RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15599
(2347 letters)
>gnl|CDD|201885 pfam01608, I_LWEQ, I/LWEQ domain. I/LWEQ domains bind to actin. It
has been shown that the I/LWEQ domains from mouse talin
and yeast Sla2p interact with F-actin. I/LWEQ domains can
be placed into four major groups based on sequence
similarity: (1) Metazoan talin; (2) Dictyostelium
TalA/TalB and SLA110; (3) metazoan Hip1p; and (4) yeast
Sla2p. The domain has four conserved blocks, the name of
the domain is derived from the initial conserved amino
acid of each of the four blocks.
Length = 194
Score = 230 bits (590), Expect = 3e-69
Identities = 89/200 (44%), Positives = 135/200 (67%), Gaps = 8/200 (4%)
Query: 2123 FDEMILEAAKSIAAATSALVKAASASQRELIDAGRMSRRPLTSSDDGQWSEDDGQWSEGL 2182
+E ILEAAK+I A +ALVKAA+A+QRE++ G+ S+ ++ + + +W+EGL
Sbjct: 1 VNEAILEAAKAITDAVAALVKAATAAQREIVAQGK------GSASRTEFYKKNSRWTEGL 54
Query: 2183 ISAARLVAAATHTFVEAANSVVQGAGTEEKLISSAKQVASSTAQLLVACKVKADPESDAT 2242
ISAA+ VA AT+ VEAA+ VVQG G+EE+LI ++ +VA+STAQL+ A +VKAD S A
Sbjct: 55 ISAAKAVAGATNILVEAADGVVQGTGSEEELIVASNEVAASTAQLVAASRVKADFNSKAQ 114
Query: 2243 HRLQSAGNAVKRATDNLVRAAQQAIQQDEE-RSLVLNR-KMVGGIAQEINARSEVLRIER 2300
RL++A AV A LV A +Q ++++E+ + L++ + G QE+ + E+L++E
Sbjct: 115 DRLEAASKAVTNACKALVAAVKQGLEKEEDQEDVDLSKLTLHEGKTQEMEQQVEILKLEN 174
Query: 2301 QLEEARGRLTAIRQAKYKLK 2320
+LEEAR RL IR+A Y+
Sbjct: 175 ELEEARKRLGEIRKAHYRDD 194
Score = 43.0 bits (102), Expect = 6e-04
Identities = 24/89 (26%), Positives = 48/89 (53%), Gaps = 2/89 (2%)
Query: 802 AQDVETAVEVMMSSSDRLLAASGDAPEMVRQARILGQATAQLIQAIKGDAENEPDSELQR 861
A+ V A +++ ++D ++ +G E++ + + +TAQL+ A + A+ +S+ Q
Sbjct: 58 AKAVAGATNILVEAADGVVQGTGSEEELIVASNEVAASTAQLVAASRVKAD--FNSKAQD 115
Query: 862 RLLAAAKNLAEATARMVEAARQCASHPQD 890
RL AA+K + A +V A +Q +D
Sbjct: 116 RLEAASKAVTNACKALVAAVKQGLEKEED 144
Score = 34.1 bits (79), Expect = 0.43
Identities = 16/77 (20%), Positives = 37/77 (48%), Gaps = 2/77 (2%)
Query: 1195 AANAIKHACNTLTNPSTTQQQILTAATVIAKHTSSLCNACRIASSKTTNPVAKRHFVQSA 1254
A N + A + + + ++++++ A+ +A T+ L A R+ + + A+ ++
Sbjct: 64 ATNILVEAADGVVQGTGSEEELIVASNEVAASTAQLVAASRVKADFNSK--AQDRLEAAS 121
Query: 1255 KDVANSTANLVQEIKAL 1271
K V N+ LV +K
Sbjct: 122 KAVTNACKALVAAVKQG 138
Score = 32.6 bits (75), Expect = 1.5
Identities = 38/169 (22%), Positives = 66/169 (39%), Gaps = 36/169 (21%)
Query: 1797 ENILKTAKALVEDTKTLVAGAASSQEQLAVAAQNAVSTIVQL--------------AEVV 1842
E IL+ AKA+ + LV A ++Q ++ VA ++ + A+ V
Sbjct: 3 EAILEAAKAITDAVAALVKAATAAQREI-VAQGKGSASRTEFYKKNSRWTEGLISAAKAV 61
Query: 1843 KFGAASL---------GSNNPEAQVLLINAVKDVTTALGDLIQATKAASGKTINDPCMNH 1893
L G+ + E LI A +V + L+ A++ + N +
Sbjct: 62 AGATNILVEAADGVVQGTGSEEE---LIVASNEVAASTAQLVAASRVKA--DFNSKAQDR 116
Query: 1894 LKESAKVMVTNVT-SLLKTVKAV----EDEHTRGTRALESTIEAIAQEI 1937
L+ ++K VTN +L+ VK ED+ L + E QE+
Sbjct: 117 LEAASKA-VTNACKALVAAVKQGLEKEEDQEDVDLSKL-TLHEGKTQEM 163
>gnl|CDD|214607 smart00307, ILWEQ, I/LWEQ domain. Thought to possess an F-actin
binding function.
Length = 200
Score = 204 bits (520), Expect = 8e-60
Identities = 93/205 (45%), Positives = 132/205 (64%), Gaps = 9/205 (4%)
Query: 2118 DETLNFDEMILEAAKSIAAATSALVKAASASQRELIDAGRMSRRPLTSSDDGQWSEDDGQ 2177
L DE ILEAAK+I A +ALVKAA+ +QRE++ GR + G++ + + +
Sbjct: 1 GVELEVDESILEAAKAITKAIAALVKAATNAQREIVAQGR------GGASPGEFYKKNSR 54
Query: 2178 WSEGLISAARLVAAATHTFVEAANSVVQGAGTEEKLISSAKQVASSTAQLLVACKVKADP 2237
W+EGLISAA+ VAAAT+ VEAA+ VV G G+EE+LI +AK+VA+STAQL+ A +VKAD
Sbjct: 55 WTEGLISAAKAVAAATNVLVEAADGVVTGKGSEEELIVAAKEVAASTAQLVAASRVKADK 114
Query: 2238 ESDATHRLQSAGNAVKRATDNLVRAAQQAI---QQDEERSLVLNRKMVGGIAQEINARSE 2294
+S A RLQ+A AV AT NLV A + + ++ EE + G QE+ + E
Sbjct: 115 DSQAQDRLQAASKAVTNATANLVAAVKSGMIFDEEQEEEEDFSKLSLHEGKTQEMEQQVE 174
Query: 2295 VLRIERQLEEARGRLTAIRQAKYKL 2319
+L++E +LE AR +L IR+ Y+L
Sbjct: 175 ILKLENELEAARKKLAEIRKQHYEL 199
Score = 43.5 bits (103), Expect = 5e-04
Identities = 31/108 (28%), Positives = 55/108 (50%), Gaps = 4/108 (3%)
Query: 802 AQDVETAVEVMMSSSDRLLAASGDAPEMVRQARILGQATAQLIQAIKGDAENEPDSELQR 861
A+ V A V++ ++D ++ G E++ A+ + +TAQL+ A + A+ DS+ Q
Sbjct: 63 AKAVAAATNVLVEAADGVVTGKGSEEELIVAAKEVAASTAQLVAASRVKAD--KDSQAQD 120
Query: 862 RLLAAAKNLAEATARMVEAARQCASHPQDIMKQEALVTTVEELRQAAT 909
RL AA+K + ATA +V A + D ++E + L + T
Sbjct: 121 RLQAASKAVTNATANLVAAVKSGMI--FDEEQEEEEDFSKLSLHEGKT 166
Score = 40.0 bits (94), Expect = 0.006
Identities = 44/182 (24%), Positives = 68/182 (37%), Gaps = 28/182 (15%)
Query: 673 EMQDTLLSLAKAVANTTAALVLKAKSVASTLPPNQQTS----------------VITSAT 716
E+ +++L AKA+ AALV A + + + +I++A
Sbjct: 5 EVDESILEAAKAITKAIAALVKAATNAQREIVAQGRGGASPGEFYKKNSRWTEGLISAAK 64
Query: 717 KCALATSQLV-ACTKVVAPTLENPACQQQLMAAVKEVANAVEGLVAMCN-ETCTDENLNK 774
A AT+ LV A VV +++L+ A KEVA + LVA + D
Sbjct: 65 AVAAATNVLVEAADGVVTGK----GSEEELIVAAKEVAASTAQLVAASRVKADKDSQAQD 120
Query: 775 DLTKAAAEVTKTLNQLLNHIKVTTTEPAQDVETAVEVMMSSSDRLLAASGDAPEMVRQAR 834
L A+ VT L+ +K + E +S G EM +Q
Sbjct: 121 RLQAASKAVTNATANLVAAVKSGMIFDEEQEEEEDFSKLS------LHEGKTQEMEQQVE 174
Query: 835 IL 836
IL
Sbjct: 175 IL 176
Score = 38.1 bits (89), Expect = 0.028
Identities = 30/140 (21%), Positives = 60/140 (42%), Gaps = 24/140 (17%)
Query: 1153 NVSDSICGLCEGVAQA------------SYLVAISEATSNTAN---------KGLIDQTQ 1191
V +SI + + +A +VA ++ +GLI +
Sbjct: 5 EVDESILEAAKAITKAIAALVKAATNAQREIVAQGRGGASPGEFYKKNSRWTEGLISAAK 64
Query: 1192 -FSRAANAIKHACNTLTNPSTTQQQILTAATVIAKHTSSLCNACRIASSKTTNPVAKRHF 1250
+ A N + A + + ++++++ AA +A T+ L A R+ + K + A+
Sbjct: 65 AVAAATNVLVEAADGVVTGKGSEEELIVAAKEVAASTAQLVAASRVKADK--DSQAQDRL 122
Query: 1251 VQSAKDVANSTANLVQEIKA 1270
++K V N+TANLV +K+
Sbjct: 123 QAASKAVTNATANLVAAVKS 142
>gnl|CDD|241305 cd10569, FERM_C_Talin, Talin FERM domain C-lobe/F3. Talin (also
called filopodin) plays an important role in initiating
actin filament growth in motile cell protrusions. It is
responsible for linking the cytoplasmic domains of
integrins to the actin-based cytoskeleton, and is
involved in vinculin, integrin and actin interactions.
At the leading edge of motile cells, talin colocalises
with the hyaluronan receptor layilin in transient
adhesions, some of which become more stable focal
adhesions (FA). During this maturation process, layilin
is replaced with integrins, where localized production
of PI(4,5)P(2) by type 1 phosphatidyl inositol phosphate
kinase type 1gamma (PIPK1gamma) is thought to play a
role in FA assembly. Talins are composed of a N-terminal
region FERM domain which us made up of 3 subdomains (N,
alpha-, and C-lobe-or- A-lobe, B-lobe, C-lobe -or- F1,
F2, F3) connected by short linkers, a talin rod which
binds vinculin, and a conserved C-terminal with actin-
and integrin-binding sites. There are 2 additional
actin-binding domains, one in the talin rod and the
other in the FERM domain. Both the F2 and F3 FERM
subdomains contribute to F-actin binding. Subdomain F3
of the FERM domain contains overlapping binding sites
for integrin cytoplasmic domains and for the type 1
gamma isoform of PIP-kinase (phosphatidylinositol
4-phosphate 5-kinase). The FERM domain has a cloverleaf
tripart structure . F3 within the FERM domain is part of
the PH domain family. The FERM domain is found in the
cytoskeletal-associated proteins such as ezrin, moesin,
radixin, 4.1R, and merlin. These proteins provide a link
between the membrane and cytoskeleton and are involved
in signal transduction pathways. The FERM domain is also
found in protein tyrosine phosphatases (PTPs) , the
tyrosine kinases FAK and JAK, in addition to other
proteins involved in signaling. This domain is
structurally similar to the PH and PTB domains and
consequently is capable of binding to both peptides and
phospholipids at different sites.
Length = 92
Score = 192 bits (490), Expect = 2e-57
Identities = 77/92 (83%), Positives = 84/92 (91%)
Query: 316 GVTFFLVKEKMKGKNKLVPRLLGVTKDSVLRLDERTKEIMKTWPLTTVRRWGASSNVFTL 375
GVTFFLVKEKMKGKNKLVPRLLG+TK+SVLR+DE TKE++K WPLTT++RW AS FTL
Sbjct: 1 GVTFFLVKEKMKGKNKLVPRLLGITKESVLRVDEETKEVLKVWPLTTIKRWAASPKSFTL 60
Query: 376 DFGDYSDNYYSVQTTEAEQIQQLIAGYIDIIL 407
DFGDYSDNYYSVQTTE EQI QLIAGYIDIIL
Sbjct: 61 DFGDYSDNYYSVQTTEGEQISQLIAGYIDIIL 92
>gnl|CDD|214604 smart00295, B41, Band 4.1 homologues. Also known as
ezrin/radixin/moesin (ERM) protein domains. Present in
myosins, ezrin, radixin, moesin, protein tyrosine
phosphatases. Plasma membrane-binding domain. These
proteins play structural and regulatory roles in the
assembly and stabilization of specialized plasmamembrane
domains. Some PDZ domain containing proteins bind one or
more of this family. Now includes JAKs.
Length = 201
Score = 188 bits (479), Expect = 4e-54
Identities = 76/237 (32%), Positives = 109/237 (45%), Gaps = 41/237 (17%)
Query: 89 TLKVRMLDGTLKTLLVDDSQPVANLMVVICTKIGITNHDEYSLVRENPEDEVENKPNFGT 148
LKV +LDGT VD S L+ +C K+GI + + L E+P
Sbjct: 1 VLKVYLLDGTTLEFEVDSSTTAEELLETVCRKLGIRESEYFGLQFEDP------------ 48
Query: 149 LTLKRKKEEKERDLKMEQLRKKLKTDDEVNWIDFSKTLREQGID-ENEPVLLRRKFFFSD 207
+D +W+D +KTL +Q + E + R KF+ D
Sbjct: 49 ------------------------DEDLRHWLDPAKTLLDQDVKSEPLTLYFRVKFYPPD 84
Query: 208 GNIDSHDPVQLNLLYVQARDAVLDGTHPVTQDLACQLAGIQTHIQFGDYNPSKHKPP-FL 266
N DP +LNLLY+Q R+ +L+G P ++ A LA + +FGDY+ H L
Sbjct: 85 PNQLKEDPTRLNLLYLQVRNDILEGRLPCPEEEALLLAALALQAEFGDYDEELHDLRGEL 144
Query: 267 DLKEFLPQSY---VKVKGIEKKIFSEHKNHVGLSELDAKVLYTKTCRSLPTYGVTFF 320
LK FLP+ K+K ++I HK +GLS +AK+ Y + R LPTYGV F
Sbjct: 145 SLKRFLPKQLLDSRKLKEWRERIVELHKELIGLSPEEAKLKYLELARKLPTYGVELF 201
Score = 31.1 bits (71), Expect = 4.5
Identities = 21/84 (25%), Positives = 37/84 (44%), Gaps = 9/84 (10%)
Query: 6 LKICIVDRNVTKTMQFDPSTSVYDACRIIRDK--ISEANFGEAKDYGLFLSDGDVKKGVW 63
LK+ ++D T + D ST+ + + K I E+ + +GL D D W
Sbjct: 2 LKVYLLD-GTTLEFEVDSSTTAEELLETVCRKLGIRESEY-----FGLQFEDPDEDLRHW 55
Query: 64 LEPGRNLEYYILRNGDE-LEYRRK 86
L+P + L +++ L +R K
Sbjct: 56 LDPAKTLLDQDVKSEPLTLYFRVK 79
>gnl|CDD|213393 cd12150, talin-RS, rod-segment of the talin C-terminal domain. The
talin rod-segment characterize by this model interacts
with its N-terminal FERM domain to mask its
integrin-binding site and interferes with interactions
between the FERM domain and the cellular membrane. Talin
is a large and ubiquitous cytoskeletal protein
concentrated at focal adhesion sites. It is involved in
linking integrins to the actin cytoskeleton.
Length = 172
Score = 180 bits (459), Expect = 6e-52
Identities = 80/170 (47%), Positives = 115/170 (67%), Gaps = 4/170 (2%)
Query: 1380 APGQKECDQAIEAISSRLRELDEVAMLAVSQGQIPHYNSASLQMSAEKTEQAANEILTRL 1439
APGQ+ECDQAIE +++ +RELD+ ++ A+SQG P SLQ E+ + +EIL ++
Sbjct: 2 APGQRECDQAIETLNNCIRELDQASLAAISQGLAPR-RDNSLQGFQEQMLHSVSEILDKI 60
Query: 1440 EPLRQAAKYQAESIAFSVNQLVTSFDSLASDSMNVASNLIHSKQQMTLLDQTKTVAECLL 1499
EPLR AAK +AE + +V Q+ F+ L ++ AS ++S+QQM LLDQTKTVAE L
Sbjct: 61 EPLRSAAKGEAEQLGHAVTQMAQYFEPLVQAAIGAASKTVNSQQQMALLDQTKTVAESAL 120
Query: 1500 QVLHLIKEAGGNPDAVNIHPDLDESIEATKEALSDITSSLDHF---TGVV 1546
Q+++ KEAGGNP AV+ HP +DE+ + KEA+ D+T +L+ GVV
Sbjct: 121 QLVYAAKEAGGNPKAVHAHPAVDEAAQMLKEAIEDLTQTLEEAASEAGVV 170
Score = 39.5 bits (93), Expect = 0.006
Identities = 38/170 (22%), Positives = 68/170 (40%), Gaps = 23/170 (13%)
Query: 1753 GTQACINAASTVSGIIGDLDTTIMFATAGTLHAEKENDTFADHRENILKTAKALVEDTKT 1812
G + C A T++ I +LD + A + L ++N + + E
Sbjct: 4 GQRECDQAIETLNNCIRELDQASLAAISQGLAPRRDN------------SLQGFQEQMLH 51
Query: 1813 LVAGAASSQEQLAVAAQN-------AVSTIVQLAEVVKF---GAASLGSNNPEAQVLLIN 1862
V+ E L AA+ AV+ + Q E + GAAS + N + Q+ L++
Sbjct: 52 SVSEILDKIEPLRSAAKGEAEQLGHAVTQMAQYFEPLVQAAIGAASK-TVNSQQQMALLD 110
Query: 1863 AVKDVTTALGDLIQATKAASGKTINDPCMNHLKESAKVMVTNVTSLLKTV 1912
K V + L+ A K A G + E+A+++ + L +T+
Sbjct: 111 QTKTVAESALQLVYAAKEAGGNPKAVHAHPAVDEAAQMLKEAIEDLTQTL 160
Score = 37.6 bits (88), Expect = 0.027
Identities = 31/157 (19%), Positives = 70/157 (44%), Gaps = 9/157 (5%)
Query: 930 PGQQEIEE--------ITEIIESTYEQIHTDDFPRSTKPIGRLQQELSSAATGLSETTNE 981
PGQ+E ++ I E+ +++ I PR + Q+++ + + + +
Sbjct: 3 PGQRECDQAIETLNNCIRELDQASLAAISQGLAPRRDNSLQGFQEQMLHSVSEILDKIEP 62
Query: 982 VISSVK-NPANLPASSKQYSHSLQNLVDIGMEIISTTESRETQTKMLSSLKSVSTSSSKF 1040
+ S+ K L + Q + + LV + S T + + Q +L K+V+ S+ +
Sbjct: 63 LRSAAKGEAEQLGHAVTQMAQYFEPLVQAAIGAASKTVNSQQQMALLDQTKTVAESALQL 122
Query: 1041 LSTARSAALDPSASNSKSQLSAAARNVADSINNLLNI 1077
+ A+ A +P A ++ + AA+ + ++I +L
Sbjct: 123 VYAAKEAGGNPKAVHAHPAVDEAAQMLKEAIEDLTQT 159
Score = 37.2 bits (87), Expect = 0.038
Identities = 24/87 (27%), Positives = 44/87 (50%)
Query: 821 AASGDAPEMVRQARILGQATAQLIQAIKGDAENEPDSELQRRLLAAAKNLAEATARMVEA 880
AA G+A ++ + Q L+QA G A +S+ Q LL K +AE+ ++V A
Sbjct: 66 AAKGEAEQLGHAVTQMAQYFEPLVQAAIGAASKTVNSQQQMALLDQTKTVAESALQLVYA 125
Query: 881 ARQCASHPQDIMKQEALVTTVEELRQA 907
A++ +P+ + A+ + L++A
Sbjct: 126 AKEAGGNPKAVHAHPAVDEAAQMLKEA 152
Score = 30.7 bits (70), Expect = 6.2
Identities = 26/117 (22%), Positives = 46/117 (39%), Gaps = 16/117 (13%)
Query: 1083 PGQKECDNAIRNIQSMKPFLDKPT--------EPINDMSYYECHNLIMEKSKSLGEGMTG 1134
PGQ+ECD AI + + LD+ + P D S ++ + + +
Sbjct: 3 PGQRECDQAIETLNNCIRELDQASLAAISQGLAPRRDNSLQGFQEQMLHSVSEILDKIEP 62
Query: 1135 MANHAKHSEYDAFGKCVNNVSDSICGLCEG-VAQASYLVAISEATSNTANKGLIDQT 1190
+ + AK E + G V ++ L + + AS V + + L+DQT
Sbjct: 63 LRSAAK-GEAEQLGHAVTQMAQYFEPLVQAAIGAASKTVNSQQQMA------LLDQT 112
>gnl|CDD|149993 pfam09141, Talin_middle, Talin, middle domain. Members of this
family adopt a structure consisting of five alpha
helices that fold into a bundle. They contain a Vinculin
binding site (VBS) composed of a hydrophobic surface
spanning five turns of helix four. Activation of the VBS
causes subsequent recruitment of Vinculin, which enables
maturation of small integrin/talin complexes into more
stable adhesions. Formation of the complex between VBS
and Vinculin requires prior unfolding of this middle
domain: once released from the talin hydrophobic core,
the VBS helix is then available to induce the 'bundle
conversion' conformational change within the vinculin
head domain thereby displacing the intramolecular
interaction with the vinculin tail, allowing vinculin to
bind actin.
Length = 161
Score = 177 bits (451), Expect = 4e-51
Identities = 93/160 (58%), Positives = 119/160 (74%), Gaps = 5/160 (3%)
Query: 509 QKALLSTITEGHEVITTVEKELISKAIIPDLGNDAASLKWKETTVDANKHNVSSQIAAMN 568
Q+AL+ TI+ G + + ++EL KA IP LG D AS W+E T+D +K NV S++AAM
Sbjct: 2 QQALMGTISAGIDAVNAAQEELEDKAQIPPLGQDPASKAWRENTLDVSKQNVHSRLAAMT 61
Query: 569 AATAQVVTMTSGEV--TDYSGVESAITSISHTLPEMSKGVRMLAALT---PSGDELLDAA 623
AATA VV +T+GE TDY+ V +A+T+IS LPE+SKGV++LAAL +GD+LLDAA
Sbjct: 62 AATASVVNLTAGEPADTDYTAVGAAVTTISSNLPEVSKGVKLLAALMEDDGNGDDLLDAA 121
Query: 624 RKLCFAFTDLLKAAQPHSNQPRQNLLNAATRVGEASHHVL 663
RKL AF+DLLKAAQP S +PRQNLLNAA VGEAS H+L
Sbjct: 122 RKLAGAFSDLLKAAQPESKEPRQNLLNAAGNVGEASGHLL 161
>gnl|CDD|215882 pfam00373, FERM_M, FERM central domain. This domain is the central
structural domain of the FERM domain.
Length = 113
Score = 120 bits (304), Expect = 8e-32
Identities = 49/111 (44%), Positives = 66/111 (59%), Gaps = 4/111 (3%)
Query: 214 DPVQLNLLYVQARDAVLDGTHPVTQDLACQLAGIQTHIQFGDYNPSKHKPPFLDLKE-FL 272
D V LLY+Q + +L+G P +++ A LA + +FGDYNP KH +L E FL
Sbjct: 3 DEVTRELLYLQLKRDILEGRLPCSEEEALLLAALALQAEFGDYNPEKHSSSYLKELEYFL 62
Query: 273 PQSYV---KVKGIEKKIFSEHKNHVGLSELDAKVLYTKTCRSLPTYGVTFF 320
P + K K +EK+I HKN GLS +AK+ Y + +SLPTYGVTFF
Sbjct: 63 PSRLIKKEKSKELEKRILEAHKNLRGLSPAEAKLKYLQIAQSLPTYGVTFF 113
>gnl|CDD|204093 pfam08913, VBS, Vinculin Binding Site. Vinculin binding sites are
predominantly found in talin and talin-like molecules,
enabling binding of vinculin to talin, stabilising
integrin-mediated cell-matrix junctions. Talin, in turn,
links integrins to the actin cytoskeleton. The consensus
sequence for Vinculin binding sites is
LxxAAxxVAxxVxxLIxxA, with a secondary structure
prediction of four amphipathic helices. The hydrophobic
residues that define the VBS are themselves 'masked' and
are buried in the core of a series of helical bundles
that make up the talin rod.
Length = 125
Score = 119 bits (300), Expect = 3e-31
Identities = 56/125 (44%), Positives = 77/125 (61%), Gaps = 1/125 (0%)
Query: 1629 SYVDYHTRMVGSSKEIARISQEMMTKSWSDVKSMSGLSSQLTHQYSKLCTDCIGAVASAS 1688
++VDY T MV +K IA +QEM+TKS ++ + + L++QLT Y +L D GA A+A
Sbjct: 1 TFVDYQTTMVKYAKAIAVTAQEMVTKSNTNPEELGQLANQLTSDYGQLAQDAKGAAATAE 60
Query: 1689 NPEVSGRLCGAVHDLGTACINTVTMAATCQTSGDD-YTHREFADTNRVLAEKVSQVLYAL 1747
+ E+ R+ V DLG CI V A Q S D YT +E + R ++EKVSQVL AL
Sbjct: 61 SEEIGFRIKTRVQDLGHGCIALVQKAGALQASPSDSYTKKELIECARRVSEKVSQVLAAL 120
Query: 1748 QAGSR 1752
QAG+R
Sbjct: 121 QAGNR 125
Score = 30.6 bits (69), Expect = 3.2
Identities = 22/99 (22%), Positives = 43/99 (43%), Gaps = 1/99 (1%)
Query: 978 TTNEVIS-SVKNPANLPASSKQYSHSLQNLVDIGMEIISTTESRETQTKMLSSLKSVSTS 1036
T E+++ S NP L + Q + L +T ES E ++ + ++ +
Sbjct: 19 TAQEMVTKSNTNPEELGQLANQLTSDYGQLAQDAKGAAATAESEEIGFRIKTRVQDLGHG 78
Query: 1037 SSKFLSTARSAALDPSASNSKSQLSAAARNVADSINNLL 1075
+ A + PS S +K +L AR V++ ++ +L
Sbjct: 79 CIALVQKAGALQASPSDSYTKKELIECARRVSEKVSQVL 117
Score = 29.8 bits (67), Expect = 7.6
Identities = 29/124 (23%), Positives = 55/124 (44%), Gaps = 2/124 (1%)
Query: 1791 TFADHRENILKTAKALVEDTKTLVAGAASSQEQLAVAAQNAVSTIVQLAEVVKFGAASLG 1850
TF D++ ++K AKA+ + +V + ++ E+L A S QLA+ K A+
Sbjct: 1 TFVDYQTTMVKYAKAIAVTAQEMVTKSNTNPEELGQLANQLTSDYGQLAQDAK--GAAAT 58
Query: 1851 SNNPEAQVLLINAVKDVTTALGDLIQATKAASGKTINDPCMNHLKESAKVMVTNVTSLLK 1910
+ + E + V+D+ L+Q A + L E A+ + V+ +L
Sbjct: 59 AESEEIGFRIKTRVQDLGHGCIALVQKAGALQASPSDSYTKKELIECARRVSEKVSQVLA 118
Query: 1911 TVKA 1914
++A
Sbjct: 119 ALQA 122
>gnl|CDD|241353 cd13199, FERM_C2_MyoVII, Myosin VII (MyoVII, Myo7) FERM domain
C-lobe, repeat 2. MyoVII, a MyTH-FERM myosin, is an
actin-based motor protein essential for a variety of
biological processes in the actin cytoskeleton function.
Mutations in MyoVII leads to problems in sensory
perception: deafness and blindness in humans (Usher
Syndrome), retinal defects and deafness in mice (shaker
1), and aberrant auditory and vestibular function in
zebrafish. Myosin VIIAs have plus (barbed) end-directed
motor activity on actin filaments and a characteristic
actin-activated ATPase activity. MyoVII consists of a
conserved spectrin-like, SH3 subdomain N-terminal
region, a motor/head region, a neck made of 4-5 IQ
motifs, and a tail consisting of a coiled-coil domain,
followed by a tandem repeat of myosin tail homology 4
(MyTH4) domains and partial FERM domains that are
separated by an SH3 subdomain and are thought to mediate
dimerization and binding to other proteins or cargo.
Members include: MyoVIIa, MyoVIIb, and MyoVII members
that do not have distinct myosin VIIA and myosin VIIB
genes. The FERM domain has a cloverleaf tripart
structure (FERM_N, FERM_M, FERM_C/N, alpha-, and
C-lobe/A-lobe, B-lobe, C-lobe/F1, F2, F3). The C-lobe/F3
within the FERM domain is part of the PH domain family.
The FERM domain is found in the cytoskeletal-associated
proteins such as ezrin, moesin, radixin, 4.1R, and
merlin. These proteins provide a link between the
membrane and cytoskeleton and are involved in signal
transduction pathways. The FERM domain is also found in
protein tyrosine phosphatases (PTPs) , the tyrosine
kinases FAK and JAK, in addition to other proteins
involved in signaling. This domain is structurally
similar to the PH and PTB domains and consequently is
capable of binding to both peptides and phospholipids at
different sites.
Length = 176
Score = 80.4 bits (199), Expect = 5e-17
Identities = 48/178 (26%), Positives = 85/178 (47%), Gaps = 10/178 (5%)
Query: 238 QDLACQLAGIQTHIQFGDYNPSKHKPPFLD-LKEFLPQSYVKVKGIE---KKIFSEHKNH 293
++ A QLA + ++FGD LKE +P +K++ + K I + + H
Sbjct: 1 KEDAIQLAALIYRVRFGDDK--SQFQSIPKMLKELIPADLIKLQSPDEWKKLIIAAYNKH 58
Query: 294 VGLSELDAKVLYTKTCRSLPTYGVTFFLVKEKMKGKNKLVPRLL-GVTKDSVLRLDERTK 352
G+S +AK+ + K PT+G FF VK+ L LL + K+ V +D +TK
Sbjct: 59 AGMSSEEAKLAFLKIIYRWPTFGSAFFEVKQ--TTDPNLPEILLIAINKNGVSLIDPKTK 116
Query: 353 EIMKTWPLTTVRRWGASSNVFTLDFGDY-SDNYYSVQTTEAEQIQQLIAGYIDIILKK 409
EI+ T+P T + W + + F + G+ + +T+ ++ L+ YI ++L
Sbjct: 117 EILVTYPFTKISNWSSGNTYFHMTIGNLVRGSKLLCETSLGYKMDDLLTSYISLLLSN 174
>gnl|CDD|220215 pfam09379, FERM_N, FERM N-terminal domain. This domain is the
N-terminal ubiquitin-like structural domain of the FERM
domain.
Length = 79
Score = 58.8 bits (143), Expect = 2e-10
Identities = 29/116 (25%), Positives = 43/116 (37%), Gaps = 39/116 (33%)
Query: 92 VRMLDGTLKTLLVDDSQPVANLMVVICTKIGITNHDEYSLVRENPEDEVENKPNFGTLTL 151
VR+LDGT VD S L+ +C ++G+ D + L + +K N
Sbjct: 1 VRLLDGTQLEFTVDKSATGQELLDQVCQRLGLREKDYFGL-------QFNDKKN------ 47
Query: 152 KRKKEEKERDLKMEQLRKKLKTDDEVNWIDFSKTLREQGIDENEP--VLLRRKFFF 205
E W+D K LR+QG D + P + R KF+
Sbjct: 48 ------------------------ERIWLDLDKKLRKQGKDGDPPFTLFFRVKFYP 79
>gnl|CDD|241233 cd00836, FERM_C-lobe, FERM domain C-lobe. The FERM domain has a
cloverleaf tripart structure (FERM_N, FERM_M, FERM_C/N,
alpha-, and C-lobe/A-lobe, B-lobe, C-lobe/F1, F2, F3).
The C-lobe/F3 within the FERM domain is part of the PH
domain family. The FERM domain is found in the
cytoskeletal-associated proteins such as ezrin, moesin,
radixin, 4.1R, and merlin. These proteins provide a link
between the membrane and cytoskeleton and are involved
in signal transduction pathways. The FERM domain is also
found in protein tyrosine phosphatases (PTPs), the
tyrosine kinases FAK and JAK, in addition to other
proteins involved in signaling. This domain is
structurally similar to the PH and PTB domains and
consequently is capable of binding to both peptides and
phospholipids at different sites.
Length = 91
Score = 57.8 bits (140), Expect = 5e-10
Identities = 26/95 (27%), Positives = 42/95 (44%), Gaps = 7/95 (7%)
Query: 316 GVTFFLVKEKMKGKNKLVPRLLGVTKDSVLRLDERTKEIMKTWPLTTVRRWGASSNVFTL 375
GV FF VK+K G +LGV+ + + LD+ T + + +R+ S FT+
Sbjct: 1 GVEFFDVKDKSGGS----ELILGVSLEGISVLDDNTGNPLTLFRWPEIRKISFSKKTFTI 56
Query: 376 DFGDYSDNYYSVQT---TEAEQIQQLIAGYIDIIL 407
+ + + QT EA+ I +L GY
Sbjct: 57 EIRGDKEEKLAFQTSSPREAKYIWKLCVGYHRFYR 91
>gnl|CDD|216916 pfam02174, IRS, PTB domain (IRS-1 type).
Length = 100
Score = 47.6 bits (114), Expect = 3e-06
Identities = 18/71 (25%), Positives = 39/71 (54%), Gaps = 3/71 (4%)
Query: 336 LLGVTKDSVLRLDERTKEIMKTWPLTTVRRWGASSNVFTLDFGDYSDN---YYSVQTTEA 392
L +T +++ D ++ + +WPLT++RR+G N+F+ + G ++ QT +A
Sbjct: 25 RLCLTPEALTLDDLNSRVPLVSWPLTSLRRYGRDKNLFSFEAGRRCVTGEGEFTFQTDDA 84
Query: 393 EQIQQLIAGYI 403
E+I + + +
Sbjct: 85 EEIFETVQAAM 95
>gnl|CDD|241359 cd13205, FERM_C_fermitin, Fermitin family FERM domain C-lobe.
Fermitin functions as a mediator of integrin inside-out
signalling. The recruitment of Fermitin proteins and
Talin to the membrane mediates the terminal event of
integrin signalling, via interaction with integrin beta
subunits. Fermatin has FERM domain interrupted with a
pleckstrin homology (PH) domain. Fermitin family
homologs (Fermt1, 2, and 3, also known as Kindlins) are
each encoded by a different gene. In mammalian studies,
Fermt1 is generally expressed in epithelial cells,
Fermt2 is expressed inmuscle tissues, and Fermt3 is
expressed in hematopoietic lineages. Specifically Fermt2
is expressed in smooth and striated muscle tissues in
mice and in the somites (a trunk muscle precursor) and
neural crest in Xenopus embryos. As such it has been
proposed that Fermt2 plays a role in cardiomyocyte and
neural crest differentiation. Expression of mammalian
Fermt3 is associated with hematopoietic lineages: the
anterior ventral blood islands, vitelline veins, and
early myeloid cells. In Xenopus embryos this expression,
also include the notochord and cement gland. The FERM
domain has a cloverleaf tripart structure (FERM_N,
FERM_M, FERM_C/N, alpha-, and C-lobe/A-lobe, B-lobe,
C-lobe/F1, F2, F3). This cd is not included in the
C-lobe hierarchy based on its position in the tree. One
thing to note is that unlike the other members of the
C-lobe hierarchy it contains 2 FERM M domains which
might also reflect a difference in its evolutionary
history. The C-lobe/F3 within the FERM domain is part of
the PH domain family. The FERM domain is found in the
cytoskeletal-associated proteins such as ezrin, moesin,
radixin, 4.1R, and merlin. These proteins provide a link
between the membrane and cytoskeleton and are involved
in signal transduction pathways. The FERM domain is also
found in protein tyrosine phosphatases (PTPs) , the
tyrosine kinases FAK and JAK, in addition to other
proteins involved in signaling. This domain is
structurally similar to the PH and PTB domains and
consequently is capable of binding to both peptides and
phospholipids at different sites.
Length = 89
Score = 43.5 bits (103), Expect = 6e-05
Identities = 25/94 (26%), Positives = 50/94 (53%), Gaps = 15/94 (15%)
Query: 316 GVTFFLVKEKMKGKNKLVPRLLGVTKDSVLRLDERTKEIMKTWPLTTVRRWGASSNV--- 372
G+T+F+V+ + K++L LGV + ++R+D T +++KTW +T++ W NV
Sbjct: 1 GITYFIVRFRGSKKDEL----LGVAYNRLIRMDLHTGDVLKTWRYSTMKAW----NVNWE 52
Query: 373 ---FTLDFGDYSDNYYSVQTTEAEQIQQLIAGYI 403
+ F D ++ + + + + + I GYI
Sbjct: 53 IREVIIQFED-ESIAFACLSADCKIVHEFIGGYI 85
>gnl|CDD|241357 cd13203, FERM_C1_myosin_like, Myosin-like FERM domain C-lobe,
repeat 1. These myosin-like proteins are unidentified
though they are sequence similar to myosin 1/myo1,
myosin 7/myoVII, and myosin 10/myoX. These myosin-like
proteins contain an N-terminal motor/head region and a
C-terminal tail consisting of two myosin tail homology 4
(MyTH4) and twos FERM domains. In myoX the FERM domain
forms a supramodule with its MyTH4 domain which binds to
the negatively charged E-hook region in the tails of
alpha- and beta-tubulin forming a proposed motorized
link between actin filaments and microtubules and a
similar thing might happen in these myosins. The FERM
domain has a cloverleaf tripart structure (FERM_N,
FERM_M, FERM_C/N, alpha-, and C-lobe/A-lobe, B-lobe,
C-lobe/F1, F2, F3). The first FERM_N repeat is present
in this hierarchy. The C-lobe/F3 within the FERM domain
is part of the PH domain family. The FERM domain is
found in the cytoskeletal-associated proteins such as
ezrin, moesin, radixin, 4.1R, and merlin. These proteins
provide a link between the membrane and cytoskeleton and
are involved in signal transduction pathways. The FERM
domain is also found in protein tyrosine phosphatases
(PTPs) , the tyrosine kinases FAK and JAK, in addition
to other proteins involved in signaling. This domain is
structurally similar to the PH and PTB domains and
consequently is capable of binding to both peptides and
phospholipids at different sites.
Length = 117
Score = 43.9 bits (104), Expect = 8e-05
Identities = 36/116 (31%), Positives = 50/116 (43%), Gaps = 14/116 (12%)
Query: 296 LSELDAKVLYTKTCRSLPTYGVTFFLVKEKMKG----KNKLVPRLLGVTKDSVLRLDERT 351
SEL AKVLY P YG T F V KG N L +LGV D ++ +T
Sbjct: 1 KSELQAKVLYLTCVMQYPLYGTTLFDV--TYKGFWSYPNNL---ILGVHCDGFKFVNPKT 55
Query: 352 KEIMKTWPLTTVRRWG--ASSNVFTLDFGDYSDNYYS---VQTTEAEQIQQLIAGY 402
K I+ + + + S +V TL + + +T + E+I LIA Y
Sbjct: 56 KAILAEYRYSDLESIEVDPSDDVLTLTLSQSVPDEHKCFMFETPQKEEIASLIASY 111
>gnl|CDD|241355 cd13201, FERM_C_MyoXV, Myosin XV (MyoXV/Myo15) FERM domain C-lobe.
MyoXV, a MyTH-FERM myosin, are actin-based motor
proteins essential for a variety of biological processes
in actin cytoskeleton function. Specifically MyoXV
functions in the actin organization in hair cells of the
organ of Corti. Mutations in Human MyoXVa causes
non-syndromic deafness, DFNB3 and the mouse shaker-2
mutation. MyoXV consists of a N-terminal motor/head
region, a neck made of 1-3 IQ motifs, and a tail that
consists of either a myosin tail homology 4 (MyTH4)
domains, followed by an SH3 domain, and a MyTH-FERM
domains as in rat Myo15 or two MyTH-FERM domains
separated by a SH3 domain as in human Myo15A. The
MyTH-FERM domains are thought to mediate dimerization
and binding to other proteins or cargo. The FERM domain
has a cloverleaf tripart structure (FERM_N, FERM_M,
FERM_C/N, alpha-, and C-lobe/A-lobe, B-lobe, C-lobe/F1,
F2, F3). The C-lobe/F3 within the FERM domain is part of
the PH domain family. The FERM domain is found in the
cytoskeletal-associated proteins such as ezrin, moesin,
radixin, 4.1R, and merlin. These proteins provide a link
between the membrane and cytoskeleton and are involved
in signal transduction pathways. The FERM domain is also
found in protein tyrosine phosphatases (PTPs) , the
tyrosine kinases FAK and JAK, in addition to other
proteins involved in signaling. This domain is
structurally similar to the PH and PTB domains and
consequently is capable of binding to both peptides and
phospholipids at different sites.
Length = 131
Score = 44.1 bits (105), Expect = 8e-05
Identities = 32/117 (27%), Positives = 53/117 (45%), Gaps = 8/117 (6%)
Query: 296 LSELDAKVLYTKTCRSLPTYGVTFFLVKEKMKGKNKLVPRLLGVTKDSVLRLDERTKEIM 355
LS A+ + + LP +G FF V +++ P LL V ++ + LD T E +
Sbjct: 11 LSPHQARAQFLEILSKLPLFGSNFFYV-QRVSDPRIPGPCLLAVNREGLHFLDPNTHETL 69
Query: 356 KTWPLTTV---RRWGA-SSNVFTLD--FGD-YSDNYYSVQTTEAEQIQQLIAGYIDI 405
T PL + R+ LD +G+ ++T +A +I +LIA YI+
Sbjct: 70 LTIPLKEIQSTRKLRPLEDGTPFLDIKYGNLMQQKTTRLETDQAHEISRLIAQYIEE 126
>gnl|CDD|241318 cd13164, PTB_DOK4_DOK5_DOK6, Downstream of tyrosine kinase 4, 5,
and 6 proteins phosphotyrosine-binding domain (PTBi).
The Dok family adapters are phosphorylated by different
protein tyrosine kinases. Dok proteins are involved in
processes such as modulation of cell differentiation and
proliferation, as well as in control of the cell
spreading and migration The Dok protein contains an
N-terminal pleckstrin homology (PH) domain followed by a
central phosphotyrosine binding (PTB) domain, which has
a PH-like fold, and a proline- and tyrosine-rich
C-terminal tail. The PH domain binds to acidic
phospholids and localizes proteins to the plasma
membrane, while the PTB domain mediates protein-protein
interactions by binding to phosphotyrosine-containing
motifs. The C-terminal part of Dok contains multiple
tyrosine phosphorylation sites that serve as potential
docking sites for Src homology 2-containing proteins
such as ras GTPase-activating protein and Nck, leading
to inhibition of ras signaling pathway activation and
the c-Jun N-terminal kinase (JNK) and c-Jun activation,
respectively. There are 7 mammalian Dok members: Dok-1
to Dok-7. Dok-1 and Dok-2 act as negative regulators of
the Ras-Erk pathway downstream of many
immunoreceptor-mediated signaling systems, and it is
believed that recruitment of p120 rasGAP by Dok-1 and
Dok-2 is critical to their negative regulation. Dok-3 is
a negative regulator of the activation of JNK and
mobilization of Ca2+ in B-cell receptor-mediated
signaling, interacting with SHIP-1 and Grb2. Dok-4- 6
play roles in protein tyrosine kinase(PTK)-mediated
signaling in neural cells and Dok-7 is the key
cytoplasmic activator of MuSK (Muscle-Specific Protein
Tyrosine Kinase). PTB domains have a common PH-like fold
and are found in various eukaryotic signaling molecules.
This domain was initially shown to binds peptides with a
NPXY motif with differing requirements for
phosphorylation of the tyrosine, although more recent
studies have found that some types of PTB domains can
bind to peptides lack tyrosine residues altogether. In
contrast to SH2 domains, which recognize phosphotyrosine
and adjacent carboxy-terminal residues, PTB-domain
binding specificity is conferred by residues
amino-terminal to the phosphotyrosine. PTB domains are
classified into three groups: phosphotyrosine-dependent
Shc-like, phosphotyrosine-dependent IRS-like, and
phosphotyrosine-independent Dab-like PTB domains. This
cd is part of the IRS-like subgroup.
Length = 103
Score = 42.0 bits (99), Expect = 3e-04
Identities = 25/68 (36%), Positives = 38/68 (55%), Gaps = 8/68 (11%)
Query: 336 LLGVTKDSVLRLD---ERTKEIMKTWPLTTVRRWGASSNVFTLDFG---DYSDNYYSVQT 389
LL +T +++ D R K + +WPLT++RR+G S FT + G D + ++ QT
Sbjct: 24 LLQITHENIYLWDIHNPRVK--LVSWPLTSLRRYGRDSTWFTFEAGRMCDTGEGLFTFQT 81
Query: 390 TEAEQIQQ 397
E EQI Q
Sbjct: 82 REGEQIYQ 89
>gnl|CDD|197644 smart00310, PTBI, Phosphotyrosine-binding domain (IRS1-like).
Length = 99
Score = 38.2 bits (89), Expect = 0.005
Identities = 14/45 (31%), Positives = 23/45 (51%), Gaps = 3/45 (6%)
Query: 358 WPLTTVRRWGASSNVFTLDFG---DYSDNYYSVQTTEAEQIQQLI 399
WPL ++RR+G F + G ++ QT A++I QL+
Sbjct: 46 WPLLSLRRYGRDKVFFFFEAGRRCVSGPGEFTFQTVVAQEIFQLV 90
>gnl|CDD|205692 pfam13514, AAA_27, AAA domain. This domain is found in a number of
double-strand DNA break proteins. This domain contains a
P-loop motif.
Length = 1118
Score = 39.4 bits (92), Expect = 0.032
Identities = 50/207 (24%), Positives = 83/207 (40%), Gaps = 27/207 (13%)
Query: 2115 QETDETLNFDEMILEAAKSIAAATSALVKAASASQRELIDAGRMSRRPLTSSDDGQWSED 2174
+E E L +LE A+ AA ++L + ++R L +A R S W E
Sbjct: 659 EELAELLELARQLLEEAEKQAARKASLDERLRDAERALEEA--EERHDEAQSALEAWQE- 715
Query: 2175 DGQWSEGLISAA---RLVAAATHTFVEAANSVVQGAGTEEKLISSAKQVASSTAQLLVAC 2231
QW + L+ A R A +E ++ +EKL Q A Q + A
Sbjct: 716 --QWYDALLEAGLGGRASPAGALDALELLQNI------KEKL-----QAADDLRQRIAAM 762
Query: 2232 KVK-ADPESDATHRLQSAGNAV-KRATDNLVRAAQQAIQQDEERSLVLNRKMVGGIAQEI 2289
+ A E + ++ + D RA +Q +++ + + + +A+EI
Sbjct: 763 ERDLARFEEEVEALAEAVAPEMLGTPADETARALKQRLKRARDTAAAAEK-----LAEEI 817
Query: 2290 N-ARSEVLRIERQLEEARGRLTAIRQA 2315
A EV L+EA RLTA+ +A
Sbjct: 818 EEAEKEVSEAAAALDEAEARLTALLRA 844
Score = 36.3 bits (84), Expect = 0.26
Identities = 27/116 (23%), Positives = 43/116 (37%), Gaps = 15/116 (12%)
Query: 818 RLLAASGDAPEMVRQARILGQATAQLIQAIKGDAENEPDSELQRRLLAA----------A 867
R+ A D + L +A A + G +E L++RL A A
Sbjct: 758 RIAAMERDLARFEEEVEALAEAVAP---EMLGTPADETARALKQRLKRARDTAAAAEKLA 814
Query: 868 KNLAEATARMVEAARQCASHPQDI--MKQEALVTTVEELRQAATPTLRYKLFNKSQ 921
+ + EA + EAA + + + A TT+EEL A + Y+ K
Sbjct: 815 EEIEEAEKEVSEAAAALDEAEARLTALLRAARCTTIEELLAAVERSDTYRELRKRI 870
>gnl|CDD|241239 cd01203, PTB_DOK1_DOK2_DOK3, Downstream of tyrosine kinase 1, 2,
and 3 proteins phosphotyrosine-binding domain (PTBi).
The Dok family adapters are phosphorylated by different
protein tyrosine kinases. Dok proteins are involved in
processes such as modulation of cell differentiation and
proliferation, as well as in control of the cell
spreading and migration The Dok protein contains an
N-terminal pleckstrin homology (PH) domain followed by a
central phosphotyrosine binding (PTB) domain, which has
a PH-like fold, and a proline- and tyrosine-rich
C-terminal tail. The PH domain is binds to acidic
phospholids and localizes proteins to the plasma
membrane, while the PTB domain mediates protein-protein
interactions by binding to phosphotyrosine-containing
motifs. The C-terminal part of Dok contains multiple
tyrosine phosphorylation sites that serve as potential
docking sites for Src homology 2-containing proteins
such as ras GTPase-activating protein and Nck, leading
to inhibition of ras signaling pathway activation and
the c-Jun N-terminal kinase (JNK) and c-Jun activation,
respectively. There are 7 mammalian Dok members: Dok-1
to Dok-7. Dok-1 and Dok-2 act as negative regulators of
the Ras-Erk pathway downstream of many
immunoreceptor-mediated signaling systems, and it is
believed that recruitment of p120 rasGAP by Dok-1 and
Dok-2 is critical to their negative regulation. Dok-3 is
a negative regulator of the activation of JNK and
mobilization of Ca2+ in B-cell receptor-mediated
signaling, interacting with SHIP-1 and Grb2. Dok-4- 6
play roles in protein tyrosine kinase(PTK)-mediated
signaling in neural cells and Dok-7 is the key
cytoplasmic activator of MuSK (Muscle-Specific Protein
Tyrosine Kinase). PTB domains have a common PH-like fold
and are found in various eukaryotic signaling molecules.
This domain was initially shown to binds peptides with a
NPXY motif with differing requirements for
phosphorylation of the tyrosine, although more recent
studies have found that some types of PTB domains can
bind to peptides lack tyrosine residues altogether. In
contrast to SH2 domains, which recognize phosphotyrosine
and adjacent carboxy-terminal residues, PTB-domain
binding specificity is conferred by residues
amino-terminal to the phosphotyrosine. PTB domains are
classified into three groups: phosphotyrosine-dependent
Shc-like, phosphotyrosine-dependent IRS-like, and
phosphotyrosine-independent Dab-like PTB domains. This
cd is part of the IRS-like subgroup.
Length = 99
Score = 35.2 bits (82), Expect = 0.049
Identities = 18/71 (25%), Positives = 35/71 (49%), Gaps = 3/71 (4%)
Query: 336 LLGVTKDSVLRLDERTKEIMKTWPLTTVRRWGASSNVFTLDFGDYSDN---YYSVQTTEA 392
LL D++ D TK+++ TWP +RR+G F+ + G D+ ++ +T +
Sbjct: 25 LLRAGPDALELKDPSTKQVLYTWPYRFLRRFGRDKGTFSFEAGRRCDSGEGLFTFETPQG 84
Query: 393 EQIQQLIAGYI 403
+I + + I
Sbjct: 85 NEIFRAVEAAI 95
>gnl|CDD|241356 cd13202, FERM_C_MyoX, Myosin X (MyoX, Myo10) FERM domain C-lobe.
MyoX, a MyTH-FERM myosin, is a molecular motor that has
crucial functions in the transport and/or tethering of
integrins in the actin-based extensions known as
filopodia, microtubule binding, and in netrin-mediated
axon guidance. It functions as a dimer. MyoX walks on
bundles of actin, rather than single filaments, unlike
the other unconventional myosins. MyoX is present in
organisms ranging from humans to choanoflagellates, but
not in Drosophila and Caenorhabditis elegans.MyoX
consists of a N-terminal motor/head region, a neck made
of 3 IQ motifs, and a tail consisting of a coiled-coil
domain, a PEST region, 3 PH domains, a myosin tail
homology 4 (MyTH4), and a FERM domain at its very
C-terminus. The MyoX FERM domain binds to the NPXY motif
of several beta-integrins, a key family of cell surface
receptors that are involved in cell adhesion and
migration. In addition the FERM domain binds to the
cytoplasmic domains of the netrin receptors DCC (deleted
in colorectal cancer) and neogenin. The FERM domain also
forms a supramodule with its MyTH4 domain which binds to
the negatively charged E-hook region in the tails of
alpha- and beta-tubulin forming a proposed motorized
link between actin filaments and microtubules. The FERM
domain has a cloverleaf tripart structure (FERM_N,
FERM_M, FERM_C/N, alpha-, and C-lobe/A-lobe, B-lobe,
C-lobe/F1, F2, F3). The C-lobe/F3 within the FERM domain
is part of the PH domain family. The FERM domain is
found in the cytoskeletal-associated proteins such as
ezrin, moesin, radixin, 4.1R, and merlin. These proteins
provide a link between the membrane and cytoskeleton and
are involved in signal transduction pathways. The FERM
domain is also found in protein tyrosine phosphatases
(PTPs) , the tyrosine kinases FAK and JAK, in addition
to other proteins involved in signaling. This domain is
structurally similar to the PH and PTB domains and
consequently is capable of binding to both peptides and
phospholipids at different sites.
Length = 111
Score = 34.6 bits (80), Expect = 0.11
Identities = 31/114 (27%), Positives = 50/114 (43%), Gaps = 4/114 (3%)
Query: 296 LSELDAKVLYTKTCRSLPTYGVTFFLVKEKMKGKNKLVPRLLGVTKDSVLRLDERTKEIM 355
+S+ DA Y R P YG T F V E K LGV+ V E +
Sbjct: 1 MSQEDAMAKYMAIIREWPGYGSTLFEV-ECNKEGGFPQELWLGVSAKGVSLYKRGEPEPL 59
Query: 356 KTWPLTTVRRWGAS-SNVFTLDFGDYSDNYYSVQTTEAEQIQQLIAGYIDIILK 408
+++P + +GA +N + + D +TT+ +I +L+ YI+ I+K
Sbjct: 60 ESFPYEKILSFGAPQANTYKIVVE--GDRELLFETTQVVEIAKLMKAYINEIVK 111
>gnl|CDD|219226 pfam06911, Senescence, Senescence-associated protein. This family
contains a number of plant senescence-associated proteins
of approximately 450 residues in length. In Hemerocallis,
petals have a genetically based program that leads to
senescence and cell death approximately 24 hours after
the flower opens, and it is believed that senescence
proteins produced around that time have a role in this
program. This family extends to the higher vertebrates
where the full-length protein is often a Spartin,
associated with mitochondrial membranes and
transportation along microtubules.
Length = 181
Score = 35.4 bits (82), Expect = 0.18
Identities = 26/147 (17%), Positives = 52/147 (35%), Gaps = 7/147 (4%)
Query: 2111 RRSLQETDETLNFDEMILEAAKSIAAATSALVKAASASQRELIDAGRMSRRPLTSSDDGQ 2170
+ T++ + E + + + A K + + + L +S G+
Sbjct: 32 ISKISPTEKPVEVSPSTKERLRRVKKLSKATAKVSKSVLNGVGKVAGNVGSSLANSVAGK 91
Query: 2171 WSEDDGQWSEGLISAARLVAAATHTFVEAANSVVQGAGTEEKLISSAKQVASSTAQLLVA 2230
DG+ E A VA A+ ++A ++V+ G K + + A++ V
Sbjct: 92 KKGKDGK-GEPNFDGALGVALAS---LDAFSTVLDGLEEAAKNVLKSLSDATTKV---VE 144
Query: 2231 CKVKADPESDATHRLQSAGNAVKRATD 2257
K + L +AGN A +
Sbjct: 145 HKYGEEAGEVTQDTLGTAGNVGLTAWN 171
>gnl|CDD|216263 pfam01044, Vinculin, Vinculin family.
Length = 850
Score = 36.2 bits (84), Expect = 0.22
Identities = 24/106 (22%), Positives = 46/106 (43%), Gaps = 13/106 (12%)
Query: 752 VANAVEGLVAMCNETCTDENLNKDLTKAAAEVTKTLNQLLN---HIKVTTTEPAQDVETA 808
+A V LV + D + DLT A V++ ++ L+ I ++ + QD+ A
Sbjct: 14 LAQQVTTLVITHEPSEKDGGASPDLTAPVAAVSQAVSNLIEVGYDIANSSPDLKQDMPPA 73
Query: 809 VEVMMSSSDRLLAASGDAPE----------MVRQARILGQATAQLI 844
+E + + + AS + ++R AR L A ++L+
Sbjct: 74 LERVEKTGQLMEQASREFASDPYSSPKRGKLIRGARGLLSAVSRLL 119
Score = 33.9 bits (78), Expect = 1.4
Identities = 26/118 (22%), Positives = 54/118 (45%), Gaps = 2/118 (1%)
Query: 958 TKPIGRLQQELSSAATGLSETTNEVISSVKNPANLPASSKQYSHSLQNLVDIGMEIISTT 1017
TK + ++ + L+ T L T +L A S ++ NL+++G +I +++
Sbjct: 4 TKTVEKILEPLAQQVTTLVITHEPSEKDGGASPDLTAPVAAVSQAVSNLIEVGYDIANSS 63
Query: 1018 ESRETQTKMLSSLKSVSTSSSKFLSTARSAALDPSASNSKSQLSAAARNVADSINNLL 1075
+ + M +L+ V + +R A DP +S + +L AR + +++ LL
Sbjct: 64 P--DLKQDMPPALERVEKTGQLMEQASREFASDPYSSPKRGKLIRGARGLLSAVSRLL 119
Score = 32.4 bits (74), Expect = 4.3
Identities = 29/207 (14%), Positives = 60/207 (28%), Gaps = 38/207 (18%)
Query: 822 ASGDAPEMVRQARILGQATAQLIQAIKGDAENEPDSELQRRLLAAAKNLAEATARMVEAA 881
+ D +V A + +++ K + +N D R+ A L+ M A
Sbjct: 512 QNADPQTLVATAGSIAGRANRVLLVAKAEMDNSEDPVYTERVKEAVDILSNTIPPMFAEA 571
Query: 882 RQCASHPQDIMKQEA-------LVTTVEELRQAATPTLRYKLFNKS-------------- 920
++ A + D ++ + V + A P + L N+S
Sbjct: 572 KEVAVNALDPGAAKSWEENNYEFLDAVRLVYDAVRPIRQAVLMNRSPPELPTDSEFERED 631
Query: 921 -----------QTN-EFEGLLPGQQEIEEITEIIESTYEQIHTDDFPRSTKPIGRLQQEL 968
+T P + + EE+ + +I +P +L
Sbjct: 632 EPADPRPPPPVETEPPPRPPPPPETDREEMRRLPPEEKAKIAA-----QVQPFLAAAHKL 686
Query: 969 SSAATGLSETTNEVISSVKNPANLPAS 995
N++I+ K +
Sbjct: 687 HREVAKWDSKGNDIIALAKRMCMIMME 713
>gnl|CDD|233973 TIGR02680, TIGR02680, TIGR02680 family protein. Members of this
protein family belong to a conserved gene four-gene
neighborhood found sporadically in a phylogenetically
broad range of bacteria: Nocardia farcinica,
Symbiobacterium thermophilum, and Streptomyces
avermitilis (Actinobacteria), Geobacillus kaustophilus
(Firmicutes), Azoarcus sp. EbN1 and Ralstonia
solanacearum (Betaproteobacteria). Proteins in this
family average over 1400 amino acids in length
[Hypothetical proteins, Conserved].
Length = 1353
Score = 36.3 bits (84), Expect = 0.24
Identities = 62/332 (18%), Positives = 113/332 (34%), Gaps = 59/332 (17%)
Query: 2019 GQEVAVQYRELLQTVLHILSRP--GDRIADS------KQALPPIS----RRIAQSLTELV 2066
G +Y LL L L +P + + +ALPP+ +A +L +L
Sbjct: 175 GFLGEERYAALLDL-LIQLRQPQLSKKPDEGVLSDALTEALPPLDDDELTDVADALEQLD 233
Query: 2067 SIAEQLKGSNWMDPDD--------------PTVIAE--TELLGAAASIDAAAKKLSSLR- 2109
++L+ ++ + T++ T L A D ++ L R
Sbjct: 234 EYRDELER---LEALERALRNFLQRYRRYARTMLRRRATRLRSAQTQYDQLSRDLGRARD 290
Query: 2110 ----PRRSLQETDETLNFDEMILEAAKSIAAATSALVKAASASQRELIDAGRMSRRPLTS 2165
R +E D E +A ++ A A + E A + +
Sbjct: 291 ELETAREEERELDARTEALEREADALRTRLEALQGSPAYQDAEELERARADAEALQAA-- 348
Query: 2166 SDDGQWSEDDGQWSEGLISAARLVAAATHTFVEAANSVVQGAGTEEKLISSAKQVASSTA 2225
++ E + +RL EA E +L ++ +Q+A +
Sbjct: 349 -----AADARQAIRE---AESRLEEERRRLDEEAGRL----DDAERELRAAREQLARAAE 396
Query: 2226 QLLVACKVKADPE-SDATHRLQSAGNAVKRATDNLVRAAQQAIQQDEERSLVLNRKM-VG 2283
+ ++ A+P+ + A LQ G A D + A + I Q E+ +L R+ V
Sbjct: 397 RAGLSPAHTAEPDAALAAQELQELG-----ALDARRQDADRVIAQRSEQVALLRRRDDVA 451
Query: 2284 GIAQEINARSEVLRIERQLEEARGRLTAIRQA 2315
A+ +A + R + EEA A
Sbjct: 452 DRAEATHAAARA-RRDELDEEAEQAAARAELA 482
>gnl|CDD|241341 cd13187, FERM_C_PTPH13, Protein tyrosine phosphatase non-receptor
13 (PTPH13) FERM domain C-lobe. There are many
functions of PTPN13 (also called PTPL1, PTP-BAS, hPTP1E,
FAP1, or PTPL1). Mice lacking PTPN13 activity have
abnormal regulation of signal transducer and activator
of transcription signaling in their T cells, mild
impairment of motor nerve repair, and a significant
reduction in the growth of retinal glia cultures. It
also plays a role in adipocyte differentiation. PTPN13
contains a kinase non-catalytic C-lobe domain (KIND), a
FERM domain with two potential phosphatidylinositol
4,5-biphosphate [PtdIns(4,5)P2]-binding motifs, 5 PDZ
domains, and a carboxy-terminal catalytic domain. There
is an nteraction between the FERM domain of PTPL1 and
PtdIns(4,5)P2 which is thought to regulate the membrane
localization of PTPN13. PDZ are protein/protein
interaction domains so there is the potential for
numerous partners that can actively participate in the
regulation of its phosphatase activity or can permit
direct or indirect recruitment of tyrosine
phosphorylated PTPL1 substrates. The FERM domain has a
cloverleaf tripart structure (FERM_N, FERM_M, FERM_C/N,
alpha-, and C-lobe/A-lobe, B-lobe, C-lobe/F1, F2, F3).
The C-lobe/F3 within the FERM domain is part of the PH
domain family. The FERM domain is found in the
cytoskeletal-associated proteins such as ezrin, moesin,
radixin, 4.1R, and merlin. These proteins provide a link
between the membrane and cytoskeleton and are involved
in signal transduction pathways. The FERM domain is also
found in protein tyrosine phosphatases (PTPs), the
tyrosine kinases FAK and JAK, in addition to other
proteins involved in signaling. This domain is
structurally similar to the PH and PTB domains and
consequently is capable of binding to both peptides and
phospholipids at different sites.
Length = 124
Score = 33.8 bits (78), Expect = 0.25
Identities = 19/46 (41%), Positives = 27/46 (58%), Gaps = 4/46 (8%)
Query: 295 GLSELDAKVLYTKTCRSLPTYGVTFFLV-KEKMKGKNKLVPRLLGV 339
GLSE +A++ + K C+ LP YGV F V +EK K+ LG+
Sbjct: 1 GLSEEEAELEFLKVCQKLPEYGVHFHRVYREK---KSSTGGIWLGI 43
>gnl|CDD|241238 cd01202, PTB_FRS2, Fibroblast growth factor receptor substrate 2
phosphotyrosine-binding domain. FRS2 (also called
Suc1-associated neurotrophic factor (SNT)-induced
tyrosine-phosphorylated target) proteins are
membrane-anchored adaptor proteins. They are composed
of an N-terminal myristoylation site followed by a
phosphotyrosine binding (PTB) domain, which has a
PH-like fold, and a C-terminal effector domain
containing multiple tyrosine and serine/threonine
phosphorylation site. The FRS2/SNT proteins show
increased tyrosine phosphorylation by activated
receptors, such as fibroblast growth factor receptor
(FGFR) and TrkA, recruit SH2 domain containing proteins
such as Grb2, and mediate signals from activated
receptors to a variety of downstream pathways. The PTB
domains of the SNT proteins directly interact with the
canonical NPXpY motif of TrkA in a
phosphorylationdependent manner, they directly bind to
the juxtamembrane region of FGFR in a
phosphorylation-independent manner. PTB domains have a
common PH-like fold and are found in various eukaryotic
signaling molecules. This domain was initially shown to
binds peptides with a NPXY motif with differing
requirements for phosphorylation of the tyrosine,
although more recent studies have found that some types
of PTB domains can bind to peptides lack tyrosine
residues altogether. In contrast to SH2 domains, which
recognize phosphotyrosine and adjacent carboxy-terminal
residues, PTB-domain binding specificity is conferred by
residues amino-terminal to the phosphotyrosine. PTB
domains are classified into three groups:
phosphotyrosine-dependent Shc-like,
phosphotyrosine-dependent IRS-like, and
phosphotyrosine-independent Dab-like PTB domains. This
cd is part of the IRS-like subgroup.
Length = 92
Score = 32.9 bits (76), Expect = 0.28
Identities = 24/77 (31%), Positives = 42/77 (54%), Gaps = 5/77 (6%)
Query: 330 NKLVPRLLGVTKDSVLRLDERTKEIMKTWPLTTVRRWGASSNVFTLDFGDYSDN---YYS 386
N++ +L VT ++ L L +R KE +K WPL +RR+G SN+F+ + G ++
Sbjct: 17 NEIGSGILEVT-ETELILYQRGKEPVK-WPLRCLRRYGYDSNLFSFESGRRCPTGPGIFA 74
Query: 387 VQTTEAEQIQQLIAGYI 403
+ AE++ L+ I
Sbjct: 75 FKCKRAEELFNLVQRLI 91
>gnl|CDD|189762 pfam00901, Orbi_VP5, Orbivirus outer capsid protein VP5.
cryoelectron microscopy indicates that VP5 is a trimer
implying that there are 360 copies of VP5 per virion.
Length = 507
Score = 35.8 bits (83), Expect = 0.30
Identities = 18/63 (28%), Positives = 31/63 (49%), Gaps = 3/63 (4%)
Query: 2245 LQSAGNAVKRATDNLVRAAQQAIQQDEERSLVLNRKMVGGIAQEINARSEVLRIERQ--L 2302
L+S VK +L R A+ ++ EER+ KM+ +I+A + +E++
Sbjct: 149 LKSYLKIVKEENKSLQRLAKALQKESEERTQD-ETKMIEEYRDKIDALKNAIEVEKEGLQ 207
Query: 2303 EEA 2305
EEA
Sbjct: 208 EEA 210
>gnl|CDD|241236 cd00934, PTB, Phosphotyrosine-binding (PTB) PH-like fold. PTB
domains have a common PH-like fold and are found in
various eukaryotic signaling molecules. This domain was
initially shown to bind peptides with a NPXY motif with
differing requirements for phosphorylation of the
tyrosine, although more recent studies have found that
some types of PTB domains can bind to peptides lack
tyrosine residues altogether. In contrast to SH2
domains, which recognize phosphotyrosine and adjacent
carboxy-terminal residues, PTB-domain binding
specificity is conferred by residues amino-terminal to
the phosphotyrosine. PTB domains are classified into
three groups: phosphotyrosine-dependent Shc-like,
phosphotyrosine-dependent IRS-like, and
phosphotyrosine-independent Dab-like PTB domains.
Length = 119
Score = 33.7 bits (77), Expect = 0.33
Identities = 18/56 (32%), Positives = 25/56 (44%), Gaps = 3/56 (5%)
Query: 321 LVKEKMKGKNKLVPRLLGVTKDSVLRLDERTKEIMKTWPLTTVRRWGA---SSNVF 373
L K K P LL V+ + V LD TKE++ PL+ + G + VF
Sbjct: 29 LALLLKSSKRKPGPVLLEVSPEGVKLLDLDTKELLLRHPLSRISYCGRDPDNPKVF 84
>gnl|CDD|130093 TIGR01021, rpsE_bact, ribosomal protein S5, bacterial/organelle type.
This model finds chloroplast ribosomal protein S5 as
well as bacterial ribosomal protein S5. A candidate
mitochondrial form (Saccharomyces cerevisiae YBR251W and
its homolog) differs substantially and is not included in
this model [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 154
Score = 34.2 bits (79), Expect = 0.37
Identities = 25/65 (38%), Positives = 30/65 (46%), Gaps = 8/65 (12%)
Query: 1826 VAAQNAVSTIVQLAEVVKFGAASLGSNNPEAQVLLINAVKDVTTALGDLIQATKAAS--G 1883
V A AV I++LA V A SLGSNNP IN V+ AL L A G
Sbjct: 96 VIAGGAVRAILELAGVKDILAKSLGSNNP------INVVRATFDALLKLKSPEDVAELRG 149
Query: 1884 KTIND 1888
K + +
Sbjct: 150 KPVEE 154
>gnl|CDD|214563 smart00213, UBQ, Ubiquitin homologues. Ubiquitin-mediated
proteolysis is involved in the regulated turnover of
proteins required for controlling cell cycle
progression.
Length = 72
Score = 31.8 bits (73), Expect = 0.54
Identities = 14/35 (40%), Positives = 16/35 (45%)
Query: 89 TLKVRMLDGTLKTLLVDDSQPVANLMVVICTKIGI 123
L V+ LDG TL V S V+ L I GI
Sbjct: 2 ELTVKTLDGKTITLEVKPSDTVSELKEKIAELTGI 36
>gnl|CDD|236769 PRK10820, PRK10820, DNA-binding transcriptional regulator TyrR;
Provisional.
Length = 520
Score = 34.3 bits (79), Expect = 0.89
Identities = 25/79 (31%), Positives = 36/79 (45%), Gaps = 8/79 (10%)
Query: 817 DRLLAASGDAPEMVRQARILGQATAQLIQAIKGDAENEPDSELQRRLLAAAKNLAEATAR 876
+++A S ++V QAR L A L+ I GD D LLA A +L +
Sbjct: 204 SQIVAVSPKMRQVVEQARKLAMLDAPLL--ITGDTGTGKD------LLAYACHLRSPRGK 255
Query: 877 MVEAARQCASHPQDIMKQE 895
A CAS P D+++ E
Sbjct: 256 KPFLALNCASIPDDVVESE 274
>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common
bacterial type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. This family
represents the SMC protein of most bacteria. The smc gene
is often associated with scpB (TIGR00281) and scpA genes,
where scp stands for segregation and condensation
protein. SMC was shown (in Caulobacter crescentus) to be
induced early in S phase but present and bound to DNA
throughout the cell cycle [Cellular processes, Cell
division, DNA metabolism, Chromosome-associated
proteins].
Length = 1179
Score = 34.3 bits (79), Expect = 1.0
Identities = 54/363 (14%), Positives = 115/363 (31%), Gaps = 53/363 (14%)
Query: 1980 DVIVAANMGRKAISDMLAVCKGCSNAAETHELCVKTLDAGQEVAVQYR----------EL 2029
D++ RKA+S +L L V LD E+A + R +L
Sbjct: 606 DLVKFDPKLRKALSYLLG-----------GVLVVDDLDNALELAKKLRPGYRIVTLDGDL 654
Query: 2030 L-----------QTVLHILSRPGDRIADSKQALPPISRRIAQSLTELVSIAEQLKGSNWM 2078
+ +T IL R I + ++ + + +IA+ L + ++L+
Sbjct: 655 VRPGGVITGGSAKTNSSILER-RREIEELEEKIEELEEKIAELEKALAELRKELE----- 708
Query: 2079 DPDDPTVIAETELLGAAASIDAAAKKLSSLRPRRSLQETDETLNFDEMILEAAKSIAAAT 2138
+ ++ EL + I A K L+ L Q + + + E I
Sbjct: 709 ELEEELEQLRKELEELSRQISALRKDLARLE-AEVEQLEERIAQLSKELTELEAEIEELE 767
Query: 2139 SALVKAASASQRELIDAGRMSRRPLTSSDDGQWSEDDGQWSEGLISAARLVAAATHTFVE 2198
L +A +A + + R + E
Sbjct: 768 ERLEEAEEELAE--AEAEIEELEAQIEQLKEELKALREA-----LDELRAELTLLN---E 817
Query: 2199 AANSVVQGAGTEEKLISSAKQVASSTAQLLVACKVKADPESDATHRLQSAGNAVKRATDN 2258
A ++ + + E+ I++ ++ + + + ++ ++ ++
Sbjct: 818 EAANLRERLESLERRIAATERRLEDLEEQI---EELSEDIESLAAEIEELEELIEELESE 874
Query: 2259 LVRAAQQAIQQDEERSLVLNRKMVGGIAQEINARSEVLRIERQLEEARGRLTAIRQAKYK 2318
L A EE +L ++ + S+ + R+LEE R +L +
Sbjct: 875 LE-ALLNERASLEEALALLRSELEELSEELRELESKRSELRRELEELREKLAQLELRLEG 933
Query: 2319 LKG 2321
L+
Sbjct: 934 LEV 936
Score = 31.2 bits (71), Expect = 9.5
Identities = 14/82 (17%), Positives = 31/82 (37%), Gaps = 4/82 (4%)
Query: 2244 RLQSAGNAVKRATDNLVRAAQQAIQQDEERSLVLNRKMVGGIAQEI----NARSEVLRIE 2299
++ ++R D R Q+ + ++ +++ + + + E+ R+E
Sbjct: 401 EIERLEARLERLEDRRERLQQEIEELLKKLEEAELKELQAELEELEEELEELQEELERLE 460
Query: 2300 RQLEEARGRLTAIRQAKYKLKG 2321
LEE R L QA +
Sbjct: 461 EALEELREELEEAEQALDAAER 482
>gnl|CDD|224455 COG1538, TolC, Outer membrane protein [Cell envelope biogenesis,
outer membrane / Intracellular trafficking and
secretion].
Length = 457
Score = 34.0 bits (78), Expect = 1.1
Identities = 36/193 (18%), Positives = 63/193 (32%), Gaps = 31/193 (16%)
Query: 2128 LEAAKSIAAATSALVKAASASQRELIDAGRMSRRPLTSSDDGQWSEDDGQWSEGLISAAR 2187
L A + A + + A R + R + P S + G +S+
Sbjct: 53 LAANPDLRVAAAEVEAA-----RAQLRIARAALLP---QLSASASYTRQTLAGGPLSSTG 104
Query: 2188 LVAAATHTFVEAANSVVQGAGTEEKLISSAK-QVASSTAQLLVACKVKADPESDATHRLQ 2246
+ + A+ ++ G + +A+ ++ AQL A RL
Sbjct: 105 TDRNSYGYGLSLASWLLDLFGRVRANVRAAEAAAKAARAQLEAA-------------RLS 151
Query: 2247 SAGNAVK-----RATDNLVRAAQQAIQQDEERSLVLNRKMVGGIAQEINARSEVLRIERQ 2301
A A + A++ + E L L K + R +VL+ E Q
Sbjct: 152 LAAEVATAYFDLLAAQEQLALAEETLA-AAEEQLELAEKRY---DAGLATRLDVLQAEAQ 207
Query: 2302 LEEARGRLTAIRQ 2314
L AR +L A +
Sbjct: 208 LASARAQLAAAQA 220
>gnl|CDD|216703 pfam01791, DeoC, DeoC/LacD family aldolase. This family includes
diverse aldolase enzymes. This family includes the
enzyme deoxyribose-phosphate aldolase EC:4.1.2.4, which
is involved in nucleotide metabolism. The family also
includes a group of related bacterial proteins of
unknown function. The family also includes tagatose
1,6-diphosphate aldolase (EC:4.1.2.40) is part of the
tagatose-6-phosphate pathway of galactose-6-phosphate
degradation.
Length = 231
Score = 33.5 bits (77), Expect = 1.1
Identities = 37/190 (19%), Positives = 62/190 (32%), Gaps = 25/190 (13%)
Query: 678 LLSLAKAVANTTAALVLKAKSVASTLPPNQQTSVITSATKCALATSQLVACTKVVAPTL- 736
+ A+ + ALV+ + P + ++ A + A+A +V
Sbjct: 43 VALAARLLGKVDIALVIGFPAGTYLTPVKGRDVLVAEA-EEAIALG--ADEVDMVVNIGA 99
Query: 737 ---ENPACQQQLMAAVKEVANAVEGL--VAMC---NETCTDENLNKDLTKAAAEVTKTLN 788
E+ +AAVKE + EGL + E D+ + L A V
Sbjct: 100 DGSEDEEQVLAEIAAVKEACHG-EGLKVILEAYLRGEEIKDKV-DPHLVAKATRVGAEAG 157
Query: 789 QLLNHIKVTTTE-PAQDVETAVEVMMSSSDR----LLAASG----DAPEMVRQARILGQA 839
+ +K +T E V++ + A+ G D V A L +A
Sbjct: 158 --ADFVKTSTGFGERGATEEDVQIFKEVVGGAPPGVKASGGIKEKDFLRTVEDAIALIEA 215
Query: 840 TAQLIQAIKG 849
A I G
Sbjct: 216 GADRIGVSAG 225
>gnl|CDD|220262 pfam09485, CRISPR_Cse2, CRISPR-associated protein Cse2
(CRISPR_cse2). Clusters of short DNA repeats with
non-homologous spacers, which are found at regular
intervals in the genomes of phylogenetically distinct
prokaryotic species, comprise a family with recognisable
features. This family is known as CRISPR (short for
Clustered, Regularly Interspaced Short Palindromic
Repeats). A number of protein families appear only in
association with these repeats and are designated Cas
(CRISPR-Associated) proteins. This family of proteins,
represented by CT1973 from Chlorobaculum tepidum, is
encoded by genes found in the CRISPR/Cas subtype Ecoli
regions of many bacteria (most of which are mesophiles),
and not in Archaea. It is designated Cse2.
Length = 143
Score = 32.0 bits (73), Expect = 1.5
Identities = 20/73 (27%), Positives = 27/73 (36%), Gaps = 4/73 (5%)
Query: 819 LLAASGDAPEMVRQARILGQATAQLIQAIKGDAENEPDSELQRRLLAAAKNLAEATARMV 878
LLA P AR LG+A A+L + D + SE + R L A E R+
Sbjct: 47 LLAHHKQDPPGHTFARSLGRALARL----RQDGDKSDVSERRFRQLLRADTPDELLRRLR 102
Query: 879 EAARQCASHPQDI 891
R +
Sbjct: 103 RLVRLLRGDGVPV 115
>gnl|CDD|241354 cd13200, FERM_C_KCBP, kinesin-like calmodulin binding protein FERM
domain C-lobe. KCBPs (also called KIPK/Kinesin-like
Calmodulin-Binding Protein-Interacting Protein Kinase),
a member of the Kinesin-14 family, is a C-terminal
microtubule motor with three unique domains including a
myosin tail homology region 4 (MyTH4), a talin-like
domain, and a calmodulin-binding domain (CBD). Binding
of the Ca2+-activated calmodulin to KCBP causes the
motor to dissociate from microtubules. The microtubule
binding of KCBP is controlled by the calcium binding
protein KIC containing a single EF-hand motif. KCBPs
are unique to land plants and green algae. The MyTH4
and talin-like domains are not found in other kinesins,
while the CBD domain is also only found in
Strongylocentrotus purpuratus kinesin-C (SpKinC). The
FERM domain has a cloverleaf tripart structure (FERM_N,
FERM_M, FERM_C/N, alpha-, and C-lobe/A-lobe, B-lobe,
C-lobe/F1, F2, F3). The C-lobe/F3 within the FERM domain
is part of the PH domain family. The FERM domain is
found in the cytoskeletal-associated proteins such as
ezrin, moesin, radixin, 4.1R, and merlin. These proteins
provide a link between the membrane and cytoskeleton and
are involved in signal transduction pathways. The FERM
domain is also found in protein tyrosine phosphatases
(PTPs) , the tyrosine kinases FAK and JAK, in addition
to other proteins involved in signaling. This domain is
structurally similar to the PH and PTB domains and
consequently is capable of binding to both peptides and
phospholipids at different sites.
Length = 189
Score = 32.4 bits (74), Expect = 1.5
Identities = 34/139 (24%), Positives = 61/139 (43%), Gaps = 6/139 (4%)
Query: 241 ACQLAGIQTHIQFGDYNPSKHKPPF-LDLKEFLPQSYVKVKGIEK---KIFSEHKNHVGL 296
A QLA +Q + G ++ L+ +LP+ + + E+ I + ++ L
Sbjct: 2 AAQLAALQIQAEIGPVLGAEPPEELGQLLERYLPKQVLITRPREEWDADIVARYRALEQL 61
Query: 297 SELDAKVLYTKTCRSLPTYGVTFFLVKEKMKGKNKLVPRL-LGVTKDSVLRLDERTKEIM 355
S+ DA+ + RSLP FF V+ L ++ LG+ K V KE +
Sbjct: 62 SKDDARQQLLRILRSLPYGNSIFFSVRRIEDPIGLLPGKIILGINKRGVHFFRPVPKEYL 121
Query: 356 KTWPLTTVRRWGASSN-VF 373
+ L + ++G+S+ VF
Sbjct: 122 HSAELRDIMQFGSSNTAVF 140
>gnl|CDD|222649 pfam14284, PcfJ, PcfJ-like protein. The PcfJ-like protein family
includes the E. faecalis PcfJ protein, which is
functionally uncharacterized. It is found in bacteria
and viruses, and is typically between 159 and 170 amino
acids in length. There is a conserved HCV sequence
motif.
Length = 169
Score = 32.3 bits (74), Expect = 1.6
Identities = 19/97 (19%), Positives = 35/97 (36%), Gaps = 32/97 (32%)
Query: 117 ICTKIGITNHDEYSLVRENPE---DEVENKPNFGTLTLKRKKEEKERDLKMEQLRKKLKT 173
+ ++G HD + + +N + D K + K+EKE+ KM + +L+
Sbjct: 8 MLRRLGKDLHDAHYVCPKNLKAAHDRAVAK--------YQAKKEKEKAEKMRKRYPELEK 59
Query: 174 DDEVNWIDFSKTLREQGIDENEPVLLRRKFFFSDGNI 210
L+ KF F+DG+
Sbjct: 60 ---------------------IFRELKSKFEFTDGDY 75
>gnl|CDD|182181 PRK09983, pflD, putative formate acetyltransferase 2; Provisional.
Length = 765
Score = 33.6 bits (77), Expect = 1.6
Identities = 19/80 (23%), Positives = 37/80 (46%), Gaps = 8/80 (10%)
Query: 834 RILGQATAQLIQAIKGDAENEPDSELQRRLLAAAKNLAEATARMV----EAARQCASHPQ 889
R+L +L+ ++ + +P++ + AA L EA+ + + E A A++
Sbjct: 163 RLLNHGLGELVAQMQQHCQQQPENHFYQ----AALLLLEASQKHILRYAELAETMAANCT 218
Query: 890 DIMKQEALVTTVEELRQAAT 909
D ++E L+T E R A
Sbjct: 219 DAQRREELLTIAEISRHNAQ 238
>gnl|CDD|223716 COG0643, CheA, Chemotaxis protein histidine kinase and related
kinases [Cell motility and secretion / Signal
transduction mechanisms].
Length = 716
Score = 33.5 bits (77), Expect = 2.0
Identities = 61/320 (19%), Positives = 101/320 (31%), Gaps = 39/320 (12%)
Query: 2021 EVAVQYRELLQTVLH---ILSRPGDRIADSKQALPPISRRIAQSLTELVSIAEQLKGSNW 2077
E+ + ELL +L L D I D + + L +L + G
Sbjct: 81 ELELT-SELLDLLLEALDALEEMLDAIEDG-EEDEEDDADLLDLLAQLAAGEGLEPG--- 135
Query: 2078 MDPDDPTVIAETELLGAAASIDAAAKKLSSLRPRRSLQETD--ETLNFDEMILEAAKSIA 2135
AE E A + L P L E + + A +A
Sbjct: 136 ---AADAEEAEEEAAVEPALAALNEELSEGLVPALELPEAEAAAAAAPELEAPPYAIDVA 192
Query: 2136 AATSALVKAASASQ--RELIDAGRMSRRPLTSSDDGQWSEDDGQWSEGLI--SAARLVAA 2191
A +K+A A+ EL + G L +D + + L L+
Sbjct: 193 LEEDAPLKSARAALLLEELEELGEEIAATLPDLEDLEAEAAFEESEVVLATEQDEELIRD 252
Query: 2192 ATHTFVEAANSVVQGAGTEEKLISSAKQVASSTAQLLVACKVKADPESDATHRLQSAGNA 2251
VEA + + +L+ A+ ++ L + A+ S A SA A
Sbjct: 253 VLELVVEAEELEIAAVELDAELLELAESEQAADDVLAAQAEPLAEK-SAAEAAKLSALEA 311
Query: 2252 VKRATDNLVRAAQQA-IQQDEER---------SLVLNRKMVGGIAQEINARSEVL----- 2296
A A + I+ D E+ LV+ R + +A E++ E L
Sbjct: 312 APAAKAAAAAAGASSSIRVDVEKLDRLMNLVGELVITRSRLSQLASELDEVREELDEALR 371
Query: 2297 ---RIERQLEEARGRLTAIR 2313
R+ L++ + IR
Sbjct: 372 QLSRLTTDLQDE---VMKIR 388
>gnl|CDD|176352 cd00196, UBQ, Ubiquitin-like proteins. Ubiquitin homologs;
Includes ubiquitin and ubiquitin-like proteins.
Ubiquitin-mediated proteolysis is part of the regulated
turnover of proteins required for controlling cell cycle
progression. Other family members are protein modifiers
that perform a wide range of functions. Ubiquitination
usually results in a covalent bond between the
C-terminus of ubiquitin and the epsilon-amino group of a
substrate lysine. The three-step mechanism requires an
activating enzyme (E1) that forms a thiol ester with the
C-terminal carboxy group, a conjugating enzyme (E2) that
transiently carries the activated ubiquitin molecule as
a thiol ester, and a ligase (E3) that transfers the
activated ubiquitin from the E2 to the substrate lysine
residue. In poly-ubiquitination, ubiquitin itself is the
substrate.
Length = 69
Score = 29.8 bits (67), Expect = 2.1
Identities = 13/49 (26%), Positives = 22/49 (44%), Gaps = 1/49 (2%)
Query: 91 KVRMLDGTLKTLLVDDSQPVANLMVVICTKIGITNHDEYSLVRENPEDE 139
KV++ DG LLV VA+L + K+G+ ++ L+
Sbjct: 1 KVKLNDGKTVELLVPSGTTVADLKEKLAKKLGL-PPEQQRLLVNGKILP 48
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 33.1 bits (76), Expect = 2.2
Identities = 55/323 (17%), Positives = 114/323 (35%), Gaps = 36/323 (11%)
Query: 2024 VQYRELLQTVLHILSRPGDRIADSKQALPPISRRIAQSLTELVSIAEQLKGSNWMDPDDP 2083
+ R+ L+ + LSR + + + ++ L + I + +EL + E+L+
Sbjct: 235 KELRKELEELEEELSRLEEELEELQEELEEAEKEIEELKSELEELREELE---------- 284
Query: 2084 TVIAETELLGAAASIDAAAKKLSSLRPRRS-----LQETDETLNFDEMILEAAKSIAAAT 2138
+ ELL I+ ++S LR R L+E +E L + +EA K
Sbjct: 285 --ELQEELLELKEEIEELEGEISLLRERLEELENELEELEERLEELKEKIEALKEELEER 342
Query: 2139 SALVKAASASQRELIDAGRMSRRPLTSSDDGQWSEDDG---QWSEGLISAARLVAAATHT 2195
L++ EL ++ L E + E L +A
Sbjct: 343 ETLLEELEQLLAEL----EEAKEELEEKLSALLEELEELFEALREELAELEAELA----- 393
Query: 2196 FVEAANSVVQGAGTEEKLISSAKQVASSTAQLLVACKVKADPESDATHRLQSAGNAVKRA 2255
E N + + E L ++++ L K + L+ ++
Sbjct: 394 --EIRNELEELKREIESLEERLERLSERLEDLKEELKELEAELEELQTELEELNEELEEL 451
Query: 2256 TDNLVRAAQQAIQQDEERSLVLNRKMVGGIAQEIN-ARSEVLRIERQLEEARGRLTAIRQ 2314
+ L + + ER L ++ + + +E++ + + R+E + ++G +
Sbjct: 452 EEQLEELRDRLKEL--ERELAELQEELQRLEKELSSLEARLDRLEAEQRASQGVRAVLEA 509
Query: 2315 AKYKLKGGDGSASD--TEPEMYE 2335
+ L G G ++ E YE
Sbjct: 510 LESGLPGVYGPVAELIKVKEKYE 532
>gnl|CDD|129794 TIGR00711, efflux_EmrB, drug resistance transporter, EmrB/QacA
subfamily. This subfamily of drug efflux proteins, a
part of the major faciliator family, is predicted to have
14 potential membrane-spanning regions. Members with
known activities include EmrB (multiple drug resistance
efflux pump) in E. coli, FarB (antibacterial fatty acid
resistance) in Neisseria gonorrhoeae, TcmA
(tetracenomycin C resistance) in Streptomyces
glaucescens, etc. In most cases, the efflux pump is
described as having a second component encoded in the
same operon, such as EmrA of E. coli [Cellular processes,
Toxin production and resistance, Transport and binding
proteins, Other].
Length = 485
Score = 32.7 bits (75), Expect = 2.7
Identities = 20/95 (21%), Positives = 38/95 (40%), Gaps = 4/95 (4%)
Query: 989 PANLPASSKQYSHSLQNLV-DIGMEIISTTESRETQTKMLSSLKSVSTSSSKFLSTA-RS 1046
P + A S+ + L IG +I+T + TQ ++++ + FLS +
Sbjct: 378 PPHKIARGSSLSNFTRQLGGSIGTALITTILTNRTQFHHSQLTETINPVNPNFLSGYSQL 437
Query: 1047 AALDPSASNSKSQLSAAARNVA--DSINNLLNICT 1079
AAL + ++ A +IN + + T
Sbjct: 438 AALGNPEQQVYALIAQQITLHAFSIAINEIFWMAT 472
>gnl|CDD|237941 PRK15315, PRK15315, outer membrane protein RatA; Provisional.
Length = 1865
Score = 32.7 bits (74), Expect = 3.0
Identities = 14/34 (41%), Positives = 23/34 (67%), Gaps = 4/34 (11%)
Query: 2150 RELIDAGRMSRRPL----TSSDDGQWSEDDGQWS 2179
R ++DAG + +RPL S DGQ+SE++ +W+
Sbjct: 609 RGVVDAGNLYKRPLLAVEASHKDGQFSENNEEWA 642
>gnl|CDD|218559 pfam05335, DUF745, Protein of unknown function (DUF745). This family
consists of several uncharacterized Drosophila
melanogaster proteins of unknown function.
Length = 188
Score = 31.5 bits (72), Expect = 3.3
Identities = 30/139 (21%), Positives = 58/139 (41%), Gaps = 10/139 (7%)
Query: 2190 AAATHTFVEAANSVVQGAGTEEKLISSAKQVASSTAQLLVACKVKADPESDATHRLQSAG 2249
AAA + A+ +Q A E ++ +Q+ Q + + + ES + + ++
Sbjct: 38 AAAYQAKSQLADKALQAAKAAEAALAGKQQLVEQLEQEVREAEAVVEEESQSLQQSEANA 97
Query: 2250 NAVKRATDNLVRAAQQ--AIQQDEERSLVLNRKMVGGIAQEI--------NARSEVLRIE 2299
A + A A+ ++ + +L ++ G QE+ A+ V +E
Sbjct: 98 TAAQAAAQQAQTQVNTLKALLKNAQANLENIEQVASGAQQELAEKTQLLEAAKRRVEVLE 157
Query: 2300 RQLEEARGRLTAIRQAKYK 2318
RQL+EAR ++A YK
Sbjct: 158 RQLKEARLDYEKTKKAAYK 176
>gnl|CDD|178129 PLN02513, PLN02513, adenylosuccinate synthase.
Length = 427
Score = 32.3 bits (74), Expect = 3.8
Identities = 14/41 (34%), Positives = 24/41 (58%)
Query: 981 EVISSVKNPANLPASSKQYSHSLQNLVDIGMEIISTTESRE 1021
E ISSV+N +LPA+++ Y ++ LV + + I R+
Sbjct: 381 EDISSVRNYDDLPAAAQAYVERIEELVGVPVHYIGVGPGRD 421
>gnl|CDD|224241 COG1322, COG1322, Predicted nuclease of restriction
endonuclease-like fold, RmuC family [General function
prediction only].
Length = 448
Score = 32.0 bits (73), Expect = 4.0
Identities = 36/177 (20%), Positives = 66/177 (37%), Gaps = 9/177 (5%)
Query: 809 VEVMMSSSDRLLAASGDAPEMVRQ----ARILGQATAQLIQAIKGDAENEPDSELQRRLL 864
+ V ++ +LL G +M+ + L A +A + LQ L
Sbjct: 13 LLVNLAFIRQLLLRLGRLEQMLGELAAVLEQLLLLLAFRAEAEQLRTFA---RSLQALNL 69
Query: 865 AAAKNLAEATARMVEAARQCASHPQDIMKQEA-LVTTVEELRQAATPTLRYKLFNKSQTN 923
+ L E AR+ + Q Q +++ A L + +EL L +L +Q N
Sbjct: 70 ELIQELNELKARLQQQLLQSREQLQLLIESLAQLSSEFQELANEIFEELNRRLAELNQQN 129
Query: 924 EFEGLLPGQQEIEEITEIIESTYEQIHTDDFPRSTKPIGRLQQELSSAATGLSETTN 980
+ L P ++ +E+ E +E + ++ + I RL E+ A T
Sbjct: 130 LKQLLKPLREVLEKFREQLEQRIHE-SAEERSTLLEEIDRLLGEIQQLAQEAGNLTA 185
>gnl|CDD|237804 PRK14725, PRK14725, pyruvate kinase; Provisional.
Length = 608
Score = 32.2 bits (74), Expect = 4.3
Identities = 31/126 (24%), Positives = 41/126 (32%), Gaps = 29/126 (23%)
Query: 776 LTKAAAEVTKTLNQLLNHIKVTTTEPAQDVETAVEVMMSSSDRLLAASGDA----PEMVR 831
L +A A V L+ +L ++ E V D LL +A P R
Sbjct: 80 LGRAEAHVLAALDAVLAVLRALLGEGPAYPPEDTAVTFEEGDELLDEHAEALLGPPPSGR 139
Query: 832 QARI---LGQATAQLIQAIKGDAENEPDSELQRRLLAAAKNLA---------EATARMVE 879
RI L A D +L RRLLAA ++A EA M+
Sbjct: 140 PTRIMVTLPTEAAD-------------DPDLVRRLLAAGMDIARINCAHDDPEAWRAMIA 186
Query: 880 AARQCA 885
R
Sbjct: 187 NVRTAE 192
>gnl|CDD|99999 cd04950, GT1_like_1, Glycosyltransferases catalyze the transfer of
sugar moieties from activated donor molecules to
specific acceptor molecules, forming glycosidic bonds.
The acceptor molecule can be a lipid, a protein, a
heterocyclic compound, or another carbohydrate residue.
This group of glycosyltransferases is most closely
related to the previously defined glycosyltransferase
family 1 (GT1). The members of this family may transfer
UDP, ADP, GDP, or CMP linked sugars. The diverse
enzymatic activities among members of this family
reflect a wide range of biological functions. The
protein structure available for this family has the GTB
topology, one of the two protein topologies observed for
nucleotide-sugar-dependent glycosyltransferases. GTB
proteins have distinct N- and C- terminal domains each
containing a typical Rossmann fold. The two domains have
high structural homology despite minimal sequence
homology. The large cleft that separates the two domains
includes the catalytic center and permits a high degree
of flexibility.
Length = 373
Score = 31.5 bits (72), Expect = 5.0
Identities = 15/60 (25%), Positives = 27/60 (45%), Gaps = 3/60 (5%)
Query: 827 PEMVRQAR---ILGQATAQLIQAIKGDAENEPDSELQRRLLAAAKNLAEATARMVEAARQ 883
PE+ R ++ + + AI+ + + +RRL AA+N +A A + A Q
Sbjct: 311 PEVRRYEDEVVLIADDPEEFVAAIEKALLEDGPARERRRLRLAAQNSWDARAAEMLEALQ 370
>gnl|CDD|179334 PRK01770, PRK01770, sec-independent translocase; Provisional.
Length = 171
Score = 30.6 bits (69), Expect = 5.8
Identities = 27/149 (18%), Positives = 42/149 (28%), Gaps = 37/149 (24%)
Query: 875 ARMVEAARQCASHPQDIMKQE-----------------------ALVTTVEELRQAATPT 911
A + A R A+ Q+ + QE L +V+EL+QAA
Sbjct: 33 AGWIRALRSLATTVQNELTQELKLQELQDSLKKVEKASLTNLSPELKASVDELKQAAESM 92
Query: 912 LRYKLFNKSQTNEFEGLLPGQQEIEEITEIIESTYEQIHTDDFPRSTKPIGRLQQELSSA 971
R N + E I + E H P + + + SS
Sbjct: 93 KRSYAANDPEKAS--------DEAHTIHNPVVKDNEAAHEGVTPAAAQT------QASSP 138
Query: 972 ATGLSETTNEVISSVKNPANLPASSKQYS 1000
T V+ + A+ S
Sbjct: 139 EQKPETTPEPVVKPAADAEPKTAAPSPSS 167
>gnl|CDD|201900 pfam01642, MM_CoA_mutase, Methylmalonyl-CoA mutase. The enzyme
methylmalonyl-CoA mutase is a member of a class of
enzymes that uses coenzyme B12 (adenosylcobalamin) as a
cofactor. The enzyme induces the formation of an adenosyl
radical from the cofactor. This radical then initiates a
free-radical rearrangement of its substrate,
succinyl-CoA, to methylmalonyl-CoA.
Length = 517
Score = 31.6 bits (72), Expect = 6.1
Identities = 29/113 (25%), Positives = 43/113 (38%), Gaps = 29/113 (25%)
Query: 2217 AKQVASSTAQLLV----ACKVKADPESDATHRLQSAGNA-VKRATDNLVRAAQQAIQQDE 2271
+ ++A +T +L +V DP G+ V+ TD + A + Q+ E
Sbjct: 342 SARIARNTQLILQEESGVARV-IDP---------WGGSYYVEELTDRIAEEAWKLFQEIE 391
Query: 2272 ERSLVLNRKMVGGIAQEINARSEVLRIE-----RQLEEARGRLTAIRQAKYKL 2319
E GG+A+ I LRIE RQ GR + KY L
Sbjct: 392 EA---------GGMAKAIEDGLPKLRIEESAARRQARIDSGREVIVGVNKYPL 435
>gnl|CDD|216983 pfam02347, GDC-P, Glycine cleavage system P-protein. This family
consists of Glycine cleavage system P-proteins
EC:1.4.4.2 from bacterial, mammalian and plant sources.
The P protein is part of the glycine decarboxylase
multienzyme complex EC:2.1.2.10 (GDC) also annotated as
glycine cleavage system or glycine synthase. GDC
consists of four proteins P, H, L and T. The reaction
catalyzed by this protein is:- Glycine + lipoylprotein
<=> S-aminomethyldihydrolipoylprotein + CO2.
Length = 429
Score = 31.2 bits (71), Expect = 6.8
Identities = 24/61 (39%), Positives = 36/61 (59%), Gaps = 15/61 (24%)
Query: 319 FFLVKEKMKGKNKLVP-RLLGVTKDS----VLRLDERTKEIMKTWPLTTVRRWGASSNVF 373
FF VKE++K K +P R++GV+KD+ LRL +T+E +RR A+SN+
Sbjct: 272 FFAVKEELKRK---MPGRIVGVSKDANGKRALRLALQTRE-------QHIRRDKATSNIC 321
Query: 374 T 374
T
Sbjct: 322 T 322
>gnl|CDD|224691 COG1777, COG1777, Predicted transcriptional regulators
[Transcription].
Length = 217
Score = 30.5 bits (69), Expect = 7.6
Identities = 18/67 (26%), Positives = 32/67 (47%), Gaps = 4/67 (5%)
Query: 818 RLLAASGDAPEMVRQARILGQATAQLIQAIKGDAENEPDSELQRRLLAA-AKNLAEATAR 876
RLL + + E+ R L + +L+ IK + E++ +R +L KN A A
Sbjct: 126 RLLEINREIEELSRAQTELQKQLNELMDRIKEEIEDKDGDMTERIVLEYLLKNGA---AD 182
Query: 877 MVEAARQ 883
+ E +R+
Sbjct: 183 VEETSRR 189
>gnl|CDD|181608 PRK09004, PRK09004, FMN-binding protein MioC; Provisional.
Length = 146
Score = 29.8 bits (68), Expect = 7.7
Identities = 18/79 (22%), Positives = 29/79 (36%), Gaps = 23/79 (29%)
Query: 1508 AGGNPDAVNIHPDLDESIEATKEALSDIT--------SSLDHFTGVVNT----------- 1548
AG PD N+ P +E ++ K LS + S D F G ++
Sbjct: 59 AGDLPD--NLQPFFEE-LQEQKPDLSQVRFAAIGIGSSEYDTFCGAIDKLEQLLKAKGAK 115
Query: 1549 -FVDSITKSMQQIPDPNQP 1566
+++ + Q P P P
Sbjct: 116 QIGETLKIDVLQHPIPEDP 134
>gnl|CDD|237037 PRK12285, PRK12285, tryptophanyl-tRNA synthetase; Reviewed.
Length = 368
Score = 30.6 bits (70), Expect = 9.4
Identities = 9/36 (25%), Positives = 13/36 (36%), Gaps = 9/36 (25%)
Query: 180 IDFSKTLREQGID---------ENEPVLLRRKFFFS 206
+D+ K E GI+ L+RR F
Sbjct: 15 VDYDKLFEEFGIEPFTEVLPELPEPHPLMRRGIIFG 50
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
0.312 0.125 0.340
Gapped
Lambda K H
0.267 0.0680 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 111,793,501
Number of extensions: 10895304
Number of successful extensions: 9446
Number of sequences better than 10.0: 1
Number of HSP's gapped: 9354
Number of HSP's successfully gapped: 153
Length of query: 2347
Length of database: 10,937,602
Length adjustment: 113
Effective length of query: 2234
Effective length of database: 5,925,600
Effective search space: 13237790400
Effective search space used: 13237790400
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 (21.9 bits)
S2: 67 (29.7 bits)