Alignments for a candidate for asnB in Mesorhizobium ciceri WSM1271

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Mesorhizobium ciceri WSM1271

Align candidate YP_004139468.1 Mesci_0245 (asparagine synthase)
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.10092.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    5.4e-85  272.2   0.0    6.3e-85  272.0   0.0    1.0  1  lcl|NCBI__GCF_000185905.1:YP_004139468.1  Mesci_0245 asparagine synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000185905.1:YP_004139468.1  Mesci_0245 asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  272.0   0.0   6.3e-85   6.3e-85       2     517 .]       3     562 ..       2     562 .. 0.85

  Alignments for each domain:
  == domain 1  score: 272.0 bits;  conditional E-value: 6.3e-85
                                 TIGR01536   2 giagivdlkakake.eeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlsegaQPlsnek 69 
                                               g+agi+   a+a   + + i++ml +++hRGPD++  w d   +  +lgh+ L   d   g  Pl  ++
  lcl|NCBI__GCF_000185905.1:YP_004139468.1   3 GVAGILLCGANAPAvAAADIQQMLARMRHRGPDGSSWWLD---TSIALGHAWLNTSDEV-GPGPLTMAG 67 
                                               6777777766666678899*********************...8***********9985.8******** PP

                                 TIGR01536  70 .evvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelf 137
                                                + +i+    + N +eL ++l   G++ ++ +D+ V+++ay  wge++ e+L+G+FAfa+wd++++ lf
  lcl|NCBI__GCF_000185905.1:YP_004139468.1  68 gRLAITADCRLDNRDELLARL---GIRDQSVADAIVLMRAYLRWGEACPEHLQGDFAFAIWDDERQSLF 133
                                               *****************8555...6889***************************************** PP

                                 TIGR01536 138 laRDrlGikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelepa 206
                                                aRD++G+kP+Yy   + +++faSEi  +l ++ i+a++++  ++ +l+   + +++t + +++ l++ 
  lcl|NCBI__GCF_000185905.1:YP_004139468.1 134 CARDHFGVKPFYYHAADRRFAFASEIGPILGVEGIRARVNERQISGFLAGLPDDPQSTPYSDIFSLPAR 202
                                               ********************************************999999889999************* PP

                                 TIGR01536 207 kal...dgeekleeywevekeevkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaia 272
                                               ++l    ++  l++yw++e +++    +++ ee+ +l+ ++v++r+++   vg++lSGGlDSs++a++a
  lcl|NCBI__GCF_000185905.1:YP_004139468.1 203 HSLtvtAQQVMLRRYWQIEPSARPL-RSDASEEFAHLFSQSVRNRMRGTSAVGAMLSGGLDSSSIACVA 270
                                               **987655566666****9888555.5678899***********************************9 PP

                                 TIGR01536 273 kkeak....sevktFsigfedskdldeskaarkvadelgtehkevliseeevlkeleevilaleeptai 337
                                                 + +     ++ tFs+ fe+ + +de  ++ +v d+  ++ + + + + + ++e+e+v+  +e  +  
  lcl|NCBI__GCF_000185905.1:YP_004139468.1 271 GLQNAaarkPKLPTFSLIFEKGSPMDERPFIDAVLDQQKVDATLIPVGNYAPFAEFERVLEEQEGTFLA 339
                                               87766678899********************************************************9* PP

                                 TIGR01536 338 rasiplyllsklarekgvkVvLsGeGaDElf.gGYeyfreakaeeale..................... 384
                                               +  + +  + + a +kg+kV+L+G G+DE+  +G    +e  +  ++                      
  lcl|NCBI__GCF_000185905.1:YP_004139468.1 340 PGLTLTRGIYRTAGAKGIKVLLDGHGGDEVVsQGHGHLHELANGGRWMdlwrevrsasntygdstlgly 408
                                               *****************************9747**9****99999998777777777777777777776 PP

                                 TIGR01536 385 ............lpeaselaekkl....llqaklakese.....lkellkakleeelkekeelkkelke 432
                                                           +               + ++ l+k  +      ++ ++  ++ +l++++el +++++
  lcl|NCBI__GCF_000185905.1:YP_004139468.1 409 lqfltlygpawrI----------ArlrhMANRALNKIRKpaqvsRARSWRDLINPDLAKRTELVDRFHR 467
                                               6666655543332..........0333333333333333000003333444445555555555555555 PP

                                 TIGR01536 433 e.......seleellrl..dlelllsdllrakDrvsmahslEvRvPflDkelvelalsippelklrdgk 492
                                               +       ++ ++l ++    + ++++  ++ D++++  ++E R+Pf Dk lve++l +p e kl++g 
  lcl|NCBI__GCF_000185905.1:YP_004139468.1 468 AgymppgvQASDALSHRwiLSNGYVPHAFEVLDKAAANFGVEPRYPFWDKPLVEFCLALPGEEKLSHGF 536
                                               57777887555555554114578999999*99************************************* PP

                                 TIGR01536 493 eKvlLreaaeellPeeileR.kKeaf 517
                                                +++Lr+a++++lPe++ +R +K  f
  lcl|NCBI__GCF_000185905.1:YP_004139468.1 537 GRYVLRRAMQGVLPEAVQWRrDKIDF 562
                                               ********************888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (640 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 11.96
//
[ok]

This GapMind analysis is from Apr 10 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