Align Putative asparagine synthetase [glutamine-hydrolyzing]; EC 6.3.5.4 (characterized)
to candidate N515DRAFT_4267 N515DRAFT_4267 asparagine synthase (glutamine-hydrolysing)
Query= SwissProt::P64248
(652 letters)
>FitnessBrowser__Dyella79:N515DRAFT_4267
Length = 655
Score = 291 bits (745), Expect = 6e-83
Identities = 227/663 (34%), Positives = 318/663 (47%), Gaps = 50/663 (7%)
Query: 1 MCGLLAFVAAPAGAAGPEGADAASAIARASHLMRHRGPDESGTWHAVDGASGGVVFGFNR 60
MCG+ A + PAGA P A+A + L+ HRGPD+ G W D ASG + R
Sbjct: 1 MCGI-AGLWIPAGA--PRERLERQALAMTTRLL-HRGPDDGGVWS--DEASG-IALAQRR 53
Query: 61 LSIIDIAHS-HQPLRWGPPEAPDRYVLVFNGEIYNYLELRDELRTQHGA-VFATDGDGEA 118
L+IID++ + HQP+ A RY VFNGEIYN+L+LR L + A ++ D E
Sbjct: 54 LAIIDLSPAGHQPMH----SACGRYAAVFNGEIYNHLDLRARLAAEGQAPMWRGHSDTET 109
Query: 119 ILAGYHHWGTE-VLQRLRGMFAFALWDTVTRELFCARDPFGIKPLFIATGAGGTAVASEK 177
++A WG E LQ GMFA ALWD R L ARD G KPL+ SE
Sbjct: 110 LVACIAAWGLEPALQACIGMFALALWDRRERSLALARDRLGEKPLYYGWQGDALLFGSEL 169
Query: 178 KCLLDLVELVGFDTEIDHRALQHYTVLQYVPEPETLHRGVRRLESGCFARIRA----DQL 233
K L GF ++D AL VP P +++RG+ +L G R++A D
Sbjct: 170 KALK---AYEGFRPDVDRDALTLLLRHNCVPAPYSIYRGIAKLRPGHVLRLQAGGPRDAE 226
Query: 234 APVITRY--FVPRFAASPITNDNDQARYDEITAVLEDSVAKHMRADVTVGAFLSGGIDST 291
RY V A P +D+ D + + SV M ADV +GAFLSGGIDS+
Sbjct: 227 PQPYWRYNDVVAAGLAEPFFG-SDRDAIDALETQIAQSVRAQMLADVPLGAFLSGGIDSS 285
Query: 292 AIAALAIRHNPRLI-TFTTGFEREGFSEIDVAVASAEAIGARHIAKVVSADEFVAALPEI 350
I AL + + R + TFT GF +G+ E A A A +G H V ++ +A +P++
Sbjct: 286 TIVALMQKQSGRPVKTFTIGFGEDGYDEATHAKAVAAHLGTEHTELYVRPEDALAVIPKL 345
Query: 351 VWYLDEPVADPALVPLFFVAREARKHVKVVLSGEGADELFGGYTIYREPLSL-RPFDYLP 409
EP AD + +P + V++ AR+HV V LSG+ DELFGGY Y + LP
Sbjct: 346 PSMYCEPFADSSQIPTYLVSQLARRHVTVALSGDAGDELFGGYNRYLAARRVWERMQRLP 405
Query: 410 KPLRRSMGKVSKPLPEGMRGKSLLHRGSLTLEERYYGNARSFSGAQLREVLP-------- 461
+R + + +P + R + L +R + +L VL
Sbjct: 406 SFVRHAAAGALRAVPPATWDR-WYERARVLLPKRMHVATPGDKAQKLAGVLALSSGEQFF 464
Query: 462 -GFRPDWTHTDVTAPVYAESA-------GWDPVARMQH----IDLFTWLRGDILVKADKI 509
W+ + AE + W +H +D ++ DILVK D+
Sbjct: 465 HQLTSQWSDPENLVQGAAEPSTLLTDPQAWPQTDSFEHWMMAMDAQAYMADDILVKVDRA 524
Query: 510 TMANSLELRVPFLDPEVFAVASRLPAGAKITRTTTKYALRRALEPIVPAHVLHRPKLGFP 569
MANSLE RVP LDP V A+A R+P KI K+ LR+ L VP ++ RPK GF
Sbjct: 525 AMANSLETRVPLLDPRVVALAWRMPLHLKIRDGQGKWLLRQVLYRHVPKELIERPKQGFG 584
Query: 570 VPIRHWLRAGELLEWAYATV--GSSQAGHLVDIAAVYRMLDEHRCGSSDHSRRLWTMLIF 627
VP+ WLR G L +WA + + G + + A + R+ +EH G + +LW +L+F
Sbjct: 585 VPLDSWLR-GPLRDWAESLLDEGRLRREGYLRHAPIRRVWNEHLSGKRNWQHQLWNVLMF 643
Query: 628 MLW 630
W
Sbjct: 644 QAW 646
Lambda K H
0.323 0.138 0.428
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: 1142
Number of extensions: 63
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: 652
Length of database: 655
Length adjustment: 38
Effective length of query: 614
Effective length of database: 617
Effective search space: 378838
Effective search space used: 378838
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 54 (25.4 bits)
Align candidate N515DRAFT_4267 N515DRAFT_4267 (asparagine synthase (glutamine-hydrolysing))
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.5237.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
3.9e-141 457.4 0.0 4.7e-141 457.2 0.0 1.1 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_4267 N515DRAFT_4267 asparagine syntha
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_4267 N515DRAFT_4267 asparagine synthase (glutamine-hydrolysing)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 457.2 0.0 4.7e-141 4.7e-141 1 517 [] 2 583 .. 2 583 .. 0.86
Alignments for each domain:
== domain 1 score: 457.2 bits; conditional E-value: 4.7e-141
TIGR01536 1 Cgiagivdlkakake.eeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQP 64
Cgiag+ + +e e+++ +m+ +l hRGPD+ gvw+d + ++ +l++rRLaiidls + +QP
lcl|FitnessBrowser__Dyella79:N515DRAFT_4267 2 CGIAGLWIPAGAPRErLERQALAMTTRLLHRGPDDGGVWSD-EASGIALAQRRLAIIDLSPAgHQP 66
*****988888877777789999******************.799***************998*** PP
TIGR01536 65 lsnek.evvivfnGEIYNheeLreeleekGye..FetksDtEViLaayeewg.eelverLeGmFAf 126
++++ +++ vfnGEIYNh +Lr++l ++G ++++sDtE ++a + +wg e +++ GmFA+
lcl|FitnessBrowser__Dyella79:N515DRAFT_4267 67 MHSACgRYAAVFNGEIYNHLDLRARLAAEGQApmWRGHSDTETLVACIAAWGlEPALQACIGMFAL 132
****99************************85449******************************* PP
TIGR01536 127 alwdekkgelflaRDrlGikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlqlvpt 192
alwd++++ l+laRDrlG kPLYy+ ++++llf+SE+Kal a + +++ +d++al+ ll ++ vp
lcl|FitnessBrowser__Dyella79:N515DRAFT_4267 133 ALWDRRERSLALARDRLGEKPLYYGWQGDALLFGSELKALKAYEGFRPDVDRDALTLLLRHNCVPA 198
****************************************************************** PP
TIGR01536 193 ektlfkevkelepakal......dgeeklee..ywevekee.......vkeseeelveelrelled 243
+ ++++++ +l+p+++l +++ yw+ ++ + s++++++ l+ + +
lcl|FitnessBrowser__Dyella79:N515DRAFT_4267 199 PYSIYRGIAKLRPGHVLrlqaggPRDAE--PqpYWRYNDVVaaglaepFFGSDRDAIDALETQIAQ 262
*****************98765333333..246**999988889999988999************* PP
TIGR01536 244 avkkrlvadvpvgvllSGGlDSslvaaiakkeaksevktFsigfedskdldeskaarkvadelgte 309
+v++++ advp+g++lSGG+DSs+++a+++k++ ++vktF+igf ++ +de+++a++va++lgte
lcl|FitnessBrowser__Dyella79:N515DRAFT_4267 263 SVRAQMLADVPLGAFLSGGIDSSTIVALMQKQSGRPVKTFTIGFG-EDGYDEATHAKAVAAHLGTE 327
*********************************************.******************** PP
TIGR01536 310 hkevliseeevlkeleevilaleeptairasiplyllsklarekgvkVvLsGeGaDElfgGYeyfr 375
h+e+++ +e++l+ ++++ + ep+a++++ip+yl+s+lar++ v+V+LsG+ +DElfgGY+++
lcl|FitnessBrowser__Dyella79:N515DRAFT_4267 328 HTELYVRPEDALAVIPKLPSMYCEPFADSSQIPTYLVSQLARRH-VTVALSGDAGDELFGGYNRYL 392
********************************************.********************9 PP
TIGR01536 376 eakaeeale...................................lpeaselaekkl.......... 396
a + +e l
lcl|FitnessBrowser__Dyella79:N515DRAFT_4267 393 AARR--VWErmqrlpsfvrhaaagalravppatwdrwyerarvlL----------Pkrmhvatpgd 446
9754..333334677777777777777766666666655555552..........03334444444 PP
TIGR01536 397 ................llqaklakeselkellkakleeelkekeelkkelkeeseleellrldlel 446
+ +++ + s+ ++l++ e ++ ++ ++ +++s + ++ d++
lcl|FitnessBrowser__Dyella79:N515DRAFT_4267 447 kaqklagvlalssgeqFFHQLTSQWSDPENLVQ-GAAEPSTLLTDPQAWPQTDSFEHWMMAMDAQA 511
555556666655445333223333333333333.2222222223333333333666778999**** PP
TIGR01536 447 llsdllrak.DrvsmahslEvRvPflDkelvelalsippelklrdgkeKvlLreaaeellPeeile 511
++ d++++k Dr++ma+slE RvP+lD ++v la+++p lk+rdg+ K+lLr+++ +++P+e+ e
lcl|FitnessBrowser__Dyella79:N515DRAFT_4267 512 YMADDILVKvDRAAMANSLETRVPLLDPRVVALAWRMPLHLKIRDGQGKWLLRQVLYRHVPKELIE 577
****************************************************************** PP
TIGR01536 512 RkKeaf 517
R+K++f
lcl|FitnessBrowser__Dyella79:N515DRAFT_4267 578 RPKQGF 583
****99 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (517 nodes)
Target sequences: 1 (655 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: 8.72
//
[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