RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16318
(474 letters)
>gnl|CDD|215487 PLN02900, PLN02900, alanyl-tRNA synthetase.
Length = 936
Score = 128 bits (323), Expect = 2e-31
Identities = 57/146 (39%), Positives = 75/146 (51%), Gaps = 29/146 (19%)
Query: 317 EGFMSNKQFVDSVSSGTEAGILLDKSNFYAEQGGQIYDEGFMIGVNDESQIELWFSSLVN 376
+ ++ FV+SVS G E GI+LDK++FYAE GGQI D G + G
Sbjct: 504 KAILTGGGFVESVSEGDEVGIVLDKTSFYAESGGQIGDTGVLEGSGGAV----------- 552
Query: 377 LEGSKYALPIFLQFSLSNLKKKKKLVKLLHTLSHT---LRVGDKLKLHIDTARRRPIMSN 433
+S+++K V LH + T + VGD + +D RRR I N
Sbjct: 553 -------------VEVSDVQKAGGFV--LHIGTVTEGSVSVGDAVTCKVDYDRRRRIAPN 597
Query: 434 HTATHILNHALRFVLGPEADQKGSLV 459
HTATH+LN AL+ VLG DQKGSLV
Sbjct: 598 HTATHLLNSALKEVLGDHVDQKGSLV 623
Score = 76.2 bits (188), Expect = 1e-14
Identities = 35/76 (46%), Positives = 48/76 (63%), Gaps = 6/76 (7%)
Query: 6 AKLGESKVLPGDVAWRLYDTYGFPVDLTQLMVEEKGLSVDMEVYEDAKKKAQSEPESQAG 65
AK VL G A+ LYDTYGFPVDLT+LM EE+G++VDME +E A ++A+ S+A
Sbjct: 403 AKANGGPVLSGKDAFLLYDTYGFPVDLTELMAEERGVTVDMEGFEAAMEEARE--RSRAA 460
Query: 66 METSVEFCGGTHLAMA 81
+ GG + +A
Sbjct: 461 HLKA----GGGAIELA 472
Score = 63.9 bits (156), Expect = 9e-11
Identities = 24/54 (44%), Positives = 32/54 (59%)
Query: 267 GFMIGVNDEGTVVGLRYNKQFVDSVSSGTEAGILLDKSNFYAEQGGQIYDEGFM 320
+ + E V + FV+SVS G E GI+LDK++FYAE GGQI D G +
Sbjct: 492 KYDWLSDHEAVVKAILTGGGFVESVSEGDEVGIVLDKTSFYAESGGQIGDTGVL 545
Score = 61.6 bits (150), Expect = 5e-10
Identities = 24/44 (54%), Positives = 29/44 (65%)
Query: 236 FVDSVSSGTEAGILLDKSNFYAEQGGQIYDEGFMIGVNDEGTVV 279
FV+SVS G E GI+LDK++FYAE GGQI D G + G V
Sbjct: 512 FVESVSEGDEVGIVLDKTSFYAESGGQIGDTGVLEGSGGAVVEV 555
Score = 46.9 bits (112), Expect = 2e-05
Identities = 15/30 (50%), Positives = 19/30 (63%)
Query: 69 SVEFCGGTHLAMAHHVGDFCISSEEAIAKG 98
S+E CGGTH++ F + SEE IAKG
Sbjct: 698 SMELCGGTHVSNTAEAEAFKLLSEEGIAKG 727
>gnl|CDD|223092 COG0013, AlaS, Alanyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 879
Score = 114 bits (287), Expect = 5e-27
Identities = 47/146 (32%), Positives = 73/146 (50%), Gaps = 28/146 (19%)
Query: 317 EGFMSNKQFVDSVSSGTEAGILLDKSNFYAEQGGQIYDEGFMIGVNDESQIELWFSSLVN 376
+ + V ++ G E ++LD++ FYAE GGQ+ D G++ G
Sbjct: 472 LVLFVDGKEVSELNEGQEVYVVLDQTPFYAESGGQVGDTGYIFGDGGG------------ 519
Query: 377 LEGSKYALPIFLQFSLSNLKKKKKLVKLLHT---LSHTLRVGDKLKLHIDTARRRPIMSN 433
+F +++++K V ++H S L+VGD++ +D RRR +M N
Sbjct: 520 ------------RFEVTDVQKVGNGV-IVHKGKVESGELKVGDEVTAEVDEERRRRLMRN 566
Query: 434 HTATHILNHALRFVLGPEADQKGSLV 459
HTATH+L+ ALR VLG Q GSLV
Sbjct: 567 HTATHLLHAALRKVLGDHVWQAGSLV 592
Score = 81.9 bits (203), Expect = 2e-16
Identities = 27/57 (47%), Positives = 40/57 (70%)
Query: 3 QTIAKLGESKVLPGDVAWRLYDTYGFPVDLTQLMVEEKGLSVDMEVYEDAKKKAQSE 59
+ +AKL +SK L G+ A++LYDTYGFPV+LT+ + EE+GL VD +E A + +
Sbjct: 375 KELAKLKKSKTLDGEDAFKLYDTYGFPVELTEEIAEERGLKVDEPGFEYAMEAQRER 431
Score = 59.6 bits (145), Expect = 2e-09
Identities = 20/60 (33%), Positives = 33/60 (55%), Gaps = 5/60 (8%)
Query: 264 YDEGFMIGVNDEGTVVGLRYNKQFVDSVSSGTEAGILLDKSNFYAEQGGQIYDEGFMSNK 323
YD+ M E V+ L + + V ++ G E ++LD++ FYAE GGQ+ D G++
Sbjct: 462 YDDLEM-----EFKVLVLFVDGKEVSELNEGQEVYVVLDQTPFYAESGGQVGDTGYIFGD 516
Score = 53.8 bits (130), Expect = 2e-07
Identities = 15/42 (35%), Positives = 26/42 (61%)
Query: 233 NKQFVDSVSSGTEAGILLDKSNFYAEQGGQIYDEGFMIGVND 274
+ + V ++ G E ++LD++ FYAE GGQ+ D G++ G
Sbjct: 477 DGKEVSELNEGQEVYVVLDQTPFYAESGGQVGDTGYIFGDGG 518
Score = 39.9 bits (94), Expect = 0.003
Identities = 17/30 (56%), Positives = 20/30 (66%)
Query: 69 SVEFCGGTHLAMAHHVGDFCISSEEAIAKG 98
SVE CGGTH++ +G F I SEE IA G
Sbjct: 665 SVELCGGTHVSNTGDIGLFKIISEEGIAAG 694
>gnl|CDD|234701 PRK00252, alaS, alanyl-tRNA synthetase; Reviewed.
Length = 865
Score = 106 bits (268), Expect = 2e-24
Identities = 48/146 (32%), Positives = 65/146 (44%), Gaps = 40/146 (27%)
Query: 322 NKQFVDSVSSGTEAGILLDKSNFYAEQGGQIYDEGFMIG-----VNDESQIELWFSSLVN 376
+ + VDS +G E ++LDK+ FYAE GGQ+ D G + V D
Sbjct: 465 DGESVDSAKAGEEVEVVLDKTPFYAESGGQVGDTGVIEDGGVFEVTD-----------TQ 513
Query: 377 LEGSKYALPIFLQFSLSNLKKKKKLVKLLHT---LSHTLRVGDKLKLHIDTARRRPIMSN 433
K L+ +H L+VGD++ +D RRR I N
Sbjct: 514 -------------------KPPNGLI--VHRGKVEEGELKVGDEVTAEVDEERRRAIARN 552
Query: 434 HTATHILNHALRFVLGPEADQKGSLV 459
H+ATH+L+ ALR VLG Q GSLV
Sbjct: 553 HSATHLLHAALREVLGEHVTQAGSLV 578
Score = 87.8 bits (219), Expect = 2e-18
Identities = 32/86 (37%), Positives = 44/86 (51%), Gaps = 12/86 (13%)
Query: 5 IAKLGESKVLPGDVAWRLYDTYGFPVDLTQLMVEEKGLSVDMEVYE------------DA 52
+AKL KVL G+ A++LYDTYGFP+DLT + E+GL+VD E +E
Sbjct: 368 LAKLKAGKVLSGEDAFKLYDTYGFPLDLTAEIARERGLTVDEEGFEAAMEEQRERARAAR 427
Query: 53 KKKAQSEPESQAGMETSVEFCGGTHL 78
K K + + + EF G L
Sbjct: 428 KFKGDYNALEELLDDLATEFVGYDTL 453
Score = 58.9 bits (144), Expect = 3e-09
Identities = 20/49 (40%), Positives = 30/49 (61%)
Query: 274 DEGTVVGLRYNKQFVDSVSSGTEAGILLDKSNFYAEQGGQIYDEGFMSN 322
E V+ L + + VDS +G E ++LDK+ FYAE GGQ+ D G + +
Sbjct: 455 AEAKVLALFVDGESVDSAKAGEEVEVVLDKTPFYAESGGQVGDTGVIED 503
Score = 50.1 bits (121), Expect = 2e-06
Identities = 17/39 (43%), Positives = 25/39 (64%)
Query: 233 NKQFVDSVSSGTEAGILLDKSNFYAEQGGQIYDEGFMIG 271
+ + VDS +G E ++LDK+ FYAE GGQ+ D G +
Sbjct: 465 DGESVDSAKAGEEVEVVLDKTPFYAESGGQVGDTGVIED 503
Score = 38.1 bits (90), Expect = 0.009
Identities = 14/30 (46%), Positives = 19/30 (63%)
Query: 69 SVEFCGGTHLAMAHHVGDFCISSEEAIAKG 98
S+E CGGTH++ +G F I SE +A G
Sbjct: 651 SIELCGGTHVSNTGDIGLFKIVSESGVAAG 680
>gnl|CDD|232931 TIGR00344, alaS, alanine--tRNA ligase. The model describes
alanine--tRNA ligase. This enzyme catalyzes the reaction
(tRNAala + L-alanine + ATP = L-alanyl-tRNAala +
pyrophosphate + AMP) [Protein synthesis, tRNA
aminoacylation].
Length = 851
Score = 105 bits (263), Expect = 6e-24
Identities = 48/145 (33%), Positives = 71/145 (48%), Gaps = 30/145 (20%)
Query: 318 GFMSNKQFVDSVSSGTEAGILLDKSNFYAEQGGQIYDEGFMIGVNDESQIELWFSSLVNL 377
G + + VD +G ++LD++ FYAE GGQI D G++I + +
Sbjct: 468 GLFEDGKPVDEAEAGQSVYVILDQTPFYAESGGQIGDTGYLIANDGK------------- 514
Query: 378 EGSKYALPIFLQFSLSNLKKKKKLVKLLHT---LSHTLRVGDKLKLHIDTARRRPIMSNH 434
F + +++K +V H +L+VGDK+ ID RR IM NH
Sbjct: 515 ------------FRVVDVQKPNGVV--FHFGEVEGGSLKVGDKVIAVIDEKRRLRIMRNH 560
Query: 435 TATHILNHALRFVLGPEADQKGSLV 459
+ATH+L+ AL+ VLG Q GSLV
Sbjct: 561 SATHLLHAALQKVLGNHVWQAGSLV 585
Score = 70.9 bits (174), Expect = 5e-13
Identities = 27/63 (42%), Positives = 40/63 (63%), Gaps = 2/63 (3%)
Query: 6 AKLGESKVLPGDVAWRLYDTYGFPVDLTQLMVEEKGLSVDMEVYEDAKKKAQSEPESQAG 65
K K L G+ A++LYDTYGFPV+LT+ + EE+GL+VD+ +E A+ S+A
Sbjct: 375 LKKLGKKELDGEDAFKLYDTYGFPVELTKEIAEERGLTVDIPGFE--TLMAEQRERSKAA 432
Query: 66 MET 68
+T
Sbjct: 433 SQT 435
Score = 58.5 bits (142), Expect = 4e-09
Identities = 20/64 (31%), Positives = 33/64 (51%), Gaps = 1/64 (1%)
Query: 226 KRLRFSYNKQFVDSVSSGTEAGILLDKSNFYAEQGGQIYDEGFMIGVNDEGTVVG-LRYN 284
K + + + VD +G ++LD++ FYAE GGQI D G++I + + VV + N
Sbjct: 465 KVIGLFEDGKPVDEAEAGQSVYVILDQTPFYAESGGQIGDTGYLIANDGKFRVVDVQKPN 524
Query: 285 KQFV 288
Sbjct: 525 GVVF 528
Score = 39.3 bits (92), Expect = 0.004
Identities = 15/30 (50%), Positives = 17/30 (56%)
Query: 69 SVEFCGGTHLAMAHHVGDFCISSEEAIAKG 98
SVE CGGTH+ +G F I E IA G
Sbjct: 658 SVELCGGTHVRNTGEIGLFKIVKESGIAAG 687
>gnl|CDD|216484 pfam01411, tRNA-synt_2c, tRNA synthetases class II (A). Other tRNA
synthetase sub-families are too dissimilar to be
included. This family includes only alanyl-tRNA
synthetases.
Length = 551
Score = 93.5 bits (233), Expect = 3e-20
Identities = 34/85 (40%), Positives = 50/85 (58%), Gaps = 2/85 (2%)
Query: 3 QTIAKLGESKVLPGDVAWRLYDTYGFPVDLTQLMVEEKGLSVDMEVYEDAKKKAQSEPES 62
+ I L +SK LPG+ A++LYDTYGFPVDLTQ + EE+GL+VDM +E A + + S
Sbjct: 371 RLIKSLKKSKTLPGEDAFKLYDTYGFPVDLTQEIAEERGLTVDMPGFEKAMVEQRE--RS 428
Query: 63 QAGMETSVEFCGGTHLAMAHHVGDF 87
+ ++ E + L +F
Sbjct: 429 KQAVKEKGEELDVSALVELPATSEF 453
Score = 72.7 bits (179), Expect = 1e-13
Identities = 31/111 (27%), Positives = 49/111 (44%), Gaps = 26/111 (23%)
Query: 317 EGFMSNKQFVDSVSSGTEAGILLDKSNFYAEQGGQIYDEGFMIGVNDESQIELWFSSLVN 376
+ +FV V G E G++LD++ FYAE GGQI D G++IG E
Sbjct: 466 LALFKDGEFVAEVLEGQEGGVILDRTPFYAESGGQIGDTGYIIGEGGE------------ 513
Query: 377 LEGSKYALPIFLQFSLSNLKKKKKLVKLLHTLSH-TLRVGDKLKLHIDTAR 426
F +++++K +V L +L+VGD + +D R
Sbjct: 514 -------------FRVTDVQKYGGVVVHKGKLESGSLKVGDTVIAVVDEDR 551
Score = 69.2 bits (170), Expect = 2e-12
Identities = 20/50 (40%), Positives = 31/50 (62%)
Query: 272 VNDEGTVVGLRYNKQFVDSVSSGTEAGILLDKSNFYAEQGGQIYDEGFMS 321
+ E ++ L + +FV V G E G++LD++ FYAE GGQI D G++
Sbjct: 459 LEAEAKILALFKDGEFVAEVLEGQEGGVILDRTPFYAESGGQIGDTGYII 508
Score = 64.2 bits (157), Expect = 6e-11
Identities = 22/48 (45%), Positives = 30/48 (62%)
Query: 232 YNKQFVDSVSSGTEAGILLDKSNFYAEQGGQIYDEGFMIGVNDEGTVV 279
+ +FV V G E G++LD++ FYAE GGQI D G++IG E V
Sbjct: 470 KDGEFVAEVLEGQEGGVILDRTPFYAESGGQIGDTGYIIGEGGEFRVT 517
>gnl|CDD|234309 TIGR03683, A-tRNA_syn_arch, alanyl-tRNA synthetase. This family of
alanyl-tRNA synthetases is limited to the archaea, and
is a subset of those sequences identified by the model
pfam07973 covering the second additional domain (SAD) of
alanyl and threonyl tRNA synthetases.
Length = 902
Score = 73.1 bits (180), Expect = 1e-13
Identities = 39/144 (27%), Positives = 67/144 (46%), Gaps = 30/144 (20%)
Query: 315 YDEGFMSNKQFVDSVSSGTEAGILLDKSNFYAEQGGQIYDEGFMIGVNDESQIELWFSSL 374
Y++ M ++F V + ++LD++ FY E GGQ D G++I E ++
Sbjct: 506 YEDPTM--REFEAKVLGVFDNYVVLDQTAFYPEGGGQPADTGYLITNGGEYRV------- 556
Query: 375 VNLEGSKYALPIFLQFSLSNLKKKKKLVKLLHTLS-HTLRVGDKLKLHIDTARRRPIMSN 433
+++K ++ +H + ++ GD++K ID RR +M +
Sbjct: 557 ------------------VDVQKVGGVI--VHKVDGEGIKEGDEVKGEIDWERRLRLMRH 596
Query: 434 HTATHILNHALRFVLGPEADQKGS 457
HTATH+L A R VLG Q G+
Sbjct: 597 HTATHVLLAAARRVLGRHVWQAGA 620
Score = 36.5 bits (85), Expect = 0.029
Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 2/62 (3%)
Query: 220 KHTPFVKRLRF--SYNKQFVDSVSSGTEAGILLDKSNFYAEQGGQIYDEGFMIGVNDEGT 277
K P +RL + ++F V + ++LD++ FY E GGQ D G++I E
Sbjct: 496 KDLPETRRLFYEDPTMREFEAKVLGVFDNYVVLDQTAFYPEGGGQPADTGYLITNGGEYR 555
Query: 278 VV 279
VV
Sbjct: 556 VV 557
Score = 33.8 bits (78), Expect = 0.24
Identities = 10/25 (40%), Positives = 17/25 (68%)
Query: 296 EAGILLDKSNFYAEQGGQIYDEGFM 320
+ ++LD++ FY E GGQ D G++
Sbjct: 523 DNYVVLDQTAFYPEGGGQPADTGYL 547
Score = 31.9 bits (73), Expect = 0.89
Identities = 12/45 (26%), Positives = 26/45 (57%), Gaps = 1/45 (2%)
Query: 3 QTIAKLGESKV-LPGDVAWRLYDTYGFPVDLTQLMVEEKGLSVDM 46
+ + +L ++K +P D LYD++G P ++ + + E G V++
Sbjct: 422 RIVERLLKTKKEIPLDDLIELYDSHGIPPEIVKEIAAELGAEVEI 466
>gnl|CDD|237551 PRK13902, alaS, alanyl-tRNA synthetase; Provisional.
Length = 900
Score = 71.0 bits (175), Expect = 5e-13
Identities = 35/122 (28%), Positives = 58/122 (47%), Gaps = 28/122 (22%)
Query: 337 ILLDKSNFYAEQGGQIYDEGFMIGVNDESQIELWFSSLVNLEGSKYALPIFLQFSLSNLK 396
++LD++ FY E GGQ D G +I V+ + + + +++
Sbjct: 522 VVLDQTAFYPEGGGQPADTGVLI-VDGK------------------------GYKVVDVQ 556
Query: 397 KKKKLVKLLHTL-SHTLRVGDKLKLHIDTARRRPIMSNHTATHILNHALRFVLGPEADQK 455
K ++ +H L + GD+++ ID RR +M +HTATHI+ A R VLG Q
Sbjct: 557 KVGGVI--VHVLEGEPPKKGDEVRGEIDWERRYRLMRHHTATHIILAAARKVLGDHVWQA 614
Query: 456 GS 457
G+
Sbjct: 615 GA 616
Score = 35.2 bits (82), Expect = 0.073
Identities = 13/32 (40%), Positives = 18/32 (56%)
Query: 248 ILLDKSNFYAEQGGQIYDEGFMIGVNDEGTVV 279
++LD++ FY E GGQ D G +I VV
Sbjct: 522 VVLDQTAFYPEGGGQPADTGVLIVDGKGYKVV 553
Score = 34.4 bits (80), Expect = 0.15
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 299 ILLDKSNFYAEQGGQIYDEGFMS 321
++LD++ FY E GGQ D G +
Sbjct: 522 VVLDQTAFYPEGGGQPADTGVLI 544
>gnl|CDD|225427 COG2872, COG2872, Predicted metal-dependent hydrolases related to
alanyl-tRNA synthetase HxxxH domain [General function
prediction only].
Length = 241
Score = 68.2 bits (167), Expect = 5e-13
Identities = 40/136 (29%), Positives = 54/136 (39%), Gaps = 37/136 (27%)
Query: 324 QFVDSVSSGTEA--------GILLDKSNFYAEQGGQIYDEGFMIGVNDESQIELWFSSLV 375
+ DS EA I+LD++ FY GGQ D G +I E +E
Sbjct: 6 YYDDSYLKEFEATVVDVEDNEIVLDRTIFYPTGGGQPGDTGTLIWAGGEYVVE------- 58
Query: 376 NLEGSKYALPIFLQFSLSNLKKKKKLVKLLHTLSH--TLRVGDKLKLHIDTARRRPIMSN 433
K +++H L+ L+VGDK+KL ID RR M
Sbjct: 59 --------------------DVTKDGEEIVHVLAEHAKLKVGDKVKLKIDWERRYRHMRM 98
Query: 434 HTATHILNHALRFVLG 449
HTA H+L+ L V G
Sbjct: 99 HTALHLLSAVLYKVYG 114
Score = 39.3 bits (92), Expect = 0.003
Identities = 17/45 (37%), Positives = 24/45 (53%)
Query: 231 SYNKQFVDSVSSGTEAGILLDKSNFYAEQGGQIYDEGFMIGVNDE 275
SY K+F +V + I+LD++ FY GGQ D G +I E
Sbjct: 10 SYLKEFEATVVDVEDNEIVLDRTIFYPTGGGQPGDTGTLIWAGGE 54
Score = 33.9 bits (78), Expect = 0.13
Identities = 17/56 (30%), Positives = 24/56 (42%), Gaps = 4/56 (7%)
Query: 283 YNKQFVDSVSSGTEAGILLDKSNFYAEQGGQIYDEGFM----SNKQFVDSVSSGTE 334
Y K+F +V + I+LD++ FY GGQ D G + D G E
Sbjct: 11 YLKEFEATVVDVEDNEIVLDRTIFYPTGGGQPGDTGTLIWAGGEYVVEDVTKDGEE 66
>gnl|CDD|234962 PRK01584, PRK01584, alanyl-tRNA synthetase; Provisional.
Length = 594
Score = 68.6 bits (168), Expect = 2e-12
Identities = 40/110 (36%), Positives = 59/110 (53%), Gaps = 15/110 (13%)
Query: 5 IAKLGESKVLPGDVAWRLYDTYGFPVDLTQLMVEEKGLSVDMEVYEDAKKKAQSEPESQA 64
I LG SK++PGD+A++LYDTYGFP ++T+ + E G +VD E +++ KK Q S+
Sbjct: 379 IPNLGSSKIIPGDIAFKLYDTYGFPYEITEELASEYGFTVDREGFDEHFKKHQK--VSKK 436
Query: 65 GMETSVEFCGG--------THLAMAHHVGDFCIS---SEEAIAKGSNIVS 103
G + F GG T L A H+ + + KGSNI +
Sbjct: 437 GADKV--FKGGLADHSYETTKLHTATHLLHKALRLVLGDHVRQKGSNITA 484
Score = 40.5 bits (95), Expect = 0.001
Identities = 16/24 (66%), Positives = 18/24 (75%)
Query: 434 HTATHILNHALRFVLGPEADQKGS 457
HTATH+L+ ALR VLG QKGS
Sbjct: 457 HTATHLLHKALRLVLGDHVRQKGS 480
Score = 31.7 bits (72), Expect = 1.1
Identities = 11/30 (36%), Positives = 16/30 (53%)
Query: 69 SVEFCGGTHLAMAHHVGDFCISSEEAIAKG 98
S E CGG H+ +G F I E++ + G
Sbjct: 555 SKEVCGGPHVENTGELGTFKIQKEQSSSSG 584
>gnl|CDD|197931 smart00863, tRNA_SAD, Threonyl and Alanyl tRNA synthetase second
additional domain. The catalytically active form of
threonyl/alanyl tRNA synthetase is a dimer. Within the
tRNA synthetase class II dimer, the bound tRNA
interacts with both monomers making specific
interactions with the catalytic domain, the C-terminal
domain, and this SAD domain (the second additional
domain). The second additional domain is comprised of a
pair of perpendicularly orientated antiparallel beta
sheets, of four and three strands, respectively, that
surround a central alpha helix that forms the core of
the domain.
Length = 43
Score = 37.7 bits (89), Expect = 4e-04
Identities = 13/32 (40%), Positives = 16/32 (50%)
Query: 67 ETSVEFCGGTHLAMAHHVGDFCISSEEAIAKG 98
+ SVE CGGTH+ +G F I S G
Sbjct: 8 DFSVELCGGTHVPNTGEIGAFKILSVSGAYWG 39
>gnl|CDD|219676 pfam07973, tRNA_SAD, Threonyl and Alanyl tRNA synthetase second
additional domain. The catalytically active from of
threonyl/alanyl tRNA synthetase is a dimer. Within the
tRNA synthetase class II dimer, the bound tRNA
interacts with both monomers making specific
interactions with the catalytic domain, the C-terminal
domain, and this domain (the second additional domain).
The second additional domain is comprised of a pair of
perpendicularly orientated antiparallel beta sheets, of
four and three strands, respectively, that surround a
central alpha helix that forms the core of the domain.
Length = 44
Score = 37.1 bits (87), Expect = 6e-04
Identities = 11/32 (34%), Positives = 17/32 (53%)
Query: 67 ETSVEFCGGTHLAMAHHVGDFCISSEEAIAKG 98
+ V+ CGGTH+ +G F I ++ KG
Sbjct: 8 DFDVDLCGGTHVPNTGEIGAFKILKGDSKNKG 39
>gnl|CDD|239663 cd03692, mtIF2_IVc, mtIF2_IVc: this family represents the C2
subdomain of domain IV of mitochondrial translation
initiation factor 2 (mtIF2) which adopts a beta-barrel
fold displaying a high degree of structural similarity
with domain II of the translation elongation factor
EF-Tu. The C-terminal part of mtIF2 contains the entire
fMet-tRNAfmet binding site of IF-2 and is resistant to
proteolysis. This C-terminal portion consists of two
domains, IF2 C1 and IF2 C2. IF2 C2 been shown to
contain all molecular determinants necessary and
sufficient for the recognition and binding of
fMet-tRNAfMet. Like IF2 from certain prokaryotes such as
Thermus thermophilus, mtIF2lacks domain II which is
thought to be involved in binding of E.coli IF-2 to 30S
subunits.
Length = 84
Score = 32.5 bits (75), Expect = 0.062
Identities = 12/35 (34%), Positives = 15/35 (42%)
Query: 275 EGTVVGLRYNKQFVDSVSSGTEAGILLDKSNFYAE 309
EG + L+ K V V G E GI L+ N
Sbjct: 44 EGKISSLKRFKDDVKEVKKGYECGITLENFNDIKV 78
Score = 27.1 bits (61), Expect = 6.2
Identities = 9/25 (36%), Positives = 10/25 (40%)
Query: 234 KQFVDSVSSGTEAGILLDKSNFYAE 258
K V V G E GI L+ N
Sbjct: 54 KDDVKEVKKGYECGITLENFNDIKV 78
Score = 27.1 bits (61), Expect = 6.2
Identities = 9/25 (36%), Positives = 10/25 (40%)
Query: 323 KQFVDSVSSGTEAGILLDKSNFYAE 347
K V V G E GI L+ N
Sbjct: 54 KDDVKEVKKGYECGITLENFNDIKV 78
>gnl|CDD|178546 PLN02961, PLN02961, alanine-tRNA ligase.
Length = 223
Score = 33.5 bits (77), Expect = 0.14
Identities = 29/135 (21%), Positives = 55/135 (40%), Gaps = 36/135 (26%)
Query: 337 ILLDKSNFYAEQGGQIYDEGFMIGVNDESQIELWFSSLVNLEGSKYALPIFLQFSLSNLK 396
++LD++ F+ + GGQ D G ++ + +FS+ +++
Sbjct: 5 LVLDRTIFHPQGGGQPSDTGRIVISGGD-----------------------TKFSVQDVR 41
Query: 397 KKKKLVKLLHTLS-------HTLRVGDKLKLHIDTARRRPIMSNHTATHILNHALRFV-L 448
+K +V GD++ + +D +RR+ H+A H+L+ + V L
Sbjct: 42 RKDGVVYHYGVFEGSNPESASPFEAGDEVTVTVDESRRKLHSRLHSAGHLLDVCMARVGL 101
Query: 449 GPEADQKGSLVYRYH 463
GP KG YH
Sbjct: 102 GPLEPGKG-----YH 111
>gnl|CDD|234502 TIGR04212, GlyGly_RbtA, Acinetobacter rhombotarget A. Members of
this protein family are found, so far, exclusively in
the genus Acinetobacter. Members average just over 600
amino acids in length, including a 22-amino acid
C-terminal putative protein sorting recognition
sequence, GlyGly-CTERM (TIGR03501). The GlyGly-CTERM
signal always co-occurs with a subfamily of the rhomboid
family intramembrane serine proteases called
rhombosortase (TIGR03902). Members occur paired with a
second rhombosortase target, with which it also shares
an N-terminal motif CSLREA. This protein is designated
Acinetobacter rhombotarget A (rbtA).
Length = 605
Score = 32.8 bits (75), Expect = 0.47
Identities = 20/55 (36%), Positives = 27/55 (49%), Gaps = 12/55 (21%)
Query: 305 NFYAEQGGQIYDEGFMSNKQFVDSVSSGTEAGILLDKS----NFYAEQGGQIYDE 355
N YA QGG IY+ G +S + AGI+ ++ N A+QG IY E
Sbjct: 173 NGYANQGGAIYNAGQLSE--------TEKTAGIVEIRNSLIQNNKADQGAVIYSE 219
Score = 29.0 bits (65), Expect = 7.5
Identities = 22/94 (23%), Positives = 40/94 (42%), Gaps = 20/94 (21%)
Query: 254 NFYAEQGGQIYDEGFMIGVNDEGTVVGLRYNKQFVDSVSSGTEAGILLDKSNFYAEQGGQ 313
N YA QGG IY+ G +++ G V+ +S L+ + A+QG
Sbjct: 173 NGYANQGGAIYNAGQ---LSETEKTAG------IVEIRNS------LIQNNK--ADQGAV 215
Query: 314 IYDEG---FMSNKQFVDSVSSGTEAGILLDKSNF 344
IY E +S D+ ++ ++ +++F
Sbjct: 216 IYSEMPRFRISQSVIRDNKTTAASGALIYSQTSF 249
>gnl|CDD|222680 pfam14323, GxGYxYP, GxGYxY sequence motif in domain of unknown
function. This family carries a characteristic sequence
motif, GxGYxYP, but is of unknown function. Associated
families are sugar-processing domains.
Length = 463
Score = 31.9 bits (73), Expect = 0.78
Identities = 32/152 (21%), Positives = 44/152 (28%), Gaps = 31/152 (20%)
Query: 155 GVWEHGMSVGWTGVAIGALPFGLTVPLTFGPSLGLVFLAVAEFLFLVSSCG----FIGSD 210
H M W G P G T+ S LV LA + S FI
Sbjct: 247 QYGLHTMPKWWDSPNRGKFPLGWTI------SPSLVDLAPTVLNYYYKSATPNDNFISGP 300
Query: 211 TGLG-----DLSQTKHTPFVKRLRFSYNKQFVDSVSSGTEAGILLDKSNFYAEQGGQIY- 264
+G G +VK L Y ++ + + D S G Y
Sbjct: 301 SGPGYMYPSKWPDAALDDYVKLLN-EYMQR------ADLRVVTIWDNSTGGNRNVGNKYL 353
Query: 265 -----DEGFMIG---VNDEGTVVGLRYNKQFV 288
D F + ND G + R +K +
Sbjct: 354 KQPNIDGLFYLNYGAQNDYGRITWYRNSKPVI 385
>gnl|CDD|223606 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 509
Score = 31.4 bits (72), Expect = 1.1
Identities = 15/52 (28%), Positives = 19/52 (36%), Gaps = 5/52 (9%)
Query: 259 QGGQIYDEGFMIGVND-----EGTVVGLRYNKQFVDSVSSGTEAGILLDKSN 305
G I + V D EG V L+ K V V G E GI ++
Sbjct: 436 TEGVIKRGAPVRVVRDGVVIYEGEVESLKRFKDDVKEVRKGQECGIAIENYR 487
>gnl|CDD|128955 smart00715, LA, Domain in the RNA-binding Lupus La protein; unknown
function.
Length = 80
Score = 28.7 bits (65), Expect = 1.5
Identities = 18/75 (24%), Positives = 32/75 (42%), Gaps = 14/75 (18%)
Query: 366 QIELWFSSLVNLEGSKYA----------LPIFLQFSLSNLKKKKKLVKLLHTLSHTLRVG 415
Q+E +FS NL K+ +PI +++ K+ K L ++ + LR
Sbjct: 10 QVEYYFSD-ENLPRDKFLRKKMDKNDGYVPIST---IASFKRVKSLTTDVNLIVEALRSS 65
Query: 416 DKLKLHIDTARRRPI 430
KL++ D + R
Sbjct: 66 PKLEVSEDGLKVRRR 80
>gnl|CDD|218028 pfam04326, AAA_4, Divergent AAA domain. This family is related to
the pfam00004 family, and presumably has the same
function (ATP-binding).
Length = 116
Score = 28.8 bits (65), Expect = 2.5
Identities = 10/29 (34%), Positives = 18/29 (62%), Gaps = 5/29 (17%)
Query: 259 QGGQIYDEGFMIGVNDEGTVVGLRYNKQF 287
+GG + IGV+D+G VVG+ +++
Sbjct: 30 EGGYLL-----IGVDDDGEVVGINDDEKD 53
>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated.
Length = 746
Score = 29.8 bits (68), Expect = 3.3
Identities = 12/31 (38%), Positives = 16/31 (51%)
Query: 275 EGTVVGLRYNKQFVDSVSSGTEAGILLDKSN 305
EG + L+ K V V +G E GI L+ N
Sbjct: 697 EGELESLKRFKDDVKEVRAGYECGIGLENYN 727
>gnl|CDD|151874 pfam11435, She2p, RNA binding protein She2p. She2p is a RNA
binding protein which binds to RNA via a helical
hairpin. The protein is required for the actin dependent
transport of ASH1 mRNA in yeast, a form of mRNP
translocation. ASH1 mRNP requires recognition of zip
code elements by the RNA binding protein She2p. She2p
contains a globular domain consisting of a bundle of
five alpha-helices.
Length = 205
Score = 28.9 bits (65), Expect = 4.0
Identities = 17/61 (27%), Positives = 31/61 (50%), Gaps = 4/61 (6%)
Query: 3 QTIAK-LGESKVLPGDVAWRLYDTYGFPVDLTQLMVEEKGLS---VDMEVYEDAKKKAQS 58
+ I+K L E VL + + DTY V TQ ++E ++ + +EV + ++K A
Sbjct: 104 EIISKTLNEDLVLSDETIVNIEDTYNHFVKFTQWLIESLSINDPLLQIEVIQFSRKCAVE 163
Query: 59 E 59
+
Sbjct: 164 D 164
>gnl|CDD|187880 cd09749, Cmr5_III-B, CRISPR/Cas system-associated protein Cmr5.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Small alpha-helical protein; signature gene for subtype
III-B.
Length = 119
Score = 28.1 bits (63), Expect = 4.3
Identities = 16/54 (29%), Positives = 22/54 (40%), Gaps = 3/54 (5%)
Query: 388 LQFSLSNLKKKKKLVKLLHTLSHTLRVGDKLKLHIDTARRRPIMSNHTATHILN 441
L F L+ KK K KLL L+ LR DKL+ R ++ +
Sbjct: 47 LAFLLAKGKKNGKNSKLLEHLASWLRERDKLQDGKG---REALLEAIITADLKE 97
>gnl|CDD|215551 PLN03050, PLN03050, pyridoxine (pyridoxamine) 5'-phosphate oxidase;
Provisional.
Length = 246
Score = 29.1 bits (65), Expect = 4.5
Identities = 36/114 (31%), Positives = 45/114 (39%), Gaps = 19/114 (16%)
Query: 21 RLYDTYGFPVDLTQLMVEEKGLSVDMEVYEDAK-KKAQSEPESQAGMETSVEFC-----G 74
L T GF ++ QLM E GLSV VYE A +KA + P + + C G
Sbjct: 20 ELMSTPGFSLE--QLM-ELAGLSVAEAVYEVADGEKASNPPGRHPRV---LLVCGPGNNG 73
Query: 75 GTHLAMAHHVGDFCISSEEAIAKGS------NIVSYCGSKG-TFQSHSGSINDE 121
G L A H+ F K S N+V+ C G F G ND
Sbjct: 74 GDGLVAARHLAHFGYEVTVCYPKQSSKPHYENLVTQCEDLGIPFVQAIGGTNDS 127
>gnl|CDD|176020 cd08374, C2F_Ferlin, C2 domain sixth repeat in Ferlin. Ferlins are
involved in vesicle fusion events. Ferlins and other
proteins, such as Synaptotagmins, are implicated in
facilitating the fusion process when cell membranes fuse
together. There are six known human Ferlins: Dysferlin
(Fer1L1), Otoferlin (Fer1L2), Myoferlin (Fer1L3),
Fer1L4, Fer1L5, and Fer1L6. Defects in these genes can
lead to a wide range of diseases including muscular
dystrophy (dysferlin), deafness (otoferlin), and
infertility (fer-1, fertilization factor-1).
Structurally they have 6 tandem C2 domains, designated
as (C2A-C2F) and a single C-terminal transmembrane
domain, though there is a new study that disputes this
and claims that there are actually 7 tandem C2 domains
with another C2 domain inserted between C2D and C2E.
In a subset of them (Dysferlin, Myoferlin, and Fer1)
there is an additional conserved domain called DysF. C2
domains fold into an 8-standed beta-sandwich that can
adopt 2 structural arrangements: Type I and Type II,
distinguished by a circular permutation involving their
N- and C-terminal beta strands. Many C2 domains are
Ca2+-dependent membrane-targeting modules that bind a
wide variety of substances including bind phospholipids,
inositol polyphosphates, and intracellular proteins.
Most C2 domain proteins are either signal transduction
enzymes that contain a single C2 domain, such as protein
kinase C, or membrane trafficking proteins which contain
at least two C2 domains, such as synaptotagmin 1.
However, there are a few exceptions to this including
RIM isoforms and some splice variants of piccolo/aczonin
and intersectin which only have a single C2 domain. C2
domains with a calcium binding region have negatively
charged residues, primarily aspartates, that serve as
ligands for calcium ions. This cd contains the sixth C2
repeat, C2E, and has a type-II topology.
Length = 133
Score = 28.0 bits (63), Expect = 5.2
Identities = 9/32 (28%), Positives = 18/32 (56%)
Query: 335 AGILLDKSNFYAEQGGQIYDEGFMIGVNDESQ 366
+L D +N E+ IY +G++ G+ ++ Q
Sbjct: 10 RDVLNDDTNITGEKMSDIYVKGWLDGLEEDKQ 41
>gnl|CDD|180801 PRK07033, PRK07033, hypothetical protein; Provisional.
Length = 427
Score = 28.9 bits (65), Expect = 5.9
Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 1/50 (2%)
Query: 151 LSFRGVWEHGMSVGWTGVAIGALPFGLTVPLTFGPSLGLVFLAVAEFLFL 200
S RG + +S W V + + TVPL +L L LA+ F+ L
Sbjct: 200 RSVRGEYAPALSPHWRDVPVARVLLRPTVPLWVCVALAL-LLALLLFIGL 248
>gnl|CDD|233400 TIGR01412, tat_substr_1, Tat-translocated enzyme. This model
represents a small family of proteins with a typical Tat
(twin-arginine translocation) signal sequence,
suggesting that the family is exported in a folded
state, perhaps with a bound redox cofactor. Members of
this family show homology to Dyp, a dye-decolorizing
peroxidase from Geotrichum candidum that lacks any
typical heme-binding site.
Length = 414
Score = 29.0 bits (65), Expect = 6.1
Identities = 10/22 (45%), Positives = 11/22 (50%)
Query: 166 TGVAIGALPFGLTVPLTFGPSL 187
TG + P LTV FG SL
Sbjct: 121 TGESRDLGPSNLTVTFGFGHSL 142
>gnl|CDD|217896 pfam04104, DNA_primase_lrg, Eukaryotic and archaeal DNA primase,
large subunit. DNA primase is the polymerase that
synthesises small RNA primers for the Okazaki fragments
made during discontinuous DNA replication. DNA primase
is a heterodimer of two subunits, the small subunit Pri1
(48 kDa in yeast), and the large subunit Pri2 (58 kDa in
the yeast S. cerevisiae). The large subunit of DNA
primase forms interactions with the small subunit and
the structure implicates that it is not directly
involved in catalysis, but plays roles in correctly
positioning the primase/DNA complex, and in the transfer
of RNA to DNA polymerase.
Length = 217
Score = 28.1 bits (63), Expect = 9.2
Identities = 25/117 (21%), Positives = 41/117 (35%), Gaps = 15/117 (12%)
Query: 345 YAEQGGQIYDEGFMIGVNDESQIELW---FSSLVN--LEGSKYALPIFLQFSLSNLKKKK 399
+ +G+ + E + L F S + L + +LP L+ ++++K
Sbjct: 13 LVSRRRVFLKKGYAY-LPKEELLRLLVEAFRSRLEKALNLTYESLPELLEEYEEDIREK- 70
Query: 400 KLVKLLHTLSHTLRVGDKLKLHIDTARR-------RPIMSNHTATHILNHALRFVLG 449
L LL LS G +ID R ++ A L H RF L
Sbjct: 71 -LEPLLEHLSKEAEDGKISAENIDKLSPEHFPPCMRNLLEGLRAGGHLKHEGRFQLT 126
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.318 0.135 0.396
Gapped
Lambda K H
0.267 0.0906 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 23,807,038
Number of extensions: 2309393
Number of successful extensions: 2113
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2106
Number of HSP's successfully gapped: 70
Length of query: 474
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 374
Effective length of database: 6,502,202
Effective search space: 2431823548
Effective search space used: 2431823548
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 61 (27.0 bits)