RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy307
(1019 letters)
>gnl|CDD|238121 cd00200, WD40, WD40 domain, found in a number of eukaryotic
proteins that cover a wide variety of functions
including adaptor/regulatory modules in signal
transduction, pre-mRNA processing and cytoskeleton
assembly; typically contains a GH dipeptide 11-24
residues from its N-terminus and the WD dipeptide at its
C-terminus and is 40 residues long, hence the name WD40;
between GH and WD lies a conserved core; serves as a
stable propeller-like platform to which proteins can
bind either stably or reversibly; forms a propeller-like
structure with several blades where each blade is
composed of a four-stranded anti-parallel b-sheet;
instances with few detectable copies are hypothesized to
form larger structures by dimerization; each WD40
sequence repeat forms the first three strands of one
blade and the last strand in the next blade; the last
C-terminal WD40 repeat completes the blade structure of
the first WD40 repeat to create the closed ring
propeller-structure; residues on the top and bottom
surface of the propeller are proposed to coordinate
interactions with other proteins and/or small ligands; 7
copies of the repeat are present in this alignment.
Length = 289
Score = 169 bits (431), Expect = 4e-47
Identities = 83/313 (26%), Positives = 128/313 (40%), Gaps = 38/313 (12%)
Query: 328 VHTWEGHTKGISAIRWFPKSAHLLLSCSMDCRVKLWEVYKERRCVRTYYGHRQAVRDICF 387
T +GHT G++ + + P LL + S D +K+W+ + +RT GH VRD+
Sbjct: 2 RRTLKGHTGGVTCVAFSPDG-KLLATGSGDGTIKVWD-LETGELLRTLKGHTGPVRDV-- 57
Query: 388 NNTGTNFISAIRWFPKSAHLLLSCSMDCRVKLWEVYKEHRCVRTYYGHRQAVRDICFNNT 447
L S S D ++LW++ CVRT GH V + F+
Sbjct: 58 -----------AASADG-TYLASGSSDKTIRLWDLETG-ECVRTLTGHTSYVSSVAFSPD 104
Query: 448 GTNFISAGYDRYLKLWDTESGECISRFTS-RKVAYCVKFHPDE--------DKQHL--DI 496
G S+ D+ +K+WD E+G+C++ V F PD D D+
Sbjct: 105 GRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWDL 164
Query: 497 PVDMKYIADPTMHSMP--AVTSSPNNKWLACQSMDNKILIFSALNRFKLNRKKTFEGHMV 554
K +A T H+ +V SP+ + L S D I ++ L T GH
Sbjct: 165 -RTGKCVATLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWDLSTGKCL---GTLRGH-- 218
Query: 555 AGYACSLDFSPDMSYLISGDADGKCYIWDWKTTKLFKKWKAHDGVCISTLWHPHEPSKVV 614
S+ FSPD L SG DG +WD +T + + H S W P + ++
Sbjct: 219 ENGVNSVAFSPDGYLLASGSEDGTIRVWDLRTGECVQTLSGHTNSVTSLAWSP-DGKRLA 277
Query: 615 TAGWDAATAKVQD 627
+ D T ++ D
Sbjct: 278 SGSAD-GTIRIWD 289
Score = 113 bits (284), Expect = 2e-27
Identities = 65/262 (24%), Positives = 99/262 (37%), Gaps = 60/262 (22%)
Query: 371 CVRTYYGHRQAVRDICFNNTGTNFISAIRWFPKSAHLLLSCSMDCRVKLWEVYKEHRCVR 430
RT GH V + F+ G LL + S D +K+W++ +R
Sbjct: 1 LRRTLKGHTGGVTCVAFSPDG--------------KLLATGSGDGTIKVWDLETG-ELLR 45
Query: 431 TYYGHRQAVRDICFNNTGTNFISAGYDRYLKLWDTESGECISRFTS-RKVAYCVKFHPDE 489
T GH VRD+ + GT S D+ ++LWD E+GEC+ T V F PD
Sbjct: 46 TLKGHTGPVRDVAASADGTYLASGSSDKTIRLWDLETGECVRTLTGHTSYVSSVAFSPD- 104
Query: 490 DKQHLDIPVDMKYIADPTMHSMPAVTSSPNNKWLACQSMDNKILIFSALNRFKLNRKKTF 549
+ L+ S D I ++ + K T
Sbjct: 105 ------------------------------GRILSSSSRDKTIKVWD-VETGKC--LTTL 131
Query: 550 EGHMVAGYACSLDFSPDMSYLISGDADGKCYIWDWKTTKLFKKWKAHDGVCISTLWHPHE 609
GH + S+ FSPD +++ S DG +WD +T K H G S + P +
Sbjct: 132 RGHT--DWVNSVAFSPDGTFVASSSQDGTIKLWDLRTGKCVATLTGHTGEVNSVAFSP-D 188
Query: 610 PSKVVTAG-------WDAATAK 624
K++++ WD +T K
Sbjct: 189 GEKLLSSSSDGTIKLWDLSTGK 210
Score = 111 bits (279), Expect = 8e-27
Identities = 41/168 (24%), Positives = 70/168 (41%), Gaps = 18/168 (10%)
Query: 322 FLPKTQVHTWEGHTKGISAIRWFPKSAHLLLSCSMDCRVKLWEVYKERRCVRTYYGHRQA 381
+ T GHT ++++ F + S S D +KLW++ + +CV T GH
Sbjct: 122 VETGKCLTTLRGHTDWVNSVA-FSPDGTFVASSSQDGTIKLWDL-RTGKCVATLTGHTGE 179
Query: 382 VRDICFNNTGTNFISAIRWFPKSAHLLLSCSMDCRVKLWEVYKEHRCVRTYYGHRQAVRD 441
V + F+ G + S S D +KLW++ +C+ T GH V
Sbjct: 180 VNSVAFSPDGEKLL--------------SSSSDGTIKLWDLSTG-KCLGTLRGHENGVNS 224
Query: 442 ICFNNTGTNFISAGYDRYLKLWDTESGECISRFTS-RKVAYCVKFHPD 488
+ F+ G S D +++WD +GEC+ + + + PD
Sbjct: 225 VAFSPDGYLLASGSEDGTIRVWDLRTGECVQTLSGHTNSVTSLAWSPD 272
Score = 100 bits (251), Expect = 3e-23
Identities = 48/202 (23%), Positives = 69/202 (34%), Gaps = 37/202 (18%)
Query: 428 CVRTYYGHRQAVRDICFNNTGTNFISAGYDRYLKLWDTESGECISRFTSRKVAYCVKFHP 487
RT GH V + F+ G + D +K+WD E+GE +
Sbjct: 1 LRRTLKGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGELLRTL------------- 47
Query: 488 DEDKQHLDIPVDMKYIADPTMHSMPAVTSSPNNKWLACQSMDNKILIFSALNRFKLNRKK 547
K H + V +S + +LA S D I ++ L + R
Sbjct: 48 ---KGHT--------------GPVRDVAASADGTYLASGSSDKTIRLWD-LETGECVR-- 87
Query: 548 TFEGHMVAGYACSLDFSPDMSYLISGDADGKCYIWDWKTTKLFKKWKAHDGVCISTLWHP 607
T GH Y S+ FSPD L S D +WD +T K + H S + P
Sbjct: 88 TLTGH--TSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNSVAFSP 145
Query: 608 HEPSKVVTAGWDAATAKVQDAN 629
V + T K+ D
Sbjct: 146 --DGTFVASSSQDGTIKLWDLR 165
Score = 67.4 bits (165), Expect = 5e-12
Identities = 23/97 (23%), Positives = 45/97 (46%), Gaps = 16/97 (16%)
Query: 325 KTQVHTWEGHTKGISAIRWFPKSAHLLLSCSMDCRVKLWEVYKERRCVRTYYGHRQAVRD 384
+ T GH G++++ + P +LL S S D +++W++ + CV+T GH +V
Sbjct: 209 GKCLGTLRGHENGVNSVAFSPDG-YLLASGSEDGTIRVWDL-RTGECVQTLSGHTNSVTS 266
Query: 385 ICFNNTGTNFISAIRWFPKSAHLLLSCSMDCRVKLWE 421
+ ++ G L S S D +++W+
Sbjct: 267 LAWSPDGK--------------RLASGSADGTIRIWD 289
>gnl|CDD|225201 COG2319, COG2319, FOG: WD40 repeat [General function prediction
only].
Length = 466
Score = 112 bits (281), Expect = 4e-26
Identities = 66/280 (23%), Positives = 112/280 (40%), Gaps = 34/280 (12%)
Query: 328 VHTWEGHTKGISAIRWFPKSAHLLLSCSMDCRVKLWEVYKERRCVRTYYGHRQAVRDICF 387
+ T GHT +S++ + P L+ S S D ++LW++ + T GH
Sbjct: 191 LSTLAGHTDPVSSLAFSPDGGLLIASGSSDGTIRLWDLSTGKLLRSTLSGHS-------- 242
Query: 388 NNTGTNFISAIRWFPKSAHLLLSCSMDCRVKLWEVYKEHRCVRTYYGHRQAVRDICFNNT 447
S + F LL S S D ++LW++ +RT GH +V + F+
Sbjct: 243 -------DSVVSSFSPDGSLLASGSSDGTIRLWDLRSSSSLLRTLSGHSSSVLSVAFSPD 295
Query: 448 GTNFISAGYDRYLKLWDTESGECISRFT---SRKVAYCVKFHPDEDK-----------QH 493
G S D ++LWD E+G+ +S T + F PD +
Sbjct: 296 GKLLASGSSDGTVRLWDLETGKLLSSLTLKGHEGPVSSLSFSPDGSLLVSGGSDDGTIRL 355
Query: 494 LDIPVDMKYIADPTMHSMPAVTSSPNNKWLACQSMDNKILIFSALNRFKLNRKKTFEGHM 553
D+ ++ +V+ SP+ + ++ S D + ++ + + +GH
Sbjct: 356 WDLRTGKPLKTLEGHSNVLSVSFSPDGRVVSSGSTDGTVRLWDLST---GSLLRNLDGH- 411
Query: 554 VAGYACSLDFSPDMSYLISGDADGKCYIWDWKTTKLFKKW 593
SLDFSPD L SG +D +WD KT+ +
Sbjct: 412 -TSRVTSLDFSPDGKSLASGSSDNTIRLWDLKTSLKSVSF 450
Score = 107 bits (267), Expect = 2e-24
Identities = 77/322 (23%), Positives = 126/322 (39%), Gaps = 53/322 (16%)
Query: 323 LPKTQVHTWEGHTKGISAIRWFPKSAHLLLSCSMDCRVKLWEVYKERRCVRTYYG-HRQA 381
LP GH I++I F LLLS S D +KLW++ + +++ G H +
Sbjct: 53 LPDLSSLLLRGHEDSITSIA-FSPDGELLLSGSSDGTIKLWDLDNGEKLIKSLEGLHDSS 111
Query: 382 VRDICFNNTGTNFISAIRWFPKSAHLLLSCSMDCRVKLWEVYKEHRCVRTYYGHRQAVRD 441
V + ++ N I LL S S+D VKLW++ + +RT GH ++V
Sbjct: 112 VSKLALSSPDGNSI-----------LLASSSLDGTVKLWDLSTPGKLIRTLEGHSESVTS 160
Query: 442 ICFNNTGTNFISAG-YDRYLKLWDTESGECISRFT-SRKVAYCVKFHPDEDKQHLDIPVD 499
+ F+ G S D +KLWD +G+ +S + F PD
Sbjct: 161 LAFSPDGKLLASGSSLDGTIKLWDLRTGKPLSTLAGHTDPVSSLAFSPD----------- 209
Query: 500 MKYIADPTMHSMPAVTSSPNNKWLACQSMDNKILIFSALNRFKLNRKKTFEGHMVAGYAC 559
+A S D I ++ L + T GH + +
Sbjct: 210 -------------------GGLLIASGSSDGTIRLWDLSTGKLL--RSTLSGHSDSVVSS 248
Query: 560 SLDFSPDMSYLISGDADGKCYIWDWKTT-KLFKKWKAHDGVCISTLWHPHEPSKVVTAGW 618
FSPD S L SG +DG +WD +++ L + H +S + P K++ +G
Sbjct: 249 ---FSPDGSLLASGSSDGTIRLWDLRSSSSLLRTLSGHSSSVLSVAFSPD--GKLLASGS 303
Query: 619 DAATAKVQDANIVKIAVEMEKQ 640
T ++ D K+ + +
Sbjct: 304 SDGTVRLWDLETGKLLSSLTLK 325
>gnl|CDD|218231 pfam04727, ELMO_CED12, ELMO/CED-12 family. This family represents a
conserved domain which is found in a number of eukaryotic
proteins including CED-12, ELMO I and ELMO II. ELMO1 is a
component of signalling pathways that regulate
phagocytosis and cell migration and is the mammalian
orthologue of the C. elegans gene, ced-12. CED-12 is
required for the engulfment of dying cells and cell
migration. In mammalian cells, ELMO1 interacts with
Dock180 as part of the CrkII/Dock180/Rac pathway
responsible for phagocytosis and cell migration. ELMO1 is
ubiquitously expressed, although its expression is
highest in the spleen, an organ rich in immune cells.
ELMO1 has a PH domain and a polyproline sequence motif at
its C terminus which are not present in this alignment.
Length = 170
Score = 103 bits (260), Expect = 1e-25
Identities = 40/89 (44%), Positives = 51/89 (57%), Gaps = 1/89 (1%)
Query: 925 TEDFVKVVLENSCRADEHECPFGRTSVELVKHLCEILRIGDAPSEQGVNYH-PMFFTHDH 983
++F K++LE+S R EHE PF S+ + L E+LRIG E NY P+FF
Sbjct: 79 PDEFQKLLLESSHRPAEHEYPFAVASINVTSMLYELLRIGKLDQEDYKNYGFPLFFPTLL 138
Query: 984 PFEEFYCICIVLLNKTWKEMRATTEDFVK 1012
FEE YC L ++ WKEMRAT DF K
Sbjct: 139 AFEELYCALFHLFDRFWKEMRATIMDFNK 167
Score = 102 bits (257), Expect = 3e-25
Identities = 39/85 (45%), Positives = 49/85 (57%), Gaps = 1/85 (1%)
Query: 848 QVVLENSCRADEHECPFGRTSVELVKHLCEILRIGDAPSEQGVNYH-PMFFTHDHPFEEF 906
+++LE+S R EHE PF S+ + L E+LRIG E NY P+FF FEE
Sbjct: 84 KLLLESSHRPAEHEYPFAVASINVTSMLYELLRIGKLDQEDYKNYGFPLFFPTLLAFEEL 143
Query: 907 YCICIVLLNKTWKEMRATTEDFVKV 931
YC L ++ WKEMRAT DF KV
Sbjct: 144 YCALFHLFDRFWKEMRATIMDFNKV 168
Score = 46.5 bits (111), Expect = 1e-05
Identities = 15/29 (51%), Positives = 17/29 (58%)
Query: 730 EFYCICIVLLNKTWKEMRATTEDFVKVFS 758
E YC L ++ WKEMRAT DF KV
Sbjct: 142 ELYCALFHLFDRFWKEMRATIMDFNKVLE 170
>gnl|CDD|197651 smart00320, WD40, WD40 repeats. Note that these repeats are
permuted with respect to the structural repeats (blades)
of the beta propeller domain.
Length = 40
Score = 49.6 bits (119), Expect = 5e-08
Identities = 12/38 (31%), Positives = 17/38 (44%)
Query: 427 RCVRTYYGHRQAVRDICFNNTGTNFISAGYDRYLKLWD 464
++T GH V + F+ G S D +KLWD
Sbjct: 3 ELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
Score = 45.4 bits (108), Expect = 1e-06
Identities = 12/41 (29%), Positives = 21/41 (51%), Gaps = 1/41 (2%)
Query: 324 PKTQVHTWEGHTKGISAIRWFPKSAHLLLSCSMDCRVKLWE 364
+ T +GHT ++++ + P L S S D +KLW+
Sbjct: 1 SGELLKTLKGHTGPVTSVAFSPDG-KYLASGSDDGTIKLWD 40
Score = 43.5 bits (103), Expect = 7e-06
Identities = 18/42 (42%), Positives = 21/42 (50%), Gaps = 2/42 (4%)
Query: 542 KLNRKKTFEGHMVAGYACSLDFSPDMSYLISGDADGKCYIWD 583
KT +GH G S+ FSPD YL SG DG +WD
Sbjct: 1 SGELLKTLKGH--TGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
Score = 42.3 bits (100), Expect = 2e-05
Identities = 13/53 (24%), Positives = 19/53 (35%), Gaps = 14/53 (26%)
Query: 369 RRCVRTYYGHRQAVRDICFNNTGTNFISAIRWFPKSAHLLLSCSMDCRVKLWE 421
++T GH V + F+ G L S S D +KLW+
Sbjct: 2 GELLKTLKGHTGPVTSVAFSPDG--------------KYLASGSDDGTIKLWD 40
>gnl|CDD|201208 pfam00400, WD40, WD domain, G-beta repeat.
Length = 39
Score = 48.1 bits (115), Expect = 1e-07
Identities = 11/38 (28%), Positives = 18/38 (47%)
Query: 427 RCVRTYYGHRQAVRDICFNNTGTNFISAGYDRYLKLWD 464
+ +RT GH V + F+ G S D +++WD
Sbjct: 2 KLLRTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVWD 39
Score = 44.7 bits (106), Expect = 2e-06
Identities = 12/39 (30%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 325 KTQVHTWEGHTKGISAIRWFPKSAHLLLSCSMDCRVKLW 363
+ T +GHT ++++ + P +LL S S D V++W
Sbjct: 1 GKLLRTLKGHTGPVTSVAFSPDG-NLLASGSDDGTVRVW 38
Score = 43.1 bits (102), Expect = 1e-05
Identities = 16/37 (43%), Positives = 21/37 (56%), Gaps = 2/37 (5%)
Query: 547 KTFEGHMVAGYACSLDFSPDMSYLISGDADGKCYIWD 583
+T +GH G S+ FSPD + L SG DG +WD
Sbjct: 5 RTLKGH--TGPVTSVAFSPDGNLLASGSDDGTVRVWD 39
Score = 42.0 bits (99), Expect = 2e-05
Identities = 14/52 (26%), Positives = 21/52 (40%), Gaps = 14/52 (26%)
Query: 369 RRCVRTYYGHRQAVRDICFNNTGTNFISAIRWFPKSAHLLLSCSMDCRVKLW 420
+ +RT GH V + F+ G +LL S S D V++W
Sbjct: 1 GKLLRTLKGHTGPVTSVAFSPDG--------------NLLASGSDDGTVRVW 38
>gnl|CDD|241513 cd13359, PH_ELMO1_CED-12, Engulfment and cell motility protein 1
pleckstrin homology (PH) domain. DOCK2 (Dedicator of
cytokinesis 2), a hematopoietic cell-specific, atypical
GEF, controls lymphocyte migration through Rac
activation. A DOCK2-ELMO1 complex s necessary for
DOCK2-mediated Rac signaling. DOCK2 contains a SH3
domain at its N-terminus, followed by a lipid binding
DHR1 domain, and a Rac-binding DHR2 domain at its
C-terminus. ELMO1, a mammalian homolog of C. elegans
CED-12, contains the N-terminal RhoG-binding region, the
ELMO domain, the PH domain, and the C-terminal sequence
with three PxxP motifs. The C-terminal region of ELMO1,
including the Pro-rich sequence, binds the
SH3-containing region of DOCK2 forming a intermolecular
five-helix bundle along with the PH domain of ELMO1.
Autoinhibition of ELMO1 and DOCK2 is accomplished by the
interactions of the EID and EAD domains and SH3 and DHR2
domains, respectively. The interaction of DOCK2 and
ELMO1 mutually relieve their autoinhibition and results
in the activation of Rac1. The PH domain of ELMO1 does
not bind phosphoinositides due to the absence of key
binding residues. It more closely resembles the FERM
domain rather than other PH domains. PH domains have
diverse functions, but in general are involved in
targeting proteins to the appropriate cellular location
or in the interaction with a binding partner. They share
little sequence conservation, but all have a common
fold, which is electrostatically polarized. Less than
10% of PH domains bind phosphoinositide phosphates
(PIPs) with high affinity and specificity. PH domains
are distinguished from other PIP-binding domains by
their specific high-affinity binding to PIPs with two
vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2
or PtdIns(3,4,5)P3 which results in targeting some PH
domain proteins to the plasma membrane. A few display
strong specificity in lipid binding. Any specificity is
usually determined by loop regions or insertions in the
N-terminus of the domain, which are not conserved across
all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinase,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, as well as cytoskeletal associated
molecules and in lipid associated enzymes.
Length = 126
Score = 45.8 bits (109), Expect = 9e-06
Identities = 15/25 (60%), Positives = 21/25 (84%)
Query: 824 DLIQQQRLGYLVEGTRFTKYSSRGQ 848
+LI+QQRL +LVEGT F KY++R +
Sbjct: 1 ELIKQQRLNFLVEGTLFPKYNARRR 25
>gnl|CDD|240412 PTZ00420, PTZ00420, coronin; Provisional.
Length = 568
Score = 44.9 bits (106), Expect = 2e-04
Identities = 25/97 (25%), Positives = 45/97 (46%), Gaps = 8/97 (8%)
Query: 332 EGHTKGISAIRWFPKSAHLLLSCSMDCRVKLWEVYKERRCVRTYYGHRQAVRD-ICFNNT 390
+GHT I +++ P + +L S S D +++WE+ V+ ++D C
Sbjct: 71 KGHTSSILDLQFNPCFSEILASGSEDLTIRVWEIPHNDESVK-------EIKDPQCILKG 123
Query: 391 GTNFISAIRWFPKSAHLLLSCSMDCRVKLWEVYKEHR 427
IS I W P + +++ S D V +W++ E R
Sbjct: 124 HKKKISIIDWNPMNYYIMCSSGFDSFVNIWDIENEKR 160
Score = 35.3 bits (81), Expect = 0.17
Identities = 23/99 (23%), Positives = 44/99 (44%), Gaps = 21/99 (21%)
Query: 377 GHRQAVRDICFNNTGTNFISAIRWFPKSAHLLLSCSMDCRVKLWEVYKEHRCVR------ 430
GH ++ D+ FN P + +L S S D +++WE+ V+
Sbjct: 72 GHTSSILDLQFN-------------PCFSEILASGSEDLTIRVWEIPHNDESVKEIKDPQ 118
Query: 431 -TYYGHRQAVRDICFNNTGTNFI-SAGYDRYLKLWDTES 467
GH++ + I +N + S+G+D ++ +WD E+
Sbjct: 119 CILKGHKKKISIIDWNPMNYYIMCSSGFDSFVNIWDIEN 157
>gnl|CDD|176488 cd08667, APC10-ZZEF1, APC10/DOC1-like domain of uncharacterized
Zinc finger ZZ-type and EF-hand domain-containing
protein 1 (ZZEF1) and homologs. This model represents
the APC10/DOC1-like domain present in the
uncharacterized Zinc finger ZZ-type and EF-hand
domain-containing protein 1 (ZZEF1) of Mus musculus.
Members of this family contain EF-hand, APC10, CUB, and
zinc finger ZZ-type domains. ZZEF1-like APC10 domains
are homologous to the APC10 subunit/DOC1 domains present
in E3 ubiquitin ligases, which mediate substrate
ubiquitination (or ubiquitylation), and are components
of the ubiquitin-26S proteasome pathway for selective
proteolytic degradation.
Length = 131
Score = 34.9 bits (80), Expect = 0.066
Identities = 14/39 (35%), Positives = 21/39 (53%), Gaps = 1/39 (2%)
Query: 780 ANISRLTYSEITNLWQQERTSREEW-ESHAKPIVELKEL 817
A+I R+T E + WQ + ++R W KP V L+ L
Sbjct: 14 ADIDRMTDGETSTYWQSDGSARSHWIRLKMKPDVVLRHL 52
>gnl|CDD|237035 PRK12280, rplW, 50S ribosomal protein L23; Reviewed.
Length = 158
Score = 30.5 bits (69), Expect = 2.5
Identities = 11/55 (20%), Positives = 24/55 (43%)
Query: 233 PEDIEGFLGPWGGYTDEEKVSRPNEAQAAELEEYLAKKQKKGKQSEEKPLEEKTI 287
PE+ E T+E++ + + + + E+ +A+K K K ++ K
Sbjct: 92 PEESEKEQKEVSKETEEKEAIKAKKEKKEKKEKKVAEKLAKKKSTKTTKNTTKKA 146
>gnl|CDD|226710 COG4259, COG4259, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 121
Score = 29.5 bits (66), Expect = 3.2
Identities = 15/36 (41%), Positives = 16/36 (44%), Gaps = 4/36 (11%)
Query: 243 WGGYTDEE----KVSRPNEAQAAELEEYLAKKQKKG 274
W GY D K EAQ A LE+YL K K
Sbjct: 32 WEGYQDTVYEYFKGDESKEAQTAALEKYLEKIGAKN 67
>gnl|CDD|227506 COG5179, TAF1, Transcription initiation factor TFIID, subunit TAF1
[Transcription].
Length = 968
Score = 31.2 bits (70), Expect = 3.7
Identities = 19/90 (21%), Positives = 39/90 (43%)
Query: 638 EKQVPQLYQFNQTLTLSSIIQEICSGWSLSDSEQYALQFSETNNKNYITEKNRNEIKNGS 697
+ +N S+ +EI WS + + F E ++++I ++R E+KN
Sbjct: 769 SSNKKNTHIYNVAQQQSAYKEEIDRIWSKQLASLSIVNFEEPFDESFINRRHREEVKNAD 828
Query: 698 VLRLAFSASKTADDILSKLSDKNASLEEKT 727
+LR S+ I+ + D+N + +
Sbjct: 829 LLRETTMLSEKTLLIVRRTRDENGTSYREV 858
>gnl|CDD|234003 TIGR02768, TraA_Ti, Ti-type conjugative transfer relaxase TraA.
This protein contains domains distinctive of a single
strand exonuclease (N-terminus, MobA/MobL, pfam03389) as
well as a helicase domain (central region, homologous to
the corresponding region of the F-type relaxase TraI,
TIGR02760). This protein likely fills the same role as
TraI(F), nicking (at the oriT site) and unwinding the
coiled plasmid prior to conjugative transfer.
Length = 744
Score = 30.9 bits (70), Expect = 3.8
Identities = 25/109 (22%), Positives = 41/109 (37%), Gaps = 18/109 (16%)
Query: 778 FRANISRLTYSEITNLWQQERTSREEWESHAKPIVELKELITPEIVDLIQQQRLGYLVEG 837
FRA R+ Y+E+ + +Q RE W A EL ++ + R +
Sbjct: 488 FRAIAERIGYAELETIRRQ----REAWARQAS-----LELARGDVEKALAAYRDHGHITI 538
Query: 838 TRFTKYSSRGQVVLENSCRADEHECPFGRTSVEL------VKHLCEILR 880
T+ + QVV + + D E + + L V+ L E R
Sbjct: 539 HD-TREEAIEQVVAD--WKQDLREANPAGSQIMLAHTRKDVRALNEAAR 584
>gnl|CDD|180648 PRK06663, PRK06663, flagellar hook-associated protein FlgL;
Validated.
Length = 419
Score = 30.4 bits (69), Expect = 4.7
Identities = 13/50 (26%), Positives = 24/50 (48%), Gaps = 4/50 (8%)
Query: 676 FSETNNKNYI-TEKNRNEIKNGSVLRLAFSASKTADDILSKLSDKNASLE 724
S + Y+ E + I + SA T DDI++K++D +A ++
Sbjct: 206 ISSVDASGYVVKEDQKIYIDGVEI---HLSAGDTIDDIIAKINDSSAPVK 252
>gnl|CDD|224475 COG1559, COG1559, Aminodeoxychorismate lyase [Coenzyme transport
and metabolism].
Length = 342
Score = 30.3 bits (69), Expect = 5.9
Identities = 10/48 (20%), Positives = 24/48 (50%), Gaps = 11/48 (22%)
Query: 622 TAKVQDANIVKIAVE-MEKQVPQLYQF----------NQTLTLSSIIQ 658
T +I+K ++ M+K++ + ++ + LTL+SI++
Sbjct: 175 TRGTSAEDIIKRMIKAMDKKLDEAWEKRADDLPGKTPYELLTLASIVE 222
>gnl|CDD|129705 TIGR00618, sbcc, exonuclease SbcC. All proteins in this family for
which functions are known are part of an exonuclease
complex with sbcD homologs. This complex is involved in
the initiation of recombination to regulate the levels
of palindromic sequences in DNA. This family is based on
the phylogenomic analysis of JA Eisen (1999, Ph.D.
Thesis, Stanford University) [DNA metabolism, DNA
replication, recombination, and repair].
Length = 1042
Score = 30.3 bits (68), Expect = 6.2
Identities = 23/183 (12%), Positives = 56/183 (30%), Gaps = 10/183 (5%)
Query: 741 KTWKEMRATTEDFVKVFSVVREQITRALSSQPASLDKFRANISRLTYSEITNLWQQERTS 800
T ++ + T ++ + + R ++ FR +L +++ QQ
Sbjct: 382 HTLQQQKTTLTQKLQSLCKELDILQREQATIDTRTSAFRDLQGQLAHAKKQQELQQRYA- 440
Query: 801 REEWESHAKPIVELKELITPEIVDLIQQQRLGYLVEGTRFT---KYSSRGQVVLENSCRA 857
E + + ++L + + Q + T+ + + + VVL
Sbjct: 441 -ELCAAAITCTAQCEKLEKIHLQESAQSLKEREQQLQTKEQIHLQETRKKAVVLARLLEL 499
Query: 858 DEHECPFGRTSVELVKHLCEILRIG--DAPSEQGVNYHPMFFTHDHPFEEFYCICIVLLN 915
E CP + + +I G ++G + + E+ Y
Sbjct: 500 QEEPCPLCGSCIHPNPARQDIDNPGPLTRRMQRGEQTYA---QLETSEEDVYHQLTSERK 556
Query: 916 KTW 918
+
Sbjct: 557 QRA 559
>gnl|CDD|173611 PTZ00421, PTZ00421, coronin; Provisional.
Length = 493
Score = 29.5 bits (66), Expect = 9.6
Identities = 13/36 (36%), Positives = 20/36 (55%), Gaps = 1/36 (2%)
Query: 434 GHRQAVRDICFNNTGTNFI-SAGYDRYLKLWDTESG 468
GH + V + F+ + N + SAG D + +WD E G
Sbjct: 123 GHTKKVGIVSFHPSAMNVLASAGADMVVNVWDVERG 158
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
0.318 0.132 0.405
Gapped
Lambda K H
0.267 0.0728 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 50,441,890
Number of extensions: 4785122
Number of successful extensions: 4125
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4041
Number of HSP's successfully gapped: 46
Length of query: 1019
Length of database: 10,937,602
Length adjustment: 107
Effective length of query: 912
Effective length of database: 6,191,724
Effective search space: 5646852288
Effective search space used: 5646852288
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 (21.7 bits)
S2: 64 (28.4 bits)