Align asparagine synthase (glutamine-hydrolysing) 1; EC 6.3.5.4 (characterized)
to candidate PfGW456L13_2154 Asparagine synthetase [glutamine-hydrolyzing] (EC 6.3.5.4)
Query= CharProtDB::CH_005185
(632 letters)
>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2154
Length = 590
Score = 264 bits (675), Expect = 7e-75
Identities = 195/626 (31%), Positives = 301/626 (48%), Gaps = 56/626 (8%)
Query: 1 MCGFVGV--FNKHPLAQTADQEELIKQMNQMIVHRGPDSDGYFHDEHVGFGFRRLSIIDV 58
MCG G F+ P A I+++ + RGPD+ G+ V G RRL I+D+
Sbjct: 1 MCGLAGELRFDHQPADLAA-----IERITHHLAPRGPDAWGFHSQGPVALGHRRLKIMDL 55
Query: 59 ENGG-QPLSYEDETYWIIFNGEIYNYIELREELEAKGYTFNTDSDTEVLLATYRHYKEEA 117
+G QP+ + FNG IYN+ ELR ELE+ GY F + DTEVLL Y + E
Sbjct: 56 SDGSAQPMIDPQLGLSLAFNGAIYNFPELRAELESLGYAFYSGGDTEVLLKGYHAWGEAL 115
Query: 118 ASKLRGMFAFLIWNKNDHVLYGARDPFGIKPLYYTTINDQVYFASERKSLMVAQNDIE-- 175
KL GMFAF +W ++ L+ ARD G+KPLY + + ++ FAS +L+ DI
Sbjct: 116 LPKLNGMFAFAVWERDAQRLFIARDRLGVKPLYLSRTDQRLRFASALPALLKG-GDINPI 174
Query: 176 IDKEALQQYMSF-QFVPEPSTLDAHVKKVEPGSQFTIRPDGDITFKTYFKANFKPVQTEE 234
+D AL Y++F VP P TL A ++K+ P + I DG KT++ + P E
Sbjct: 175 LDPAALNHYLNFHSVVPAPRTLLAGIEKLPPATWMRIEADGRTEQKTWWTLPYGPHADET 234
Query: 235 DKLVKEVRDAIYDS----VNVHMRSDVPVGSFLSGGIDSSFIVSVAKEFH-PSLKTFSVG 289
+++ RD + DS V + R+ V VG LSGG+DSS +V + +E +L TFS+G
Sbjct: 235 KLTLEDWRDRVLDSTREAVAIRQRAAVDVGVLLSGGVDSSLLVGLLREVGVDNLSTFSIG 294
Query: 290 FEQQG---FSEVDVAKETAAALGIENISKVISPEEYMNELPKIVWHFDDPLADPAAIPLY 346
F+ G E + A G ++ I +E + +LP +P+ I Y
Sbjct: 295 FQDAGGERGDEFQYSDLIARHYGTQHHQLRIDEKEIIEQLPAAFRAMSEPMVSHDCIAFY 354
Query: 347 FVAKEAKKHVTVALSGEGADELFGGYNIYREPLSLKPFERIPSGLKKMLLHVAAVMPEGM 406
+++E KH V SG+GADELF GY+ Y + G A E
Sbjct: 355 LLSREVAKHCKVVQSGQGADELFAGYHWYPQ----------VDGASDSY----AAYREAF 400
Query: 407 RGKSLLERGCTPLQDRYIGNAKIFEESVKKQLLKHYNPNLSYRDVTKTYFTESSSYSDIN 466
+S + T +Q +++ N + D K +F + + + ++
Sbjct: 401 FDRSYDDYAAT-VQPKWL------------------TANDAAGDFVKAHFAQPGADAAVD 441
Query: 467 KMQYVDIHTWMRGDILLKADKMTMANSLELRVPFLDKVVFDVASKIPDELKTKNGTTKYL 526
K +D + D + + D MTMA LE R PFLD + +++++IP K +G K +
Sbjct: 442 KALRLDSTVMLVDDPVKRVDNMTMAWGLEARTPFLDYRLVELSARIPGRFKLPDG-GKQV 500
Query: 527 LRKAAEGIVPEHVLNRKKLGFPVPIRHWLKNEMNEWVRNIIQESQTDAYIHKDYVL-QLL 585
L++AA ++P V++RKK FPVP L+ + EWVR ++ + D + +L +LL
Sbjct: 501 LKEAARQVIPSEVIDRKKGYFPVPGLKHLQGDTLEWVRELLLDPSQDRGLFNPAMLDRLL 560
Query: 586 EDHCADKAD-NSRKIWTVLIFMIWHS 610
D K+W + +W S
Sbjct: 561 TDPQGQLTPLRGSKLWQLAALNLWLS 586
Lambda K H
0.319 0.136 0.403
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 894
Number of extensions: 43
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 632
Length of database: 590
Length adjustment: 37
Effective length of query: 595
Effective length of database: 553
Effective search space: 329035
Effective search space used: 329035
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)
Align candidate PfGW456L13_2154 (Asparagine synthetase [glutamine-hydrolyzing] (EC 6.3.5.4))
to HMM TIGR01536 (asnB: asparagine synthase (glutamine-hydrolyzing) (EC 6.3.5.4))
# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file: ../tmp/path.aa/TIGR01536.hmm
# target sequence database: /tmp/gapView.15436.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: TIGR01536 [M=517]
Accession: TIGR01536
Description: asn_synth_AEB: asparagine synthase (glutamine-hydrolyzing)
Scores for complete sequences (score includes all domains):
--- full sequence --- --- best 1 domain --- -#dom-
E-value score bias E-value score bias exp N Sequence Description
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
1.9e-126 409.0 0.0 2.2e-126 408.8 0.0 1.0 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2154 Asparagine synthetase [glutamine
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2154 Asparagine synthetase [glutamine-hydrolyzing] (EC 6.3.5.4)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 408.8 0.0 2.2e-126 2.2e-126 1 516 [. 2 520 .. 2 521 .. 0.89
Alignments for each domain:
== domain 1 score: 408.8 bits; conditional E-value: 2.2e-126
TIGR01536 1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLai 55
Cg+ag + +++ + + +ai+++++ la RGPDa g++++ ++lghrRL i
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2154 2 CGLAGELRFDHQPA-DLAAIERITHHLAPRGPDAWGFHSQ---GPVALGHRRLKI 52
9*****99988755.579******************6555...9*********** PP
TIGR01536 56 idlseg.aQPlsnek.evvivfnGEIYNheeLreeleekGyeFetksDtEViLaa 108
+dls+g aQP+ + + + fnG IYN+ eLr+ele Gy F + DtEV+L+
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2154 53 MDLSDGsAQPMIDPQlGLSLAFNGAIYNFPELRAELESLGYAFYSGGDTEVLLKG 107
****************99************************************* PP
TIGR01536 109 yeewgeelverLeGmFAfalwdekkgelflaRDrlGikPLYyaseqgkllfaSEi 163
y++wge+l+ +L+GmFAfa+w++ +++lf+aRDrlG+kPLY ++++++l faS +
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2154 108 YHAWGEALLPKLNGMFAFAVWERDAQRLFIARDRLGVKPLYLSRTDQRLRFASAL 162
******************************************************* PP
TIGR01536 164 Kallalkeikaeldkealaelltlq.lvptektlfkevkelepakal....dgee 213
all+ +i++ ld +al ++l ++ +vp ++tl +++++l+pa + dg +
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2154 163 PALLKGGDINPILDPAALNHYLNFHsVVPAPRTLLAGIEKLPPATWMrieaDGRT 217
*************************999****************99999888888 PP
TIGR01536 214 kleeywevekeevkese....eelveelrelledavkkrlvadvpvgvllSGGlD 264
+ +++w + + +++++ e+ +++ + ++av+ r +a v vgvllSGG+D
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2154 218 EQKTWWTLPYGPHADETkltlEDWRDRVLDSTREAVAIRQRAAVDVGVLLSGGVD 272
8888****9998666650000555556666678899******************* PP
TIGR01536 265 SslvaaiakkeaksevktFsigfe..dskdldeskaarkvadelgtehkevlise 317
Ssl++ ++++ ++ tFsigf+ + + de ++ +a++ gt+h+++ i+e
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2154 273 SSLLVGLLREVGVDNLSTFSIGFQdaGGERGDEFQYSDLIARHYGTQHHQLRIDE 327
***********999*********965567788889******************** PP
TIGR01536 318 eevlkeleevilaleeptairasiplyllsklarekgvkVvLsGeGaDElfgGYe 372
+e++++l+ ++a+ ep+ +++i ylls+++ ++ +kVv sG+GaDElf+GY+
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2154 328 KEIIEQLPAAFRAMSEPMVSHDCIAFYLLSREVAKH-CKVVQSGQGADELFAGYH 381
************************************.****************** PP
TIGR01536 373 yfreakaeealelpeaselaekklllqaklakeselke.llkakleeelkekeel 426
++ + + + a+++ + ++++ + ++ + + + +++ ++++
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2154 382 WYPQVDGASDSY------AAYREAFFDRSYDDYAATVQpKWLTANDAAGDFVKAH 430
****86666664......3344455555555544444413333445555667778 PP
TIGR01536 427 kkelkeeseleellrldlelllsdl.lrakDrvsmahslEvRvPflDkelvelal 480
+++ ++ +++++lrld + +l d+ +++ D ++ma++lE+R PflD +lvel +
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2154 431 FAQPGADAAVDKALRLDSTVMLVDDpVKRVDNMTMAWGLEARTPFLDYRLVELSA 485
888888899*******99988877626666************************* PP
TIGR01536 481 sippelklrdgkeKvlLreaaeellPeeileRkKea 516
+ip kl dg K +L+eaa++++P+e+ +RkK
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2154 486 RIPGRFKLPDG-GKQVLKEAARQVIPSEVIDRKKGY 520
*********98.799******************965 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (517 nodes)
Target sequences: 1 (590 residues searched)
Passed MSV filter: 1 (1); expected 0.0 (0.02)
Passed bias filter: 1 (1); expected 0.0 (0.02)
Passed Vit filter: 1 (1); expected 0.0 (0.001)
Passed Fwd filter: 1 (1); expected 0.0 (1e-05)
Initial search space (Z): 1 [actual number of targets]
Domain search space (domZ): 1 [number of targets reported over threshold]
# CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 8.18
//
[ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory