Alignments for a candidate for asnB in Sphingomonas koreensis DSMZ 15582

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Sphingomonas koreensis DSMZ 15582

Align candidate Ga0059261_3121 Ga0059261_3121 (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.15579.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.4e-119  386.4   0.0   2.1e-119  385.8   0.0    1.3  1  lcl|FitnessBrowser__Korea:Ga0059261_3121  Ga0059261_3121 asparagine syntha


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_3121  Ga0059261_3121 asparagine synthase (glutamine-hydrolyzing)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  385.8   0.0  2.1e-119  2.1e-119       1     517 []       2     560 ..       2     560 .. 0.86

  Alignments for each domain:
  == domain 1  score: 385.8 bits;  conditional E-value: 2.1e-119
                                 TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsne 68 
                                               Cgi++i + +a     +  +++ l+++ahRGPD++g + + +  +a+lg++RL+iidls + +QP+ ++
  lcl|FitnessBrowser__Korea:Ga0059261_3121   2 CGIVAISAPDAR----RFSLDATLDVIAHRGPDDRGSHVS-DGGDAALGQNRLSIIDLSCAgHQPMWDH 65 
                                               888888888664....566888899***********9888.89****************888******* PP

                                 TIGR01536  69 k.evvivfnGEIYNheeLreeleek.G.yeFetksDtEViLaayeewgeelverLeGmFAfalwdekkg 134
                                               + ++vi +nGE YN+ +Lr+ele++ G + +++ sDtEV+++ +   g  ++++L+G FA+a++d++++
  lcl|FitnessBrowser__Korea:Ga0059261_3121  66 SrRYVISYNGETYNFAALRAELEARhGaIPWTGSSDTEVVIEGFAREGIPFLDKLNGIFALAIYDTADQ 134
                                               ***********************9833257999************************************ PP

                                 TIGR01536 135 elflaRDrlGikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkel 203
                                                +++ RD+lGikPL  ++++g ++f+SEiK+ll+l++ ++ l++e lae+l++ +vp+++tl++e +++
  lcl|FitnessBrowser__Korea:Ga0059261_3121 135 VMHVLRDPLGIKPLVATEQHGGIFFCSEIKGLLTLPALQRTLRRESLAEQLAFMYVPEPHTLYHEFHKV 203
                                               ********************************************************************* PP

                                 TIGR01536 204 epakal..dgeeklee...ywevekeevkeseeelveelrelledavkkrlvadvpvgvllSGGlDSsl 267
                                               ep+ ++  +  + l++   +  +++ +  + e e++e lr+++++av++++vadvpv ++lSGGlDSs+
  lcl|FitnessBrowser__Korea:Ga0059261_3121 204 EPGVCFtyRAGKLLARtplFAWLNNAQPITGEAEAIEALRHAFTAAVDRQVVADVPVSLFLSGGLDSSA 272
                                               ******973333333367754445555555578899********************************* PP

                                 TIGR01536 268 vaaiakkeaksevktFsigfe.dskdldesk....aarkvadelgtehkevliseeevlkeleevilal 331
                                               va  a +  +s    ++i+f   + +ld+++    +a+ +ad lg+++k ++ +  ++l+ l+++   +
  lcl|FitnessBrowser__Korea:Ga0059261_3121 273 VADQAVRSGASIHDAYTIAFSdADRSLDAQSddlhYAQIMADRLGIDLKVIEAD-SDFLSMLPDLAGFM 340
                                               **9999998866679******54555554437888*************999976.589*********** PP

                                 TIGR01536 332 eeptairasiplyllsklarekgvkVvLsGeGaDElfgGYeyfreakaeeale................ 384
                                               e+ ++++a+i ++l++  ar++g+kV+LsG+GaDE +gGY +++   a +++                 
  lcl|FitnessBrowser__Korea:Ga0059261_3121 341 EDGFSDPAAINTWLICAGARKQGIKVMLSGQGADEFLGGYRRYFAERALQRMPgfvrsalsatsgmlpa 409
                                               *********************************************999998888888888887777777 PP

                                 TIGR01536 385 ............lpeaselaekkl..............llqaklakeselkellkakleeel.kekeel 426
                                                           +          +              l   ++a+  +   l+ a l ++  +++++l
  lcl|FitnessBrowser__Korea:Ga0059261_3121 410 nlpgkfnalnrrF----------KrfanlaaqpprdriLGMYSWATPATIGGLFAAPLASHPgEQFQAL 468
                                               7655554444441..........0333334444445447777888888888888887776651344455 PP

                                 TIGR01536 427 kkelkeeseleellrldle.lllsdllrakDrvsmahslEvRvPflDkelvelalsippelklrdgkeK 494
                                                + l+    ++ l+  d +  lls +l   Dr+sma ++E+RvPflD +lv+++  ip++lk++  + K
  lcl|FitnessBrowser__Korea:Ga0059261_3121 469 LDGLPPGDCVDTLMAIDRQyDLLSLNLTYTDRMSMAVGVEARVPFLDFDLVRVMNAIPASLKVKGRQGK 537
                                               555666688888877776526889999999*************************************** PP

                                 TIGR01536 495 vlLreaaeellPeeileRkKeaf 517
                                               +++++a+e  lP+ei +R+K++f
  lcl|FitnessBrowser__Korea:Ga0059261_3121 538 YIFKKAMEPQLPHEIIYRSKAGF 560
                                               *********************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (631 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: 0.08u 0.01s 00:00:00.09 Elapsed: 00:00:00.08
# Mc/sec: 4.02
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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About GapMind

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis