RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15553
(489 letters)
>gnl|CDD|214764 smart00653, eIF2B_5, domain present in translation initiation
factor eIF2B and eIF5.
Length = 110
Score = 160 bits (407), Expect = 6e-48
Identities = 56/116 (48%), Positives = 71/116 (61%), Gaps = 6/116 (5%)
Query: 14 FYRYKMPKLIAKVEGKGNGIKTVIVNMADVAKAIGRPPTYPTKYFGCELGAQTKLDHKND 73
FYR+KMP EGKG KTVIVN AD+AKA+ RPP + K+ ELG Q +D K
Sbjct: 1 FYRFKMPPPQVLREGKG---KTVIVNFADIAKALNRPPDHVLKFLLAELGTQGSIDGKG- 56
Query: 74 RFIVNGSHDVVKLQDLLDGFIRKFVLCPECDNPETDLVVSAKKGTIQQVCKACGFH 129
R IVNG KLQDLL +I+++VLCPEC +P+T+L+ C+ACG
Sbjct: 57 RLIVNGRFTPKKLQDLLRRYIKEYVLCPECGSPDTELIKE--NRLFFLKCEACGAR 110
>gnl|CDD|216754 pfam01873, eIF-5_eIF-2B, Domain found in IF2B/IF5. This family
includes the N terminus of eIF-5, and the C terminus of
eIF-2 beta. This region corresponds to the whole of the
archaebacterial eIF-2 beta homologue. The region
contains a putative zinc binding C4 finger.
Length = 125
Score = 155 bits (393), Expect = 1e-45
Identities = 57/128 (44%), Positives = 78/128 (60%), Gaps = 7/128 (5%)
Query: 4 VNVNRNVTDAFYRYKMPKLIAKVEGKGNGIKTVIVNMADVAKAIGRPPTYPTKYFGCELG 63
N +R D +R++MP K+EGK IKT+IVN +D+AKA+ RPP + KY ELG
Sbjct: 5 QNPDRVAGDK-FRFEMPPPQVKIEGK---IKTIIVNFSDIAKALNRPPEHLLKYLLAELG 60
Query: 64 AQTKLDHKNDRFIVNGSHDVVKLQDLLDGFIRKFVLCPECDNPETDLVVSAKKGTIQQVC 123
Q +D K R IVNG KLQD+LD +I+++VLC EC +P+T+L+ + I C
Sbjct: 61 TQGSIDGK-GRLIVNGRFTPKKLQDVLDDYIKEYVLCHECKSPDTELIK--ENRLIFLKC 117
Query: 124 KACGFHGM 131
KACG
Sbjct: 118 KACGARRP 125
>gnl|CDD|211399 cd11561, W2_eIF5, C-terminal W2 domain of eukaryotic translation
initiation factor 5. eIF5 functions as a GTPase
acceleration protein (GAP), as well as a GDP
dissociation inhibitor (GDI) during translational
initiation in eukaryotes. The structure of this
C-terminal domain resembles that of a set of
concatenated HEAT repeats.
Length = 157
Score = 155 bits (395), Expect = 2e-45
Identities = 78/199 (39%), Positives = 107/199 (53%), Gaps = 44/199 (22%)
Query: 235 EKTEKERMDIFYTCVKTALEKNNV-DAKELLSEAERLEV-KTKAPLILAELLFADEDKIP 292
E+ E ER+D +K +++ + + KE+L EAERL+V K KA L+LAE+LF + I
Sbjct: 1 EEEEDERVDELGEFLKKNKDESGLSELKEILKEAERLDVVKDKAVLVLAEVLFDE--NIV 58
Query: 293 IQAKKHRILFFGSNQFTWRSVGFYRRQINTIATLINQCQLILLDKQSTVLRFTHEDIKAQ 352
+ KK + L L+ ++ KAQ
Sbjct: 59 KEIKKRKALL---------------------------------------LKLVTDE-KAQ 78
Query: 353 RYLLNGIEQVIALHKEKLLSMVPGILKLFYDYDILEEKVLLEWAEKTSKKYVSKELSAEI 412
+ LL GIE+ H +LL VP ILK YD DILEE+V+L+W EK SKKYVSKE S ++
Sbjct: 79 KALLGGIERFCGKHSPELLKKVPLILKALYDNDILEEEVILKWYEKVSKKYVSKEKSKKV 138
Query: 413 RSRAEPFIKWLREAEEEDS 431
R AEPF++WL EAEEE+
Sbjct: 139 RKAAEPFVEWLEEAEEEEE 157
>gnl|CDD|216850 pfam02020, W2, eIF4-gamma/eIF5/eIF2-epsilon. This domain of
unknown function is found at the C-terminus of several
translation initiation factors.
Length = 75
Score = 87.3 bits (217), Expect = 2e-21
Identities = 34/77 (44%), Positives = 50/77 (64%), Gaps = 2/77 (2%)
Query: 350 KAQRYLLNGIEQVIALHKEKLLSMVPGILKLFYDYDILEEKVLLEWAEKTSKKYVSKELS 409
AQ+ LL +E+ +L+ ++P ILKL YD DILEE+ +L+W EK+ K V E S
Sbjct: 1 DAQKDLLGALERFCGKENPELIKLLPKILKLLYDLDILEEEAILKWYEKSKK--VDGEGS 58
Query: 410 AEIRSRAEPFIKWLREA 426
++R +A+PF+ WL EA
Sbjct: 59 KKVRKQAKPFVTWLEEA 75
>gnl|CDD|214705 smart00515, eIF5C, Domain at the C-termini of GCD6, eIF-2B epsilon,
eIF-4 gamma and eIF-5.
Length = 83
Score = 78.9 bits (195), Expect = 3e-18
Identities = 37/86 (43%), Positives = 52/86 (60%), Gaps = 5/86 (5%)
Query: 341 VLRFTHEDIKAQRYLLNGIEQVIALHKEKLLSMVPGILKLFYDYDILEEKVLLEWAEKTS 400
+L+F +D + Q LL IE+ EKL ++P ILK YD DILEE+ +L+W EK
Sbjct: 3 LLKFLAKDEEEQLELLYAIEEFCVEL-EKLGKLLPKILKSLYDADILEEEAILKWYEKA- 60
Query: 401 KKYVSKELSAEIRSRAEPFIKWLREA 426
VS E ++R A+PF+ WL+EA
Sbjct: 61 ---VSAEGKKKVRKNAKPFVTWLQEA 83
>gnl|CDD|235189 PRK03988, PRK03988, translation initiation factor IF-2 subunit
beta; Validated.
Length = 138
Score = 77.3 bits (191), Expect = 6e-17
Identities = 33/114 (28%), Positives = 62/114 (54%), Gaps = 12/114 (10%)
Query: 16 RYKMPKLIAKVEGKGNGIKTVIVNMADVAKAIGRPPTYPTKYFGCELGAQTKLDHKNDRF 75
R+++PK ++EG +T+I N ++A + R P + K+ ELG ++ R
Sbjct: 27 RFEVPKPDVRIEGN----RTIIRNFKEIADRLNRDPKHVAKFLLKELGTAGNIE--GGRL 80
Query: 76 IVNG--SHDVVKLQDLLDGFIRKFVLCPECDNPETDLVVSAKKGTIQQVCKACG 127
I+ G S V+ + +D +++++V+CPEC +P+T L+ + C+ACG
Sbjct: 81 ILQGKFSPRVIN--EKIDRYVKEYVICPECGSPDTKLI--KEGRIWVLKCEACG 130
>gnl|CDD|211396 cd11558, W2_eIF2B_epsilon, C-terminal W2 domain of eukaryotic
translation initiation factor 2B epsilon. eIF2B is a
heteropentameric complex which functions as a guanine
nucleotide exchange factor in the recycling of eIF-2
during the initiation of translation in eukaryotes. The
epsilon and gamma subunits are sequence similar and both
are essential in yeast. Epsilon appears to be the
catalytically active subunit, with gamma enhancing its
activity. The C-terminal domain of the eIF2B epsilon
subunit contains bipartite motifs rich in acidic and
aromatic residues, which are responsible for the
interaction with eIF2. The structure of the domain
resembles that of a set of concatenated HEAT repeats.
Length = 169
Score = 66.9 bits (164), Expect = 4e-13
Identities = 33/98 (33%), Positives = 47/98 (47%), Gaps = 3/98 (3%)
Query: 334 LLDKQSTVLRFTHEDIKAQRYLLNGIEQVIALHKEKLLSMVPGILKLFYDYDILEEKVLL 393
LL K +L + Q LL +E+ L E+ + +L YD DILEE+ +L
Sbjct: 75 LLSKWGPLLENYVKSQDDQVELLLALEEF-CLESEEGGPLFAKLLHALYDLDILEEEAIL 133
Query: 394 EWAEKTSKKYVSKELSAEIRSRAEPFIKWLREAEEEDS 431
EW E + E ++R + FI+WL EAEEE
Sbjct: 134 EWWE--EPDAGADEEMKKVRELVKKFIEWLEEAEEESD 169
>gnl|CDD|183451 PRK12336, PRK12336, translation initiation factor IF-2 subunit
beta; Provisional.
Length = 201
Score = 67.3 bits (165), Expect = 6e-13
Identities = 34/114 (29%), Positives = 57/114 (50%), Gaps = 8/114 (7%)
Query: 16 RYKMPKLIAKVEGKGNGIKTVIVNMADVAKAIGRPPTYPTKYFGCELGAQTKLDHKNDRF 75
R+ +P+ +EGK T++ N ++A A+ R P + K+ ELG K++ R
Sbjct: 23 RFSIPEPKIFIEGK----TTILTNFGEIADALNRDPDHLMKFLQRELGTAGKIE--GGRA 76
Query: 76 IVNGSHDVVKLQDLLDGFIRKFVLCPECDNPETDLVVSAKKGTIQQVCKACGFH 129
+ NG +Q +D ++ ++V+C EC P+T LV + C ACG H
Sbjct: 77 VFNGKFTEEDIQAAIDAYVDEYVICSECGLPDTRLVKE--DRVLMLRCDACGAH 128
>gnl|CDD|129411 TIGR00311, aIF-2beta, translation initiation factor aIF-2, beta
subunit, putative. The trusted cutoff is set high
enough to select only archaeal members. The suggested
cutoff is set to include most eukaryotic members but
largely exclude the related eIF-5 [Protein synthesis,
Translation factors].
Length = 133
Score = 63.3 bits (154), Expect = 4e-12
Identities = 37/113 (32%), Positives = 63/113 (55%), Gaps = 10/113 (8%)
Query: 16 RYKMPKLIAKVEGKGNGIKTVIVNMADVAKAIGRPPTYPTKYFGCELGAQTKLDHKNDRF 75
R+++PK +EG +T+I N +VAKA+ R + KY ELG L+ R
Sbjct: 22 RFEVPKAYIVIEGN----RTIIQNFREVAKALNRDEQHLLKYLLKELGTAGNLE--GGRL 75
Query: 76 IVNGSHDVVKLQDLLDGFIRKFVLCPECDNPETDLVVSAKKGTIQQV-CKACG 127
I+ G L + ++ ++RK+V+C EC+ P+T ++ K+G + + C+ACG
Sbjct: 76 ILQGKFTHFLLNERIEDYVRKYVICRECNRPDTRII---KEGRVSLLKCEACG 125
>gnl|CDD|224517 COG1601, GCD7, Translation initiation factor 2, beta subunit
(eIF-2beta)/eIF-5 N-terminal domain [Translation,
ribosomal structure and biogenesis].
Length = 151
Score = 60.5 bits (147), Expect = 5e-11
Identities = 32/112 (28%), Positives = 61/112 (54%), Gaps = 7/112 (6%)
Query: 16 RYKMPKLIAKVEGKGNGIKTVIVNMADVAKAIGRPPTYPTKYFGCELGAQTKLDHKNDRF 75
R+++P+ EG +T+I N D+A+A+ R P + K+ ELG +D K R
Sbjct: 29 RFRIPEPEINREGN----RTIIRNFGDIAEALNRDPEHLVKFLKKELGTAGSIDGK-GRL 83
Query: 76 IVNGSHDVVKLQDLLDGFIRKFVLCPECDNPETDLVVSAKKGTIQQVCKACG 127
++ G ++ + ++ +I ++V C EC +P+T+L+ + + C+ACG
Sbjct: 84 VLQGKFSDSEIVNEIERYIAEYVKCKECGSPDTELIKEER--LLFLKCEACG 133
>gnl|CDD|211398 cd11560, W2_eIF5C_like, C-terminal W2 domain of the eukaryotic
translation initiation factor 5C and similar proteins.
eIF5C appears to be essential for the initiation of
protein translation; its actual function, and
specifically that of the C-terminal W2 domain, are not
well understood. The Drosophila ortholog, kra
(krasavietz) or exba (extra bases), may be involved in
translational inhibition in neural development. The
structure of this C-terminal domain resembles that of a
set of concatenated HEAT repeats.
Length = 194
Score = 48.0 bits (115), Expect = 2e-06
Identities = 28/80 (35%), Positives = 42/80 (52%), Gaps = 5/80 (6%)
Query: 350 KAQRYLLNGIEQVIALHKEKLLSMVPGILKLFYDYDILEEKVLLEWAEKTSKKYVSKELS 409
+A+ LLN I Q K + + I+KL Y D+L E +L+W +K K
Sbjct: 120 RAELALLNKI-QEYCYENMKFMKVFQKIVKLLYKADVLSEDAILKWYKKGHS---PKGKQ 175
Query: 410 AEIRSRAEPFIKWLREAEEE 429
++ EPF++WL+EAEEE
Sbjct: 176 VFLKQ-MEPFVEWLQEAEEE 194
>gnl|CDD|211395 cd11473, W2, C-terminal domain of eIF4-gamma/eIF5/eIF2b-epsilon.
This domain is found at the C-terminus of several
translation initiation factors, including the epsilon
chain of eIF2b, where it has been found to catalyze the
conversion of eIF2.GDP to its active eIF2.GTP form. The
structure of the domain resembles that of a set of
concatenated HEAT repeats.
Length = 135
Score = 39.8 bits (93), Expect = 6e-04
Identities = 29/88 (32%), Positives = 44/88 (50%), Gaps = 3/88 (3%)
Query: 311 RSVGFYRRQINTIATLINQCQLIL-LDKQSTVLR-FTHEDIKAQRYLLNGIEQV-IALHK 367
+ + +L + QL+L L K VLR K Q YLL IE++ + L
Sbjct: 47 LTAVVNAVESADSISLTQKEQLVLVLKKYGPVLRELLKLIKKDQLYLLLKIEKLCLQLKL 106
Query: 368 EKLLSMVPGILKLFYDYDILEEKVLLEW 395
+L+S++ IL L YD D+L E+ +L W
Sbjct: 107 SELISLLEKILDLLYDADVLSEEAILSW 134
>gnl|CDD|219293 pfam07093, SGT1, SGT1 protein. This family consists of several
eukaryotic SGT1 proteins. Human SGT1 or hSGT1 is known
to suppress GCR2 and is highly expressed in the muscle
and heart. The function of this family is unknown
although it has been speculated that SGT1 may be
functionally analogous to the Gcr2p protein of
Saccharomyces cerevisiae which is known to be a
regulatory factor of glycolytic gene expression.
Length = 557
Score = 35.5 bits (82), Expect = 0.074
Identities = 19/74 (25%), Positives = 30/74 (40%), Gaps = 11/74 (14%)
Query: 425 EAEEEDSDSEESDDDLEI-----------EYNDRARVTLQTETIKPKVIKKDEDEDGTND 473
++++ D D +E DD+ E EY D+ L+ + G D
Sbjct: 484 DSDDADEDDDEDDDEDEDSSSDSTLEELEEYMDQMDAELKQTDSSNNADISNSGSSGAED 543
Query: 474 KDEDEDGTNDVDID 487
D+D +G VDID
Sbjct: 544 DDDDIEGVEPVDID 557
>gnl|CDD|211397 cd11559, W2_eIF4G1_like, C-terminal W2 domain of eukaryotic
translation initiation factor 4 gamma 1 and similar
proteins. eIF4G1 is a component of the multi-subunit
eukaryotic translation initiation factor 4F, which
facilitates recruitment of the mRNA to the ribosome, a
rate-limiting step during translation initiation. This
C-terminal domain, whose structure resembles that of a
set of concatenated HEAT repeats, has been associated
with binding to/recruiting the kinase Mnk1, which
phosphorylates eIF4E.
Length = 134
Score = 31.5 bits (72), Expect = 0.44
Identities = 19/72 (26%), Positives = 33/72 (45%), Gaps = 8/72 (11%)
Query: 330 CQLILLDKQSTVL-RFTHEDIKAQRYLLNGIEQVIALHKEK---LLSMVPGILKLFYDYD 385
+ LL+K + +L ++ +D + Q L + Q + E LL YD D
Sbjct: 62 KEKALLEKYAPLLQKYLDDDEQLQLQALYAL-QALVHTLEFPKGLLLR---FFDALYDED 117
Query: 386 ILEEKVLLEWAE 397
++EE+ L+W E
Sbjct: 118 VIEEEAFLKWKE 129
>gnl|CDD|237047 PRK12298, obgE, GTPase CgtA; Reviewed.
Length = 390
Score = 31.8 bits (73), Expect = 0.77
Identities = 15/68 (22%), Positives = 33/68 (48%), Gaps = 9/68 (13%)
Query: 419 FIKWLREAEEEDSDSEESDDDLEIEYNDRARVTLQTETIKPKVIKKDEDEDGTNDKDEDE 478
+ ++ E E+++ E+ + +E ++D R L+ + +E++D D D DE
Sbjct: 328 LMTFIEENPREEAEEAEAPEKVEFMWDDYHREQLE---------EVEEEDDDDWDDDWDE 378
Query: 479 DGTNDVDI 486
D V++
Sbjct: 379 DDDEGVEV 386
>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family. Emg1 and Nop14 are novel
proteins whose interaction is required for the
maturation of the 18S rRNA and for 40S ribosome
production.
Length = 809
Score = 31.9 bits (73), Expect = 0.99
Identities = 22/66 (33%), Positives = 33/66 (50%), Gaps = 3/66 (4%)
Query: 425 EAEEEDSDSEESDDDL--EIEYNDRARVTLQTETIKPKVIKKDEDEDGTNDKDED-EDGT 481
E +EE+ DS+ES DDL E E +D L + + D++ D D+D E+
Sbjct: 287 EDDEEEEDSKESADDLDDEFEPDDDDNFGLGQGEEDEEEEEDGVDDEDEEDDDDDLEEEE 346
Query: 482 NDVDID 487
DVD+
Sbjct: 347 EDVDLS 352
Score = 30.7 bits (70), Expect = 2.0
Identities = 15/60 (25%), Positives = 26/60 (43%), Gaps = 13/60 (21%)
Query: 424 REAEEEDSDSEESDDDLEIEYNDRARVTLQTETIKPKVIKKDEDEDGTNDKDEDEDGTND 483
E +D D E+ DDDLE E D + +E+++ D D+++D +
Sbjct: 326 EEDGVDDEDEEDDDDDLEEEEED-------------VDLSDEEEDEEDEDSDDEDDEEEE 372
>gnl|CDD|216661 pfam01719, Rep_2, Plasmid replication protein. This family
consists of various bacterial plasmid replication (Rep)
proteins. These proteins are essential for replication
of plasmids, the Rep proteins are topoisomerases that
nick the positive stand at the plus origin of
replication and also at the single-strand conversion
sequence.
Length = 191
Score = 30.4 bits (69), Expect = 1.5
Identities = 28/129 (21%), Positives = 49/129 (37%), Gaps = 19/129 (14%)
Query: 287 DEDKIPIQAKKHRILFFGSNQFTWRSVGFYRRQINTIATLINQCQL--ILLDKQSTVLRF 344
+ED P + H IL F + T+ V I I L+N I+ +
Sbjct: 47 NEDGEPKKPHYHIILVFKNPV-TYSQV------IKLIKRLLNSPAPVEIVGSIKGAYRYL 99
Query: 345 THEDIKAQRY--------LLNG--IEQVIALHKEKLLSMVPGILKLFYDYDILEEKVLLE 394
THE ++Y NG I++ + L + L ++ ++ + I E L +
Sbjct: 100 THETKNPEKYQYDKSDIVAGNGFDIDRYLTLTESDKLDILNEVIDFIDENGITEFSDLTD 159
Query: 395 WAEKTSKKY 403
+A +Y
Sbjct: 160 YARSNGPEY 168
>gnl|CDD|177447 PHA02664, PHA02664, hypothetical protein; Provisional.
Length = 534
Score = 30.7 bits (69), Expect = 1.7
Identities = 15/62 (24%), Positives = 24/62 (38%)
Query: 424 REAEEEDSDSEESDDDLEIEYNDRARVTLQTETIKPKVIKKDEDEDGTNDKDEDEDGTND 483
R A + + +D D+E E +D + ++D D DE DG +D
Sbjct: 413 RAAAAAAAANAPADQDVEAEAHDEFDQDPGAPAHADRADSDEDDMDEQESGDERADGEDD 472
Query: 484 VD 485
D
Sbjct: 473 SD 474
>gnl|CDD|219922 pfam08595, RXT2_N, RXT2-like, N-terminal. The family represents
the N-terminal region of RXT2-like proteins. In S.
cerevisiae, RXT2 has been demonstrated to be involved in
conjugation with cellular fusion (mating) and invasive
growth. A high throughput localisation study has
localised RXT2 to the nucleus.
Length = 141
Score = 29.7 bits (67), Expect = 1.8
Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 3/49 (6%)
Query: 442 IEYNDRARVTLQTETIK---PKVIKKDEDEDGTNDKDEDEDGTNDVDID 487
+EYN R L + IK P I +D + +D+D+++D D + D
Sbjct: 24 VEYNGYERDVLSRKRIKFNNPPRIDEDGGDIDDDDEDDEDDEEADAEDD 72
>gnl|CDD|218752 pfam05793, TFIIF_alpha, Transcription initiation factor IIF, alpha
subunit (TFIIF-alpha). Transcription initiation factor
IIF, alpha subunit (TFIIF-alpha) or RNA polymerase
II-associating protein 74 (RAP74) is the large subunit
of transcription factor IIF (TFIIF), which is essential
for accurate initiation and stimulates elongation by RNA
polymerase II.
Length = 528
Score = 30.7 bits (69), Expect = 2.0
Identities = 19/58 (32%), Positives = 29/58 (50%), Gaps = 7/58 (12%)
Query: 425 EAEEED--SDSEESDDDLEIEYNDRARVTLQTETIKPKVIKKDEDEDGTNDKDEDEDG 480
E EED SDS S +D E +R L E I++DED + + ++ +E+G
Sbjct: 280 EGREEDYISDSSASGNDPE----EREDK-LSPEIPAKPEIEQDEDSEESEEEKNEEEG 332
>gnl|CDD|113603 pfam04837, MbeB_N, MbeB-like, N-term conserved region. This family
represents an N-terminal conserved region of MbeB/MobB
proteins. These proteins are essential for specific
plasmid transfer.
Length = 52
Score = 27.4 bits (61), Expect = 2.3
Identities = 13/42 (30%), Positives = 24/42 (57%)
Query: 228 LTISEDLEKTEKERMDIFYTCVKTALEKNNVDAKELLSEAER 269
L +++ E+ KE+ + VK+A EK+ +E L E+E+
Sbjct: 5 LDLAKTFEQKSKEQAESTEEMVKSAFEKHEKSVREALKESEK 46
>gnl|CDD|236410 PRK09202, nusA, transcription elongation factor NusA; Validated.
Length = 470
Score = 30.2 bits (69), Expect = 2.6
Identities = 25/101 (24%), Positives = 41/101 (40%), Gaps = 9/101 (8%)
Query: 384 YDILEEKVLLEWAEKTSKKYVSKELSAEIRSRAEPFIKWLREAEEEDSDSEESDDDLEIE 443
+ LEE + E + +E E+R RA+ + E E + + +DD L +E
Sbjct: 377 FSSLEELAYVPVEELLEIEGFDEETVEELRERAKEAL----ETEALAQEEKLADDLLSLE 432
Query: 444 YNDRARVTLQTETIKPKVIKKDED-EDGTNDKDEDEDGTND 483
DR + K IK ED + D+ D +G +
Sbjct: 433 GLDRE----LAFKLAEKGIKTLEDLAEQAVDELIDIEGDEE 469
>gnl|CDD|216786 pfam01921, tRNA-synt_1f, tRNA synthetases class I (K). This family
includes only lysyl tRNA synthetases from prokaryotes.
Length = 357
Score = 29.5 bits (67), Expect = 3.6
Identities = 11/36 (30%), Positives = 15/36 (41%), Gaps = 2/36 (5%)
Query: 97 FVLCPEC--DNPETDLVVSAKKGTIQQVCKACGFHG 130
+CP+C + A+ GTI C CG G
Sbjct: 171 LPICPKCGRVLTTPVVEYDAEGGTITYKCDECGHEG 206
>gnl|CDD|115196 pfam06524, NOA36, NOA36 protein. This family consists of several
NOA36 proteins which contain 29 highly conserved
cysteine residues. The function of this protein is
unknown.
Length = 314
Score = 29.5 bits (66), Expect = 4.0
Identities = 23/89 (25%), Positives = 37/89 (41%), Gaps = 17/89 (19%)
Query: 404 VSKELSAEIRSRAEPFIKWLREAEEEDSDSEESDDDL-----EIEYNDRARVTLQTETIK 458
+K+LS RS K+ R+ SD ++ +Y D V E+
Sbjct: 221 ETKDLSMSTRS-----YKFGRQTRGFRSDDDQGYGRYKQNLSSNKYGDFKGVNYGYES-- 273
Query: 459 PKVIKKDEDEDGTNDKDEDEDGTNDVDID 487
D++ +ND DE+EDG +D + D
Sbjct: 274 -----DDDEGSSSNDYDEEEDGDDDDNED 297
>gnl|CDD|233044 TIGR00600, rad2, DNA excision repair protein (rad2). All proteins
in this family for which functions are known are flap
endonucleases that generate the 3' incision next to DNA
damage as part of nucleotide excision repair. This
family is related to many other flap endonuclease
families including the fen1 family. 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 = 1034
Score = 29.9 bits (67), Expect = 4.1
Identities = 15/79 (18%), Positives = 32/79 (40%), Gaps = 5/79 (6%)
Query: 409 SAEIRSRAEPFIKWLREAEEEDSDSEESDDDLEIEYNDRARVTLQTETIKPKVIKKDEDE 468
SA++ + P E+E+E+S+S+ S +++ + TL+ + + +E
Sbjct: 632 SADLLLISNPMEVEPMESEKEESESDGSFIEVDSVSS-----TLELQVPSKSQPTDESEE 686
Query: 469 DGTNDKDEDEDGTNDVDID 487
+ N E D
Sbjct: 687 NAENKVASIEGEHRKEIED 705
>gnl|CDD|178752 PLN03213, PLN03213, repressor of silencing 3; Provisional.
Length = 759
Score = 29.8 bits (66), Expect = 4.2
Identities = 26/114 (22%), Positives = 49/114 (42%), Gaps = 3/114 (2%)
Query: 152 AVQGSSLTEGKRPKRISKKQESNGDMTKSDEESDPTVVAPEKVADEVNDDDGGWLAD-VS 210
AV+ + + S + D ++++ +A + D+V DD LAD V
Sbjct: 481 AVENDTAIDSMADDTASNSMAESDDGDNVEDDTAIDSMADDTANDDVGSDDSESLADTVI 540
Query: 211 EEAVRARALDLSSGVKGLTIS--EDLEKTEKERMDIFYTCVKTALEKNNVDAKE 262
+ +V A LD + +G + ++EK E D+ +++N VD +E
Sbjct: 541 DTSVDAVPLDFVANTEGDSGDGKSNVEKHENGAEDLNAEKESLVVKENVVDEEE 594
>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 = 28.3 bits (64), Expect = 4.6
Identities = 17/66 (25%), Positives = 26/66 (39%), Gaps = 9/66 (13%)
Query: 292 PIQAKKHRIL------FFGSNQFTWRSVGFYRRQINTIATLINQCQLILLDK--QSTVLR 343
P QA+ + FGSN F + V R + +N+ L LD T+L
Sbjct: 13 PHQARAQFLEILSKLPLFGSNFFYVQRVSDPRIPGPCLLA-VNREGLHFLDPNTHETLLT 71
Query: 344 FTHEDI 349
++I
Sbjct: 72 IPLKEI 77
>gnl|CDD|131554 TIGR02502, type_III_YscX, type III secretion protein, YscX family.
Members of this family are encoded within bacterial type
III secretion gene clusters. Among all species with type
III secretion, those with this protein are found among
those that target animal rather than plant cells. The
member of this family in Yersinia was shown by mutation
to be required for type III secretion of Yops effector
proteins and therefore is believe to be part of the
secretion machinery [Protein fate, Protein and peptide
secretion and trafficking, Cellular processes,
Pathogenesis].
Length = 121
Score = 28.2 bits (63), Expect = 4.8
Identities = 16/77 (20%), Positives = 32/77 (41%), Gaps = 9/77 (11%)
Query: 292 PIQAKKHRILFFGSNQFTWRSV---GFYRRQINTIATLINQCQLILLDKQSTVLRFTHED 348
P + +L F Q + + YR+ ++ + L+ + L + +L+ T D
Sbjct: 48 PARQSDQYLLAFAKPQLNFHGLLRPEDYRQALDNLQQLLQESGSANLQAAAELLQSTQLD 107
Query: 349 IKAQRYL---LNGIEQV 362
+R L LN + +V
Sbjct: 108 ---ERLLQMALNLLHKV 121
>gnl|CDD|227693 COG5406, COG5406, Nucleosome binding factor SPN, SPT16 subunit
[Transcription / DNA replication, recombination, and
repair / Chromatin structure and dynamics].
Length = 1001
Score = 29.6 bits (66), Expect = 4.9
Identities = 17/55 (30%), Positives = 30/55 (54%), Gaps = 5/55 (9%)
Query: 425 EAEEEDSDSEESDDDLEIEYNDRARVTLQTETIKPKVIKKDEDEDGTNDKDEDED 479
E+EEE S+ E S DD E ++ +E + +DE E+ ++D+++ ED
Sbjct: 933 ESEEEVSEYEASSDDESDETDEDEESDESSED-----LSEDESENDSSDEEDGED 982
>gnl|CDD|236716 PRK10564, PRK10564, maltose regulon periplasmic protein;
Provisional.
Length = 303
Score = 29.2 bits (66), Expect = 5.0
Identities = 14/31 (45%), Positives = 20/31 (64%), Gaps = 1/31 (3%)
Query: 245 FYTCVKTALEKNNVD-AKELLSEAERLEVKT 274
F +K A++K +VD A +LL EAERL +
Sbjct: 260 FNQAIKQAVKKGDVDKALKLLDEAERLGSTS 290
>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 = 29.6 bits (67), Expect = 5.2
Identities = 27/142 (19%), Positives = 62/142 (43%), Gaps = 1/142 (0%)
Query: 316 YRRQINTIATLINQCQLILLDKQSTVLRFTHEDIKAQRYLLNGIEQVIALHKEKLLSMVP 375
++ + + + +L + + + + E + A ++ +EQ + +E+L ++
Sbjct: 258 LTAELQELEEKLEELRLEVSELEEEIEELQKE-LYALANEISRLEQQKQILRERLANLER 316
Query: 376 GILKLFYDYDILEEKVLLEWAEKTSKKYVSKELSAEIRSRAEPFIKWLREAEEEDSDSEE 435
+ +L + LE K+ E + +EL E+ S + E EE +S EE
Sbjct: 317 QLEELEAQLEELESKLDELAEELAELEEKLEELKEELESLEAELEELEAELEELESRLEE 376
Query: 436 SDDDLEIEYNDRARVTLQTETI 457
++ LE + A++ LQ ++
Sbjct: 377 LEEQLETLRSKVAQLELQIASL 398
>gnl|CDD|216194 pfam00922, Phosphoprotein, Vesiculovirus phosphoprotein.
Length = 283
Score = 29.1 bits (65), Expect = 5.4
Identities = 21/104 (20%), Positives = 38/104 (36%), Gaps = 14/104 (13%)
Query: 383 DYDILEEKV--LLEWAEKTSKKYVSK-ELSAEIRSRAEPFIKWLREAEEEDSDSEESDDD 439
+Y L++ + + E E+ + K + E S E + ++ E DS++E S +D
Sbjct: 9 NYPRLDQTLSEIEEMEEQRADKSSTFQEDSVEEHTSPSYYL----AEELSDSETEPSIED 64
Query: 440 LEIEYNDRARVTLQTETIKPKVIKKDEDEDGTNDKDEDEDGTND 483
+ Y E ++ D D D D D
Sbjct: 65 DQGLYTQLPPA----EQVEG---FIQGPLDDIADDDIDVVFEED 101
>gnl|CDD|218333 pfam04931, DNA_pol_phi, DNA polymerase phi. This family includes
the fifth essential DNA polymerase in yeast EC:2.7.7.7.
Pol5p is localised exclusively to the nucleolus and
binds near or at the enhancer region of rRNA-encoding
DNA repeating units.
Length = 784
Score = 29.1 bits (65), Expect = 6.1
Identities = 21/62 (33%), Positives = 30/62 (48%), Gaps = 13/62 (20%)
Query: 423 LREAEEEDSDS-EESDDDLEIEYNDRARVTLQTETIKPKVIK-KDEDEDGTNDKDEDEDG 480
L E EEED D EE+DDD + + E I+ + + + EDG D+ ED+
Sbjct: 644 LFEGEEEDEDDLEETDDDED-----------ECEAIEDSESESESDGEDGEEDEQEDDAE 692
Query: 481 TN 482
N
Sbjct: 693 AN 694
>gnl|CDD|240226 PTZ00007, PTZ00007, (NAP-L) nucleosome assembly protein -L;
Provisional.
Length = 337
Score = 29.0 bits (65), Expect = 6.7
Identities = 19/79 (24%), Positives = 32/79 (40%), Gaps = 15/79 (18%)
Query: 407 ELSAEIRSRAEPF-IKW-LREAEEEDSDSEESDDDLEIEYNDRARVTLQTETIKPKVIKK 464
E+ IR + P+ + W L EA +EDSD +DD + + D +
Sbjct: 258 EIGITIRDKLIPYAVYWFLGEAIDEDSDYSSDEDDDDYDSYDSSD-------------SA 304
Query: 465 DEDEDGTNDKDEDEDGTND 483
D + D +E++D
Sbjct: 305 SSDSNSDVDTNEEDDRGEK 323
>gnl|CDD|220759 pfam10446, DUF2457, Protein of unknown function (DUF2457). This is
a family of uncharacterized proteins.
Length = 449
Score = 28.8 bits (64), Expect = 7.6
Identities = 20/64 (31%), Positives = 29/64 (45%), Gaps = 16/64 (25%)
Query: 425 EAEEEDSDSEESDDDLEIEYNDRARVTLQTETIKPKVIKKDEDEDGTNDKDEDEDGTNDV 484
EA EE+ D EE DDD + E D D+D+D ++ ++D+D T
Sbjct: 48 EAMEEEDDDEEDDDDDDDEDEDDD----------------DDDDDEDDEDEDDDDSTLHD 91
Query: 485 DIDA 488
D A
Sbjct: 92 DSSA 95
>gnl|CDD|131353 TIGR02300, FYDLN_acid, TIGR02300 family protein. Members of this
family are bacterial proteins with a conserved motif
[KR]FYDLN, sometimes flanked by a pair of CXXC motifs,
followed by a long region of low complexity sequence in
which roughly half the residues are Asp and Glu,
including multiple runs of five or more acidic residues.
The function of members of this family is unknown.
Length = 129
Score = 27.6 bits (61), Expect = 7.8
Identities = 24/101 (23%), Positives = 40/101 (39%), Gaps = 8/101 (7%)
Query: 389 EKVLLEWAEKTSKKYVSKELSAEIRSRAEPFIKWLREAEEEDSDSEESDDDLEIEYNDRA 448
E+ E A K+ + E A +P I E + S E D+ E + A
Sbjct: 34 EQFPPEEALKSRRVRADDEKEAVAVKEVDPEI-----DEAAELVSLEEADE---EVDPGA 85
Query: 449 RVTLQTETIKPKVIKKDEDEDGTNDKDEDEDGTNDVDIDAI 489
+ + D+D+D T +DE++D +D DI +
Sbjct: 86 PTPAGGDDLAEDEDIADDDDDVTFLEDEEDDDIDDEDIIGV 126
>gnl|CDD|217502 pfam03343, SART-1, SART-1 family. SART-1 is a protein involved in
cell cycle arrest and pre-mRNA splicing. It has been
shown to be a component of U4/U6 x U5 tri-snRNP complex
in human, Schizosaccharomyces pombe and Saccharomyces
cerevisiae. SART-1 is a known tumour antigen in a range
of cancers recognised by T cells.
Length = 603
Score = 29.0 bits (65), Expect = 7.9
Identities = 20/76 (26%), Positives = 36/76 (47%), Gaps = 2/76 (2%)
Query: 415 RAEPFIKWLREAEEEDSDSEESDDDLEIEYNDRARV--TLQTETIKPKVIKKDEDEDGTN 472
R E + + E ED + ++D I ++ + +LQ E ++ K KDE + +
Sbjct: 364 RPEDIARQIAEERSEDEEEAAENNDNGIVIDETSEFVRSLQKEPLEEKPENKDESVEEIS 423
Query: 473 DKDEDEDGTNDVDIDA 488
D +ED++ D D D
Sbjct: 424 DAEEDDEDEEDEDGDG 439
>gnl|CDD|220714 pfam10357, Kin17_mid, Domain of Kin17 curved DNA-binding protein.
Kin17_mid is the conserved central 169 residue region of
a family of Kin17 proteins. Towards the N-terminal end
there is a zinc-finger domain, and in human and mouse
members there is a RecA-like domain further downstream.
The Kin17 protein in humans forms intra-nuclear foci
during cell proliferation and is re-distributed in the
nucleoplasm during the cell cycle.
Length = 127
Score = 27.2 bits (61), Expect = 10.0
Identities = 13/51 (25%), Positives = 25/51 (49%), Gaps = 2/51 (3%)
Query: 419 FIKWLREAEEEDSDSEESDDDLEIEYNDRARVTLQTETIKPKVIKKDEDED 469
F+K+L E EE++ I Y DR+ L+ + K K+++ ++
Sbjct: 67 FVKYL--GREGKCKVEETEKGWFITYIDRSPEALKRQEELRKKEKQEKTDE 115
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
0.314 0.133 0.377
Gapped
Lambda K H
0.267 0.0762 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 25,059,593
Number of extensions: 2509947
Number of successful extensions: 2874
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2661
Number of HSP's successfully gapped: 113
Length of query: 489
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 388
Effective length of database: 6,457,848
Effective search space: 2505645024
Effective search space used: 2505645024
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: 42 (22.0 bits)
S2: 61 (27.2 bits)