Align candidate Echvi_1262 Echvi_1262 (asparagine synthase (glutamine-hydrolyzing))
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.26600.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-110 355.9 0.0 2.7e-110 355.7 0.0 1.0 1 lcl|FitnessBrowser__Cola:Echvi_1262 Echvi_1262 asparagine synthase ( Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cola:Echvi_1262 Echvi_1262 asparagine synthase (glutamine-hydrolyzing) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 355.7 0.0 2.7e-110 2.7e-110 1 517 [] 2 528 .. 2 528 .. 0.84 Alignments for each domain: == domain 1 score: 355.7 bits; conditional E-value: 2.7e-110 TIGR01536 1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsnek.evv 72 Cgi +++l e+ai++m+ + ahRGPD++ w++ + + l+ +RL +dls+ +QPl+ ++ + + lcl|FitnessBrowser__Cola:Echvi_1262 2 CGINLAMNLPGS---GEDAIQQMMAATAHRGPDHSD-WCK-ITGQLFLAGNRLKTVDLSDWsNQPLQINQgAHT 70 777777777553...5689****************9.***.789****************99********999* PP TIGR01536 73 ivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelflaRDrlGik 146 +v+nG +YN +eLr+el e+G +Fe++sD+EV+L+ ++ +g ++rL+Gm+A+++++++++ +++aRD+ G+k lcl|FitnessBrowser__Cola:Echvi_1262 71 LVWNGALYNADELRNELLEDGESFESRSDSEVLLRWLKRHGISGINRLQGMYALVFVEREEKSIIIARDPHGKK 144 ************************************************************************** PP TIGR01536 147 PLYyaseqgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelepakal..dgeekleey 218 PLYy ++ lf+SE+++++a+ +ik++ldk+ l+++l+ + ++k++f++v+++ p+kal d +++ lcl|FitnessBrowser__Cola:Echvi_1262 145 PLYYFHQNHLWLFSSEARGIIAAGQIKRQLDKTQLTPYLYTRHSFPDKSFFQQVQQIVPGKALqlDFGGNIRA- 217 ******************************************99******************96644444444. PP TIGR01536 219 wevekee.vkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaiakkeaksevktFsigfedsk 291 e ++ +++ e +e++r+ll+da+ k+ +ad pvgvllSGG DSsl+ + +e + +++tF+ +fe +k lcl|FitnessBrowser__Cola:Echvi_1262 218 -EHRTVIpQATLELPRKEHFRSLLTDATLKHFRADIPVGVLLSGGADSSLLLDTWMRETDLPLHTFTARFE-QK 289 .22222225555567889*****************************************************.66 PP TIGR01536 292 dldesk...aarkvadelgtehkevliseeevlkeleevilaleeptairasiplyllsklarekgvkVvLsGe 362 l++ + +ar+va++ + h+evli+++ + ++l+e i +l++p+ ++as+ +++++++a+e+ vk+++sG lcl|FitnessBrowser__Cola:Echvi_1262 290 YLKKYQdpiHARQVAEKYRCVHHEVLITPALLRAQLPEYIASLDQPVGDSASFLSWMIAREAKEH-VKILISGA 362 666554666********************************************************.******** PP TIGR01536 363 GaDElfgGYeyfreakaeeale..lpeaselaekkl.......llqaklakeselkellkakleeelkekeelk 427 GaDElfgGY++++ +k+ + + +as++ + ++ +k+ak ++ e + ++l+++ +++ lcl|FitnessBrowser__Cola:Echvi_1262 363 GADELFGGYNRHEAFKQYLQHKaiALKASKV----MgklsflgRHFQKIAKGIRKDEATTFLNFSALRNIPADQ 432 ***********98864443333221222222....233444554444444444444444433344444444333 PP TIGR01536 428 kelkee......seleellrldlellls.dllrakDrvsmahslEvRvPflDkelvelalsippelklrdgkeK 494 +e + +++l+ d ++l d l+ D ++mah++E R+P+lDk+lv+l +s+ e l+ k K lcl|FitnessBrowser__Cola:Echvi_1262 433 REAFLAyypkgvPPYKAALEWDRSYYLVnDILKIHDNALMAHGVEGRAPYLDKNLVSLSMSLTEEQHLSL-KPK 505 33333356667967777777777666650556667***************************99999875.556 PP TIGR01536 495 vlLreaaeellPeeileRkKeaf 517 +re+++e e+++ RkK +f lcl|FitnessBrowser__Cola:Echvi_1262 506 QWIRELLRETGLEKVAVRKKFGF 528 66799999976799999999988 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (517 nodes) Target sequences: 1 (598 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: 8.79 // [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