Alignments for a candidate for asnB in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Echinicola vietnamensis KMM 6221, DSM 17526

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.10551.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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.02
# Mc/sec: 12.15
//
[ok]

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

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Steps (tab-delimited)
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Protein sequences (fasta format)
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SQLite3 databases

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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