Alignments for a candidate for leuA in Azoarcus olearius BH72

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuA in Azoarcus olearius BH72

Align 2-isopropylmalate synthase (EC 2.3.3.13) (characterized)
to candidate WP_011766887.1 AZO_RS15865 2-isopropylmalate synthase

Query= BRENDA::Q9JZG1
         (517 letters)



>NCBI__GCF_000061505.1:WP_011766887.1
          Length = 511

 Score =  696 bits (1797), Expect = 0.0
 Identities = 348/496 (70%), Positives = 416/496 (83%)

Query: 7   VIIFDTTLRDGEQSPGAAMTKEEKIRVARQLEKLGVDIIEAGFAAASPGDFEAVNAIAKT 66
           +IIFDTTLRDGEQSPGA+MT++EK+R+ARQLE++ VD+IEAGFAAAS GDFE+V +IA+ 
Sbjct: 5   LIIFDTTLRDGEQSPGASMTRDEKLRIARQLERMRVDVIEAGFAAASNGDFESVRSIAEA 64

Query: 67  ITKSTVCSLSRAIERDIRQAGEAVAPAPKKRIHTFIATSPIHMEYKLKMKPKQVIEAAVK 126
           I +STVCSL+RA E DIR+AGEA+ PA + RIHTFIATSPIHME KL+M P QV+E AVK
Sbjct: 65  IKESTVCSLARANENDIRRAGEAIRPAARGRIHTFIATSPIHMEKKLRMTPDQVVEQAVK 124

Query: 127 AVKIAREYTDDVEFSCEDALRSEIDFLAEICGAVIEAGATTINIPDTVGYSIPYKTEEFF 186
           A+  AREYTDD+EFS EDA RSEIDFL  I  AVI+AGA TIN+PDTVGY++P +     
Sbjct: 125 AIGWAREYTDDIEFSAEDAGRSEIDFLCRIFDAVIKAGAKTINVPDTVGYNVPEQYAATL 184

Query: 187 RELIAKTPNGGKVVWSAHCHNDLGLAVANSLAALKGGARQVECTVNGLGERAGNASVEEI 246
           R LI + PN  KV+WS HCHNDLGLAV+NSLAA+  GARQVECT+NGLGERAGNAS+EEI
Sbjct: 185 RTLIERVPNADKVIWSVHCHNDLGLAVSNSLAAVMAGARQVECTINGLGERAGNASLEEI 244

Query: 247 VMALKVRHDLFGLETGIDTTQIVPSSKLVSTITGYPVQPNKAIVGANAFSHESGIHQDGV 306
           VMA++ R D+F + T IDTTQIVP+SKLVS ITGYPVQPNKAIVGANAF+HESGIHQDGV
Sbjct: 245 VMAVRTRADVFPVSTNIDTTQIVPASKLVSQITGYPVQPNKAIVGANAFAHESGIHQDGV 304

Query: 307 LKHRETYEIMSAESVGWATNRLSLGKLSGRNAFKTKLADLGIELESEEALNAAFARFKEL 366
           LKHRETYEIM AE VGW  N+L LGK SGRNAF+ +L +LGIE+ SEE LN AFARFKEL
Sbjct: 305 LKHRETYEIMRAEDVGWGANKLVLGKHSGRNAFRARLQELGIEIGSEEQLNHAFARFKEL 364

Query: 367 ADKKREIFDEDLHALVSDEMGSMNAESYKFISQKISTETGEEPRADIVFSIKGEEKRASA 426
           ADKK EIFDEDLHAL+SDE  +   E ++ ++ +  +ETGE PRA++  +I G+E R+ A
Sbjct: 365 ADKKHEIFDEDLHALMSDEAVTPEQEHFRLVATRFHSETGETPRAEVTLAIGGQETRSQA 424

Query: 427 TGSGPVDAIFKAIESVAQSGAALQIYSVNAVTQGTESQGETSVRLARGNRVVNGQGADTD 486
            GSGPVDA FKAIESVA SG+ L +YSVNA+T GT++QGE +VRLA+  RVVNGQGADTD
Sbjct: 425 EGSGPVDAAFKAIESVAGSGSELLLYSVNAITTGTDAQGEVTVRLAKDGRVVNGQGADTD 484

Query: 487 VLVATAKAYLSALSKL 502
           ++VA+AKAYL+AL+KL
Sbjct: 485 IIVASAKAYLNALNKL 500


Lambda     K      H
   0.313    0.129    0.352 

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: 721
Number of extensions: 19
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: 517
Length of database: 511
Length adjustment: 35
Effective length of query: 482
Effective length of database: 476
Effective search space:   229432
Effective search space used:   229432
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 52 (24.6 bits)

Align candidate WP_011766887.1 AZO_RS15865 (2-isopropylmalate synthase)
to HMM TIGR00973 (leuA: 2-isopropylmalate synthase (EC 2.3.3.13))

# 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/TIGR00973.hmm
# target sequence database:        /tmp/gapView.466433.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00973  [M=494]
Accession:   TIGR00973
Description: leuA_bact: 2-isopropylmalate synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.3e-224  732.1   4.4   1.5e-224  732.0   4.4    1.0  1  NCBI__GCF_000061505.1:WP_011766887.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000061505.1:WP_011766887.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  732.0   4.4  1.5e-224  1.5e-224       2     494 .]       5     498 ..       4     498 .. 0.99

  Alignments for each domain:
  == domain 1  score: 732.0 bits;  conditional E-value: 1.5e-224
                             TIGR00973   2 vlifdttlrdGeqapgasltveeklqiakalerlgvdiieaGfpvsskgdfeavqkiarevknarvvglarav 74 
                                           ++ifdttlrdGeq+pgas+t +ekl+ia++ler+ vd+ieaGf+++s+gdfe+v+ ia+++k+++v++lara 
  NCBI__GCF_000061505.1:WP_011766887.1   5 LIIFDTTLRDGEQSPGASMTRDEKLRIARQLERMRVDVIEAGFAAASNGDFESVRSIAEAIKESTVCSLARAN 77 
                                           58*********************************************************************** PP

                             TIGR00973  75 ekdidaaaealkpaekkrihtfiatsdihleaklkktkdevlerivkavkyaknfvddvefsaedagrtelef 147
                                           e+di  a ea++pa++ rihtfiats+ih+e+kl++t d+v+e++vka+ +a++++dd+efsaedagr+e++f
  NCBI__GCF_000061505.1:WP_011766887.1  78 ENDIRRAGEAIRPAARGRIHTFIATSPIHMEKKLRMTPDQVVEQAVKAIGWAREYTDDIEFSAEDAGRSEIDF 150
                                           ************************************************************************* PP

                             TIGR00973 148 larvveaaieaGattiniPdtvGyalPaeygelikelkenvPnidkailsvhchddlGlavanslaavknGar 220
                                           l+r+++a+i+aGa tin+PdtvGy +P++y++ +++l e+vPn dk+i svhch+dlGlav+nslaav +Gar
  NCBI__GCF_000061505.1:WP_011766887.1 151 LCRIFDAVIKAGAKTINVPDTVGYNVPEQYAATLRTLIERVPNADKVIWSVHCHNDLGLAVSNSLAAVMAGAR 223
                                           ************************************************************************* PP

                             TIGR00973 221 qvectinGiGeraGnaaleevvmalkvrkdflnvetgintkeiyrtsrlvskltgmlvqrnkaivGdnafahe 293
                                           qvectinG+GeraGna+lee+vma+++r d+++v+t+i+t +i  +s+lvs++tg +vq+nkaivG+nafahe
  NCBI__GCF_000061505.1:WP_011766887.1 224 QVECTINGLGERAGNASLEEIVMAVRTRADVFPVSTNIDTTQIVPASKLVSQITGYPVQPNKAIVGANAFAHE 296
                                           ************************************************************************* PP

                             TIGR00973 294 sGihqdGvlknketyeilspesiGlkkeklvlgkrsGraalkkrleelGfkl.deeeldklfekfkeladkkk 365
                                           sGihqdGvlk++etyei+++e++G  ++klvlgk+sGr+a++ rl+elG+++ +ee+l+++f +fkeladkk+
  NCBI__GCF_000061505.1:WP_011766887.1 297 SGIHQDGVLKHRETYEIMRAEDVGWGANKLVLGKHSGRNAFRARLQELGIEIgSEEQLNHAFARFKELADKKH 369
                                           ***************************************************846788**************** PP

                             TIGR00973 366 evfdedlealvleelrqeeeeklkleklqvqsgeesvptatvklkvkgeekeaaatGnGpvdavykaiekile 438
                                           e+fdedl+al+++e +++e+e+++l+  + +s + + p a v+l++ g+e+++ a G+Gpvda +kaie + +
  NCBI__GCF_000061505.1:WP_011766887.1 370 EIFDEDLHALMSDEAVTPEQEHFRLVATRFHSETGETPRAEVTLAIGGQETRSQAEGSGPVDAAFKAIESVAG 442
                                           ************************************************************************* PP

                             TIGR00973 439 levklleysitakgegkdalgevkvvlelngkkysGrgvatdiveasakayvnaln 494
                                              +ll ys++a ++g+da+gev+v+l  +g+ ++G+g++tdi+ asakay+naln
  NCBI__GCF_000061505.1:WP_011766887.1 443 SGSELLLYSVNAITTGTDAQGEVTVRLAKDGRVVNGQGADTDIIVASAKAYLNALN 498
                                           *******************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (494 nodes)
Target sequences:                          1  (511 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 24.35
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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 2024 update 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 original 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