Alignments for a candidate for asd in Mycolicibacterium vanbaalenii PYR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for asd in Mycolicibacterium vanbaalenii PYR-1

Align aspartate-semialdehyde dehydrogenase (EC 1.2.1.11) (characterized)
to candidate WP_011782622.1 MVAN_RS27655 aspartate-semialdehyde dehydrogenase

Query= BRENDA::P9WNX5
         (345 letters)



>NCBI__GCF_000015305.1:WP_011782622.1
          Length = 344

 Score =  575 bits (1483), Expect = e-169
 Identities = 297/341 (87%), Positives = 310/341 (90%)

Query: 5   IGIVGATGQVGQVMRTLLDERDFPASAVRFFASARSQGRKLAFRGQEIEVEDAETADPSG 64
           IG+VGATGQVGQVMRTLL ERDFPA+ VRFFASARS G+KL FRGQEIEVEDA TADPSG
Sbjct: 4   IGVVGATGQVGQVMRTLLAERDFPATGVRFFASARSAGKKLGFRGQEIEVEDASTADPSG 63

Query: 65  LDIALFSAGSAMSKVQAPRFAAAGVTVIDNSSAWRKDPDVPLVVSEVNFERDAHRRPKGI 124
           LDIALFSAG+ MS+VQAPRFA AG  VIDNSSAWRKDPDVPLVVSEVNFERDA  RPKGI
Sbjct: 64  LDIALFSAGATMSRVQAPRFAGAGAVVIDNSSAWRKDPDVPLVVSEVNFERDAGNRPKGI 123

Query: 125 IANPNCTTMAAMPVLKVLHDEARLVRLVVSSYQAVSGSGLAGVAELAEQARAVIGGAEQL 184
           IANPNCTTMAAMPVLK LHDEA L RL+VSSYQAVSGSGLAGV ELA QARAVI G EQL
Sbjct: 124 IANPNCTTMAAMPVLKPLHDEAGLTRLIVSSYQAVSGSGLAGVEELAGQARAVIDGVEQL 183

Query: 185 VYDGGALEFPPPNTYVAPIAFNVVPLAGSLVDDGSGETDEDQKLRFESRKILGIPDLLVS 244
           V+DG AL+FPPPN YVAPIAFNVVPLAGSLVDDGSGETDEDQKLR ESRKILGIP+L VS
Sbjct: 184 VHDGSALQFPPPNKYVAPIAFNVVPLAGSLVDDGSGETDEDQKLRNESRKILGIPELAVS 243

Query: 245 GTCVRVPVFTGHSLSINAEFAQPLSPERARELLDGATGVQLVDVPTPLAAAGVDESLVGR 304
           GTCVRVPVFTGHSLSINAEF+QPLS  RA+E+L GA GV LVDVPTPLAAAG D+SLVGR
Sbjct: 244 GTCVRVPVFTGHSLSINAEFSQPLSVARAKEILAGAAGVTLVDVPTPLAAAGADDSLVGR 303

Query: 305 IRRDPGVPDGRGLALFVSGDNLRKGAALNTIQIAELLTADL 345
           IRRDPGVPD RGLALFVSGDNLRKGAALNTIQIAELL A L
Sbjct: 304 IRRDPGVPDDRGLALFVSGDNLRKGAALNTIQIAELLAAQL 344


Lambda     K      H
   0.317    0.135    0.382 

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: 539
Number of extensions: 12
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 345
Length of database: 344
Length adjustment: 29
Effective length of query: 316
Effective length of database: 315
Effective search space:    99540
Effective search space used:    99540
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate WP_011782622.1 MVAN_RS27655 (aspartate-semialdehyde dehydrogenase)
to HMM TIGR01296 (asd: aspartate-semialdehyde dehydrogenase (EC 1.2.1.11))

# 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/TIGR01296.hmm
# target sequence database:        /tmp/gapView.2752.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01296  [M=339]
Accession:   TIGR01296
Description: asd_B: aspartate-semialdehyde dehydrogenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.1e-148  479.9   0.0   2.4e-148  479.7   0.0    1.0  1  lcl|NCBI__GCF_000015305.1:WP_011782622.1  MVAN_RS27655 aspartate-semialdeh


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015305.1:WP_011782622.1  MVAN_RS27655 aspartate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  479.7   0.0  2.4e-148  2.4e-148       1     338 [.       3     342 ..       3     343 .. 0.99

  Alignments for each domain:
  == domain 1  score: 479.7 bits;  conditional E-value: 2.4e-148
                                 TIGR01296   1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsa 69 
                                               ++++vGatG+vGq+++++L+er+fp+  ++++as+rsaGkk+ f+g+e+eve+a++++++g+dialfsa
  lcl|NCBI__GCF_000015305.1:WP_011782622.1   3 RIGVVGATGQVGQVMRTLLAERDFPATGVRFFASARSAGKKLGFRGQEIEVEDASTADPSGLDIALFSA 71 
                                               599****************************************************************** PP

                                 TIGR01296  70 GgsvskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkp 138
                                               G+++s+++ap++a ag++viDn+sa+r+d+dvPLvv+evn+e+++  ++kgiianPnC+t+++++vLkp
  lcl|NCBI__GCF_000015305.1:WP_011782622.1  72 GATMSRVQAPRFAGAGAVVIDNSSAWRKDPDVPLVVSEVNFERDAGNRPKGIIANPNCTTMAAMPVLKP 140
                                               ********************************************************************* PP

                                 TIGR01296 139 lkdeaklkrvvvstYqavsGaGkkgveeLknqtkavlegkekepeida....lkakkfakqiafnaipl 203
                                               l+dea+l r++vs+YqavsG+G +gveeL+ q++av++g e+ +++++    ++++k++++iafn++pl
  lcl|NCBI__GCF_000015305.1:WP_011782622.1 141 LHDEAGLTRLIVSSYQAVSGSGLAGVEELAGQARAVIDGVEQLVHDGSalqfPPPNKYVAPIAFNVVPL 209
                                               ********************************************9996678899*************** PP

                                 TIGR01296 204 idklkedG..ytkeelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLke 270
                                               +++l++dG  +t+e++kl++e+rkilgi++l vs+tcvrvPvftghs+s+++ef+++lsv ++ke+L +
  lcl|NCBI__GCF_000015305.1:WP_011782622.1 210 AGSLVDDGsgETDEDQKLRNESRKILGIPELAVSGTCVRVPVFTGHSLSINAEFSQPLSVARAKEILAG 278
                                               *******9889********************************************************** PP

                                 TIGR01296 271 apgvvviddpsenlyptPleavgkdevfvgrirkD..lskekglalfvvaDnlrkGaalnavqiaelli 337
                                               a gv+++d+p      tPl+a+g d+++vgrir+D  +++++glalfv++DnlrkGaaln++qiaell 
  lcl|NCBI__GCF_000015305.1:WP_011782622.1 279 AAGVTLVDVP------TPLAAAGADDSLVGRIRRDpgVPDDRGLALFVSGDNLRKGAALNTIQIAELLA 341
                                               *********9......**************************************************997 PP

                                 TIGR01296 338 k 338
                                               +
  lcl|NCBI__GCF_000015305.1:WP_011782622.1 342 A 342
                                               5 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (339 nodes)
Target sequences:                          1  (344 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.25
//
[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