 62 ELDPDNAKAYYNLGLAYYKLGKYEEA 87
Score = 55.1 bits (133), Expect = 1e-09
Identities = 32/99 (32%), Positives = 51/99 (51%)
Query: 168 AATNLSFIYFLQGEVEQAEKMAEEACTADTYNSAAFVNLGNCAMAREDYVKGKELYVHAL 227
A NL +Y+ G+ ++A + E+A D N+ A+ NL Y + E Y AL
Sbjct: 2 ALLNLGNLYYKLGDYDEALEYYEKALELDPDNADAYYNLAAAYYKLGKYEEALEDYEKAL 61
Query: 228 DNDATCIEALYNLGLAHKHLNEYSDSLECFHKLQAIVPS 266
+ D +A YNLGLA+ L +Y ++LE + K + P+
Sbjct: 62 ELDPDNAKAYYNLGLAYYKLGKYEEALEAYEKALELDPN 100
Score = 40.1 bits (94), Expect = 2e-04
Identities = 26/97 (26%), Positives = 42/97 (43%), Gaps = 6/97 (6%)
Query: 235 EALYNLGLAHKHLNEYSDSLECFHKLQAIVPSMPEVLYQIASLYEITGDVEQASDVNENL 294
EAL NLG + L +Y ++LE + K + P + Y +A+ Y G E+A + E
Sbjct: 1 EALLNLGNLYYKLGDYDEALEYYEKALELDPDNADAYYNLAAAYYKLGKYEEALEDYEKA 60
Query: 295 L------LEAVRNDALSQLHREMKHEAEKCILTSAKL 325
L +A N L+ EA + + +L
Sbjct: 61 LELDPDNAKAYYNLGLAYYKLGKYEEALEAYEKALEL 97
Score = 38.9 bits (91), Expect = 4e-04
Identities = 25/95 (26%), Positives = 44/95 (46%), Gaps = 3/95 (3%)
Query: 139 INKAVTFLRMNDVSQAVDVLKSC---DEMTSSAATNLSFIYFLQGEVEQAEKMAEEACTA 195
+N + ++ D +A++ + D + A NL+ Y+ G+ E+A + E+A
Sbjct: 4 LNLGNLYYKLGDYDEALEYYEKALELDPDNADAYYNLAAAYYKLGKYEEALEDYEKALEL 63
Query: 196 DTYNSAAFVNLGNCAMAREDYVKGKELYVHALDND 230
D N+ A+ NLG Y + E Y AL+ D
Sbjct: 64 DPDNAKAYYNLGLAYYKLGKYEEALEAYEKALELD 98
>gnl|CDD|222112 pfam13414, TPR_11, TPR repeat.
Length = 69
Score = 40.4 bits (95), Expect = 6e-05
Identities = 26/68 (38%), Positives = 34/68 (50%), Gaps = 1/68 (1%)
Query: 199 NSAAFVNLGNCAMAREDYVKGKELYVHALDNDATCIEALYNLGLAHKHLNE-YSDSLECF 257
N+ A NLGN DY + E Y AL+ D EA YNL LA+ L + Y ++LE
Sbjct: 2 NAEALKNLGNALFKLGDYDEAIEAYEKALELDPDNAEAYYNLALAYLKLGKDYEEALEDL 61
Query: 258 HKLQAIVP 265
K + P
Sbjct: 62 EKALELDP 69
Score = 34.6 bits (80), Expect = 0.009
Identities = 19/64 (29%), Positives = 30/64 (46%), Gaps = 1/64 (1%)
Query: 168 AATNLSFIYFLQGEVEQAEKMAEEACTADTYNSAAFVNLGNCAMAR-EDYVKGKELYVHA 226
A NL F G+ ++A + E+A D N+ A+ NL + +DY + E A
Sbjct: 5 ALKNLGNALFKLGDYDEAIEAYEKALELDPDNAEAYYNLALAYLKLGKDYEEALEDLEKA 64
Query: 227 LDND 230
L+ D
Sbjct: 65 LELD 68
Score = 30.0 bits (68), Expect = 0.30
Identities = 17/49 (34%), Positives = 24/49 (48%)
Query: 235 EALYNLGLAHKHLNEYSDSLECFHKLQAIVPSMPEVLYQIASLYEITGD 283
EAL NLG A L +Y +++E + K + P E Y +A Y G
Sbjct: 4 EALKNLGNALFKLGDYDEAIEAYEKALELDPDNAEAYYNLALAYLKLGK 52
>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 = 42.4 bits (100), Expect = 5e-04
Identities = 26/120 (21%), Positives = 44/120 (36%)
Query: 168 AATNLSFIYFLQGEVEQAEKMAEEACTADTYNSAAFVNLGNCAMAREDYVKGKELYVHAL 227
A L+ +Y G E+A E+A + + L + + K + A
Sbjct: 535 AILALAGLYLRTGNEEEAVAWLEKAAELNPQEIEPALALAQYYLGKGQLKKALAILNEAA 594
Query: 228 DNDATCIEALYNLGLAHKHLNEYSDSLECFHKLQAIVPSMPEVLYQIASLYEITGDVEQA 287
D EA LG A + + ++ F KL A+ P L +A Y + + +A
Sbjct: 595 DAAPDSPEAWLMLGRAQLAAGDLNKAVSSFKKLLALQPDSALALLLLADAYAVMKNYAKA 654
Score = 37.8 bits (88), Expect = 0.012
Identities = 34/150 (22%), Positives = 62/150 (41%), Gaps = 3/150 (2%)
Query: 141 KAVTFLRMNDVSQAVDVLKSCDEM---TSSAATNLSFIYFLQGEVEQAEKMAEEACTADT 197
++ L D S+A+ L++ ++ A L Y G+ ++A A++
Sbjct: 403 LGISKLSQGDPSEAIADLETAAQLDPELGRADLLLILSYLRSGQFDKALAAAKKLEKKQP 462
Query: 198 YNSAAFVNLGNCAMAREDYVKGKELYVHALDNDATCIEALYNLGLAHKHLNEYSDSLECF 257
N++ LG + + D K +E + AL + A NL D+++ F
Sbjct: 463 DNASLHNLLGAIYLGKGDLAKAREAFEKALSIEPDFFPAAANLARIDIQEGNPDDAIQRF 522
Query: 258 HKLQAIVPSMPEVLYQIASLYEITGDVEQA 287
K+ I P + +A LY TG+ E+A
Sbjct: 523 EKVLTIDPKNLRAILALAGLYLRTGNEEEA 552
Score = 34.3 bits (79), Expect = 0.15
Identities = 29/113 (25%), Positives = 50/113 (44%)
Query: 176 YFLQGEVEQAEKMAEEACTADTYNSAAFVNLGNCAMAREDYVKGKELYVHALDNDATCIE 235
Y G++E A+K E+A D + A + L A+A + + + L L D ++
Sbjct: 135 YLGLGQLELAQKSYEQALAIDPRSLYAKLGLAQLALAENRFDEARALIDEVLTADPGNVD 194
Query: 236 ALYNLGLAHKHLNEYSDSLECFHKLQAIVPSMPEVLYQIASLYEITGDVEQAS 288
AL G L +L + K A+ P+ VL +A++ G+ E+A
Sbjct: 195 ALLLKGDLLLSLGNIELALAAYRKAIALRPNNIAVLLALATILIEAGEFEEAE 247
Score = 32.7 bits (75), Expect = 0.44
Identities = 24/128 (18%), Positives = 46/128 (35%)
Query: 162 DEMTSSAATNLSFIYFLQGEVEQAEKMAEEACTADTYNSAAFVNLGNCAMAREDYVKGKE 221
D + A L+ + + ++A + +E TAD N A + G+ ++ +
Sbjct: 155 DPRSLYAKLGLAQLALAENRFDEARALIDEVLTADPGNVDALLLKGDLLLSLGNIELALA 214
Query: 222 LYVHALDNDATCIEALYNLGLAHKHLNEYSDSLECFHKLQAIVPSMPEVLYQIASLYEIT 281
Y A+ I L L E+ ++ + L P+ P Y A +
Sbjct: 215 AYRKAIALRPNNIAVLLALATILIEAGEFEEAEKHADALLKKAPNSPLAHYLKALVDFQK 274
Query: 282 GDVEQASD 289
+ E A +
Sbjct: 275 KNYEDARE 282
Score = 30.1 bits (68), Expect = 2.9
Identities = 30/150 (20%), Positives = 63/150 (42%), Gaps = 5/150 (3%)
Query: 142 AVTFLRMNDVSQAVDVLKSCDE-MTSSAATN--LSFIYFLQGEVEQAEKMAEEACTADTY 198
+++LR +A+ K ++ +A+ + L IY +G++ +A + E+A + +
Sbjct: 438 ILSYLRSGQFDKALAAAKKLEKKQPDNASLHNLLGAIYLGKGDLAKAREAFEKALSIEPD 497
Query: 199 NSAAFVNLGNCAMAREDYVKGKELYVHALDNDATCIEALYNL-GLAHKHLNEYSDSLECF 257
A NL + + + + L D + A+ L GL + NE +++
Sbjct: 498 FFPAAANLARIDIQEGNPDDAIQRFEKVLTIDPKNLRAILALAGLYLRTGNE-EEAVAWL 556
Query: 258 HKLQAIVPSMPEVLYQIASLYEITGDVEQA 287
K + P E +A Y G +++A
Sbjct: 557 EKAAELNPQEIEPALALAQYYLGKGQLKKA 586
Score = 28.5 bits (64), Expect = 7.6
Identities = 36/187 (19%), Positives = 55/187 (29%), Gaps = 35/187 (18%)
Query: 144 TFLRMNDVSQAVDVLKSC--DEMTSSAATNLSFIYFLQGEVEQAEKMAEEACTADTYNSA 201
+LR D A+ + +S A L G +A K E ++
Sbjct: 712 LYLRQKDYPAAIQAYRKALKRAPSSQNAIKLHRALLASGNTAEAVKTLEAWLKTHPNDAV 771
Query: 202 AFVNLGNCAMAREDYVKGKELY----------VHALDNDATCIEALYN---LGLAHKHLN 248
L +A++DY K + Y L+N A L + L A + L
Sbjct: 772 LRTALAELYLAQKDYDKAIKHYQTVVKKAPDNAVVLNNLAWLYLELKDPRALEYAERALK 831
Query: 249 --------------------EYSDSLECFHKLQAIVPSMPEVLYQIASLYEITGDVEQAS 288
E +L K I P + Y +A TG +A
Sbjct: 832 LAPNIPAILDTLGWLLVEKGEADRALPLLRKAVNIAPEAAAIRYHLALALLATGRKAEAR 891
Query: 289 DVNENLL 295
+ LL
Sbjct: 892 KELDKLL 898
Score = 28.5 bits (64), Expect = 9.4
Identities = 29/182 (15%), Positives = 55/182 (30%), Gaps = 9/182 (4%)
Query: 134 AQDLEINKAVTFLRMNDVSQAVDVLKSCDEMTSSAATNLSFI------YFLQGEVEQAEK 187
+ + A +L + +A+ +L +E +A + G++ +A
Sbjct: 566 EIEPALALAQYYLGKGQLKKALAIL---NEAADAAPDSPEAWLMLGRAQLAAGDLNKAVS 622
Query: 188 MAEEACTADTYNSAAFVNLGNCAMAREDYVKGKELYVHALDNDATCIEALYNLGLAHKHL 247
++ ++ A + L + ++Y K AL+ EA L
Sbjct: 623 SFKKLLALQPDSALALLLLADAYAVMKNYAKAITSLKRALELKPDNTEAQIGLAQLLLAA 682
Query: 248 NEYSDSLECFHKLQAIVPSMPEVLYQIASLYEITGDVEQASDVNENLLLEAVRNDALSQL 307
+ + LQ P LY D A L A + +L
Sbjct: 683 KRTESAKKIAKSLQKQHPKAALGFELEGDLYLRQKDYPAAIQAYRKALKRAPSSQNAIKL 742
Query: 308 HR 309
HR
Sbjct: 743 HR 744
>gnl|CDD|223861 COG0790, COG0790, FOG: TPR repeat, SEL1 subfamily [General function
prediction only].
Length = 292
Score = 41.2 bits (96), Expect = 5e-04
Identities = 31/153 (20%), Positives = 56/153 (36%), Gaps = 9/153 (5%)
Query: 100 LTSAKLIAPSIEDNFSNGYNWCVQSIRNSAHSSLAQDLEINKAVTFLRMNDVSQAVD-VL 158
L+ L A + E+ S + + +++A + D ++A+
Sbjct: 7 LSGKSLFAAAEENAVSTLGKLLSEG-GDPLMAAVALKSALLNGAGSAYPPDYAKALKSYE 65
Query: 159 KSCDEMTSSAATNLSFIYFLQGEVEQAEKMAEE--ACTADTYNSAAFVNLGNCAMARE-- 214
K+ + ++A L +Y V + + A + C A + A NLG
Sbjct: 66 KAAELGDAAALALLGQMYGAGKGVSRDKTKAADWYRCAAADGLAEALFNLGLMYANGRGV 125
Query: 215 --DYVKGKELYVHALD-NDATCIEALYNLGLAH 244
D VK + Y A + A+Y LGLA+
Sbjct: 126 PLDLVKALKYYEKAAKLGNVEAALAMYRLGLAY 158
>gnl|CDD|176974 CHL00033, ycf3, photosystem I assembly protein Ycf3.
Length = 168
Score = 40.0 bits (94), Expect = 7e-04
Identities = 25/86 (29%), Positives = 41/86 (47%), Gaps = 12/86 (13%)
Query: 223 YVHALDN--DATCIEA--------LYNLGLAHKHLNEYSDSLECFHKLQAIVPSMPEVLY 272
Y AL N +A +E LYN+GL H E++ +LE + + P +P+ L
Sbjct: 51 YAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQALERNPFLPQALN 110
Query: 273 QIASLYEITGDVEQASDVNENLLLEA 298
+A + G EQA + ++ + EA
Sbjct: 111 NMAVICHYRG--EQAIEQGDSEIAEA 134
>gnl|CDD|225605 COG3063, PilF, Tfp pilus assembly protein PilF [Cell motility and
secretion / Intracellular trafficking and secretion].
Length = 250
Score = 40.1 bits (94), Expect = 0.001
Identities = 30/116 (25%), Positives = 44/116 (37%), Gaps = 4/116 (3%)
Query: 177 FL--QGEVEQAEKMAEEACTADTY--NSAAFVNLGNCAMAREDYVKGKELYVHALDNDAT 232
FL QG E+A + E A Y S NLG CA+ + + +E AL+ D
Sbjct: 112 FLCAQGRPEEAMQQFERALADPAYGEPSDTLENLGLCALKAGQFDQAEEYLKRALELDPQ 171
Query: 233 CIEALYNLGLAHKHLNEYSDSLECFHKLQAIVPSMPEVLYQIASLYEITGDVEQAS 288
AL L H +Y+ + + Q + E L + + GD A
Sbjct: 172 FPPALLELARLHYKAGDYAPARLYLERYQQRGGAQAESLLLGIRIAKRLGDRAAAQ 227
>gnl|CDD|205602 pfam13424, TPR_12, Tetratricopeptide repeat.
Length = 78
Score = 37.0 bits (86), Expect = 0.002
Identities = 20/78 (25%), Positives = 30/78 (38%), Gaps = 7/78 (8%)
Query: 196 DTYNSAAFVNLGNCAMAREDYVKGKELYVHAL-------DNDATCIEALYNLGLAHKHLN 248
+AA NL DY + EL AL ++ AL NL + L
Sbjct: 1 HPDLAAALNNLALVLRRLGDYDEALELLEKALELARELGEDHPETARALNNLARLYLALG 60
Query: 249 EYSDSLECFHKLQAIVPS 266
+Y ++LE K A+ +
Sbjct: 61 DYDEALEYLEKALALREA 78
Score = 32.0 bits (73), Expect = 0.098
Identities = 20/72 (27%), Positives = 31/72 (43%), Gaps = 11/72 (15%)
Query: 236 ALYNLGLAHKHLNEYSDSLECFHKLQAIVPSMPE-------VLYQIASLYEITGDVEQAS 288
AL NL L + L +Y ++LE K + + E L +A LY GD ++A
Sbjct: 7 ALNNLALVLRRLGDYDEALELLEKALELARELGEDHPETARALNNLARLYLALGDYDEA- 65
Query: 289 DVNENLLLEAVR 300
L +A+
Sbjct: 66 ---LEYLEKALA 74
>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 = 39.2 bits (92), Expect = 0.002
Identities = 33/117 (28%), Positives = 49/117 (41%), Gaps = 8/117 (6%)
Query: 177 FL--QGEVEQAEKMAEEACTADTYN--SAAFVNLGNCAMAREDYVKGKELYVHALDNDAT 232
FL QG+ EQA + E+A Y + + N G CA+ D+ K ++ AL D
Sbjct: 108 FLCQQGKYEQAMQQFEQAIEDPLYPQPARSLENAGLCALKAGDFDKAEKYLTRALQIDPQ 167
Query: 233 CIEALYNLGLAHKHLN--EYSDSLECFHKLQAIVPSMPEVLYQIASLYEITGDVEQA 287
E+L L LA + +Y D+ + Q E L+ + GDV A
Sbjct: 168 RPESL--LELAELYYLRGQYKDARAYLERYQQTYNQTAESLWLGIRIARALGDVAAA 222
Score = 36.5 bits (85), Expect = 0.014
Identities = 38/170 (22%), Positives = 66/170 (38%), Gaps = 6/170 (3%)
Query: 123 QSIRNSAHSSLAQDLEINKAVTFLRMNDVSQAVDVLKSC---DEMTSSAATNLSFIYFLQ 179
+S R + + A+ + + A+ +L D+ A + L D A L+ Y
Sbjct: 20 RSSRTTDRNKAAK-IRVQLALGYLEQGDLEVAKENLDKALEHDPDDYLAYLALALYYQQL 78
Query: 180 GEVEQAEKMAEEACTADTYNSAAFVNLGNCAMAREDYVKGKELYVHAL-DNDATCIEALY 238
GE+E+AE A T + N N G + Y + + + A+ D
Sbjct: 79 GELEKAEDSFRRALTLNPNNGDVLNNYGTFLCQQGKYEQAMQQFEQAIEDPLYPQPARSL 138
Query: 239 -NLGLAHKHLNEYSDSLECFHKLQAIVPSMPEVLYQIASLYEITGDVEQA 287
N GL ++ + + + I P PE L ++A LY + G + A
Sbjct: 139 ENAGLCALKAGDFDKAEKYLTRALQIDPQRPESLLELAELYYLRGQYKDA 188
Score = 29.2 bits (66), Expect = 3.9
Identities = 10/59 (16%), Positives = 18/59 (30%)
Query: 165 TSSAATNLSFIYFLQGEVEQAEKMAEEACTADTYNSAAFVNLGNCAMAREDYVKGKELY 223
+ + N G+ ++AEK A D + + L R Y +
Sbjct: 134 PARSLENAGLCALKAGDFDKAEKYLTRALQIDPQRPESLLELAELYYLRGQYKDARAYL 192
>gnl|CDD|179448 PRK02603, PRK02603, photosystem I assembly protein Ycf3;
Provisional.
Length = 172
Score = 38.1 bits (89), Expect = 0.003
Identities = 27/90 (30%), Positives = 43/90 (47%), Gaps = 4/90 (4%)
Query: 207 GNCAMAREDYVKGKELYVHAL---DNDATCIEALYNLGLAHKHLNEYSDSLECFHKLQAI 263
G A A +Y + E Y AL ++ LYN+G+ + E+ +LE +H+ +
Sbjct: 42 GMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALEL 101
Query: 264 VPSMPEVLYQIASLYEITGD-VEQASDVNE 292
P P L IA +Y G+ E+A D +E
Sbjct: 102 NPKQPSALNNIAVIYHKRGEKAEEAGDQDE 131
>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 = 33.6 bits (78), Expect = 0.008
Identities = 14/34 (41%), Positives = 21/34 (61%)
Query: 234 IEALYNLGLAHKHLNEYSDSLECFHKLQAIVPSM 267
EALYNLG A+ L +Y ++LE + K + P+
Sbjct: 1 AEALYNLGNAYLKLGDYDEALEYYEKALELDPNN 34
>gnl|CDD|201277 pfam00515, TPR_1, Tetratricopeptide repeat.
Length = 34
Score = 32.8 bits (76), Expect = 0.015
Identities = 12/26 (46%), Positives = 18/26 (69%)
Query: 234 IEALYNLGLAHKHLNEYSDSLECFHK 259
+ALYNLG A+ L +Y ++LE + K
Sbjct: 1 AKALYNLGNAYLKLGKYDEALEYYEK 26
>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 = 31.7 bits (73), Expect = 0.034
Identities = 15/31 (48%), Positives = 21/31 (67%)
Query: 235 EALYNLGLAHKHLNEYSDSLECFHKLQAIVP 265
EALYNLGLA+ L +Y ++LE + K + P
Sbjct: 2 EALYNLGLAYYKLGDYEEALEAYEKALELDP 32
>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 = 33.4 bits (77), Expect = 0.078
Identities = 20/93 (21%), Positives = 35/93 (37%)
Query: 177 FLQGEVEQAEKMAEEACTADTYNSAAFVNLGNCAMAREDYVKGKELYVHALDNDATCIEA 236
+ QG ++A K+ + D YNS ++ L C ++Y + + Y A D
Sbjct: 28 YQQGRYDEALKLFQLLAAYDPYNSRYWLGLAACCQMLKEYEEAIDAYALAAALDPDDPRP 87
Query: 237 LYNLGLAHKHLNEYSDSLECFHKLQAIVPSMPE 269
++ L E +L+ I PE
Sbjct: 88 YFHAAECLLALGEPESALKALDLAIEICGENPE 120
Score = 32.3 bits (74), Expect = 0.16
Identities = 17/78 (21%), Positives = 30/78 (38%), Gaps = 4/78 (5%)
Query: 240 LGLAHKHLNEYSDSLECFHKLQAIVPSMPEVLYQIASLYEITGDVEQASDVNENLLLEAV 299
L + L EY ++++ + A+ P P + A G+ E A L A+
Sbjct: 57 LAACCQMLKEYEEAIDAYALAAALDPDDPRPYFHAAECLLALGEPESA----LKALDLAI 112
Query: 300 RNDALSQLHREMKHEAEK 317
+ + E+K AE
Sbjct: 113 EICGENPEYSELKERAEA 130
>gnl|CDD|222123 pfam13432, TPR_16, Tetratricopeptide repeat.
Length = 65
Score = 30.3 bits (69), Expect = 0.24
Identities = 14/59 (23%), Positives = 19/59 (32%)
Query: 210 AMAREDYVKGKELYVHALDNDATCIEALYNLGLAHKHLNEYSDSLECFHKLQAIVPSMP 268
A+ DY + AL EAL LG A +++ A P P
Sbjct: 7 ALRAGDYDEALAALEAALARYPLAAEALLLLGEALLRQGRLAEAAALLRAALAADPDDP 65
>gnl|CDD|205553 pfam13374, TPR_10, Tetratricopeptide repeat.
Length = 42
Score = 29.1 bits (66), Expect = 0.40
Identities = 11/30 (36%), Positives = 18/30 (60%)
Query: 165 TSSAATNLSFIYFLQGEVEQAEKMAEEACT 194
T+++ NL+ QG E+AE++ EEA
Sbjct: 1 TAASLNNLARALRAQGRYEEAEELLEEALA 30
>gnl|CDD|223533 COG0457, NrfG, FOG: TPR repeat [General function prediction only].
Length = 291
Score = 32.1 bits (71), Expect = 0.51
Identities = 48/213 (22%), Positives = 81/213 (38%), Gaps = 13/213 (6%)
Query: 162 DEMTSSAATNLSFIYFLQGEVEQAEKMAEEA--CTADTYNSAAFVNLGNCAMAREDYVKG 219
+ + L+ G +E+A ++ E+A + A +NLG A Y +
Sbjct: 55 NSDLAGLLLLLALALLKLGRLEEALELLEKALELELLPNLAEALLNLGLLLEALGKYEEA 114
Query: 220 KELYVHALDNDATCIEALYNLGL-AHKHLNEYSDSLECFHKLQAIVPS---MPEVLYQIA 275
EL AL D A L L A L +Y ++LE + K + P + E L +
Sbjct: 115 LELLEKALALDPDPDLAEALLALGALYELGDYEEALELYEKALELDPELNELAEALLALG 174
Query: 276 SLYEITGDVEQA-------SDVNENLLLEAVRNDALSQLHREMKHEAEKCILTSAKLIAP 328
+L E G E+A +N + EA+ N L L EA + + +L
Sbjct: 175 ALLEALGRYEEALELLEKALKLNPDDDAEALLNLGLLYLKLGKYEEALEYYEKALELDPD 234
Query: 329 SIEDNFSNGYNWCVQSIRNSAHSSLAQDLEINK 361
+ E ++ A +L + LE++
Sbjct: 235 NAEALYNLALLLLELGRYEEALEALEKALELDP 267
>gnl|CDD|183140 PRK11447, PRK11447, cellulose synthase subunit BcsC; Provisional.
Length = 1157
Score = 32.0 bits (73), Expect = 0.71
Identities = 19/53 (35%), Positives = 29/53 (54%)
Query: 179 QGEVEQAEKMAEEACTADTYNSAAFVNLGNCAMAREDYVKGKELYVHALDNDA 231
+ QAE++ ++A D +S A + LG+ AMAR+DY + Y AL D
Sbjct: 364 ANNLAQAERLYQQARQVDNTDSYAVLGLGDVAMARKDYAAAERYYQQALRMDP 416
>gnl|CDD|185257 PRK15359, PRK15359, type III secretion system chaperone protein
SscB; Provisional.
Length = 144
Score = 30.0 bits (67), Expect = 1.3
Identities = 17/57 (29%), Positives = 25/57 (43%)
Query: 202 AFVNLGNCAMAREDYVKGKELYVHALDNDATCIEALYNLGLAHKHLNEYSDSLECFH 258
A + L M ++Y Y HAL DA+ E +Y G+ K + E + E F
Sbjct: 60 AHIALAGTWMMLKEYTTAINFYGHALMLDASHPEPVYQTGVCLKMMGEPGLAREAFQ 116
>gnl|CDD|237080 PRK12370, PRK12370, invasion protein regulator; Provisional.
Length = 553
Score = 31.0 bits (70), Expect = 1.5
Identities = 34/157 (21%), Positives = 61/157 (38%), Gaps = 6/157 (3%)
Query: 147 RMNDVSQAVDVLKSCDEMTSSAATNL--SFIYFLQGEVEQAEKMAEEACTADTYNSAAFV 204
+N + + L+ E+ +L + Q +A A+ Y S A +
Sbjct: 252 ELNSIDSTMVYLRGKHELNQYTPYSLQQALKLLTQCVNMSPNSIAPYCALAECYLSMAQM 311
Query: 205 NLGNCAMAREDYVKGKELYVHALDNDATCIEALYNLGLAHKHLNEYSDSLECFHKLQAIV 264
+ + A +K KE + A + D +AL LGL + +EY F + +
Sbjct: 312 GIFDKQNA---MIKAKEHAIKATELDHNNPQALGLLGLINTIHSEYIVGSLLFKQANLLS 368
Query: 265 PSMPEVLYQIASLYEITGDVEQA-SDVNENLLLEAVR 300
P ++ Y + G +E+A +NE L L+ R
Sbjct: 369 PISADIKYYYGWNLFMAGQLEEALQTINECLKLDPTR 405
>gnl|CDD|227343 COG5010, TadD, Flp pilus assembly protein TadD, contains TPR
repeats [Intracellular trafficking and secretion].
Length = 257
Score = 29.7 bits (67), Expect = 2.4
Identities = 19/109 (17%), Positives = 35/109 (32%), Gaps = 7/109 (6%)
Query: 226 ALDNDATCIEALYNLGLAHKHLNEYSDSLECFHKLQAIVPSMPEVLYQIASLYEITGDVE 285
+ E L G + +++ K + P+ E + + + G +
Sbjct: 92 SAIAYPKDRELLAAQGKNQIRNGNFGEAVSVLRKAARLAPTDWEAWNLLGAALDQLGRFD 151
Query: 286 QA-SDVNENLLL-----EAVRNDALSQLHREMKHEAEKCILTSAKLIAP 328
+A + L L N +S L R +AE +L A L
Sbjct: 152 EARRAYRQALELAPNEPSIANNLGMSLLLRGDLEDAET-LLLPAYLSPA 199
>gnl|CDD|240167 cd05144, RIO2_C, RIO kinase family; RIO2, C-terminal catalytic
domain. The RIO kinase catalytic domain family is part
of a larger superfamily, that includes the catalytic
domains of other kinases such as the typical
serine/threonine/tyrosine protein kinases (PKs),
aminoglycoside phosphotransferase, choline kinase, and
phosphoinositide 3-kinase (PI3K). RIO kinases are
atypical protein serine kinases containing a kinase
catalytic signature, but otherwise show very little
sequence similarity to typical PKs. Serine kinases
catalyze the transfer of the gamma-phosphoryl group from
ATP to serine residues in protein substrates. The RIO
catalytic domain is truncated compared to the catalytic
domains of typical PKs, with deletions of the loops
responsible for substrate binding. RIO2 is present in
archaea and eukaryotes. It contains an N-terminal winged
helix (wHTH) domain and a C-terminal RIO kinase
catalytic domain. The wHTH domain is primarily seen in
DNA-binding proteins, although some wHTH domains may be
involved in RNA recognition. RIO2 is essential for
survival and is necessary for rRNA cleavage during 40S
ribosomal subunit maturation. The biological substrates
of RIO2 are still unknown.
Length = 198
Score = 29.4 bits (67), Expect = 2.7
Identities = 13/44 (29%), Positives = 20/44 (45%), Gaps = 8/44 (18%)
Query: 215 DYVKGKELY-VHALDNDATC-------IEALYNLGLAHKHLNEY 250
+Y+ G ELY V L++ I Y G+ H L+E+
Sbjct: 111 EYIDGVELYRVRVLEDPEEVLDEILEEIVKAYKHGIIHGDLSEF 154
>gnl|CDD|185741 cd09000, GH43_XYL_1, Glycosyl hydrolase family 43,
beta-D-xylosidase. This glycosyl hydrolase family 43
(GH43) includes mostly enzymes that have been
characterized to have beta-1,4-xylosidase
(beta-D-xylosidase;xylan 1,4-beta-xylosidase; EC
3.2.1.37) activity. They are part of an array of
hemicellulases that are involved in the final breakdown
of plant cell-wall whereby they degrade xylan. They
hydrolyze beta-1,4 glycosidic bonds between two xylose
units in short xylooligosaccharides. These are inverting
enzymes (i.e. they invert the stereochemistry of the
anomeric carbon atom of the substrate) that have an
aspartate as the catalytic general base, a glutamate as
the catalytic general acid and another aspartate that is
responsible for pKa modulation and orienting the
catalytic acid. A common structural feature of GH43
enzymes is a 5-bladed beta-propeller domain that
contains the catalytic acid and catalytic base. A long
V-shaped groove, partially enclosed at one end, forms a
single extended substrate-binding surface across the
face of the propeller.
Length = 288
Score = 29.4 bits (67), Expect = 3.3
Identities = 10/19 (52%), Positives = 14/19 (73%), Gaps = 2/19 (10%)
Query: 396 YFLVSSEFQYLPTSEVPIY 414
Y+LV+S F+Y P VPI+
Sbjct: 20 YYLVTSSFEYFPG--VPIF 36
>gnl|CDD|237004 PRK11863, PRK11863, N-acetyl-gamma-glutamyl-phosphate reductase;
Provisional.
Length = 313
Score = 29.4 bits (67), Expect = 3.9
Identities = 11/13 (84%), Positives = 11/13 (84%)
Query: 237 LYNLGLAHKHLNE 249
LY LGLAHKHL E
Sbjct: 172 LYGLGLAHKHLPE 184
>gnl|CDD|178069 PLN02450, PLN02450, 1-aminocyclopropane-1-carboxylate synthase.
Length = 468
Score = 29.0 bits (65), Expect = 5.1
Identities = 17/32 (53%), Positives = 21/32 (65%), Gaps = 1/32 (3%)
Query: 375 VDVLKSCDEMTSSAATNLSFIYFLVSSEFQYL 406
V + S DEM SAAT +S + LVSS+ QYL
Sbjct: 281 VGAIYSNDEMVVSAATKMS-SFGLVSSQTQYL 311
>gnl|CDD|225504 COG2956, COG2956, Predicted N-acetylglucosaminyl transferase
[Carbohydrate transport and metabolism].
Length = 389
Score = 28.9 bits (65), Expect = 5.6
Identities = 40/171 (23%), Positives = 58/171 (33%), Gaps = 23/171 (13%)
Query: 162 DEMTSSAATNLSFIYFLQGEVEQAEKMAEEACTA--DTYNS--AAF-VNLGNCAMAREDY 216
E A L IY E E+A +AE TY A F L A+A D
Sbjct: 137 GEFAEGALQQLLNIYQATREWEKAIDVAERLVKLGGQTYRVEIAQFYCELAQQALASSDV 196
Query: 217 VKGKELYVHALDNDATCIEALYNLGLAHKHLNEYSDSLECFHKLQAIVPS----MPEVLY 272
+ +EL AL D C+ A LG +Y ++E L+ ++ + EVL
Sbjct: 197 DRARELLKKALQADKKCVRASIILGRVELAKGDYQKAVE---ALERVLEQNPEYLSEVLE 253
Query: 273 QIASLYEITGDVEQASDVNENLLLEAVRN-------DALSQLHREMKHEAE 316
+ Y G + N L A+ L+ L +
Sbjct: 254 MLYECYAQLGKPAEG----LNFLRRAMETNTGADAELMLADLIELQEGIDA 300
>gnl|CDD|217864 pfam04053, Coatomer_WDAD, Coatomer WD associated region. This
region is composed of WD40 repeats.
Length = 429
Score = 28.7 bits (65), Expect = 5.7
Identities = 13/56 (23%), Positives = 23/56 (41%), Gaps = 5/56 (8%)
Query: 146 LRMNDVSQAVDVLKSCDEMTSSAATNLSFIYFLQGEVEQAEKMAEEACTADTYNSA 201
L ++ A + + + L +Y G E+ +K+A+ A YNSA
Sbjct: 344 LSQGNIKLAEEAYQKAKDFDK-----LLLLYLSTGNKEKLKKLAKIAEERGDYNSA 394
>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 = 5.7
Identities = 21/80 (26%), Positives = 32/80 (40%), Gaps = 5/80 (6%)
Query: 179 QGEVEQAEKMAEEACTADTYNSAAFVNLGNCAMAREDYVKGKELY-VHALDNDATCIEAL 237
QG E A +AE+ N A++ L C + Y + EL LDN + C
Sbjct: 2 QGNYENAIFLAEKLLALTPSNEDAYL-LAQCYFLQGQYKRAYELLRKLKLDNSSGC---R 57
Query: 238 YNLGLAHKHLNEYSDSLECF 257
Y L L +Y +++
Sbjct: 58 YLLAQCLLKLGKYDEAIAVL 77
>gnl|CDD|221956 pfam13174, TPR_6, Tetratricopeptide repeat.
Length = 33
Score = 25.1 bits (56), Expect = 8.4
Identities = 10/31 (32%), Positives = 16/31 (51%)
Query: 235 EALYNLGLAHKHLNEYSDSLECFHKLQAIVP 265
+ALY L LA+ L + ++ E +L P
Sbjct: 1 DALYKLALAYLKLGDTDEAKEALERLLKRYP 31
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
0.316 0.128 0.358
Gapped
Lambda K H
0.267 0.0867 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 20,340,404
Number of extensions: 1892808
Number of successful extensions: 1755
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1745
Number of HSP's successfully gapped: 62
Length of query: 425
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 325
Effective length of database: 6,502,202
Effective search space: 2113215650
Effective search space used: 2113215650
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 60 (26.6 bits)