Alignments for a candidate for hcs in Azorhizobium caulinodans ORS 571

GapMind for Amino acid biosynthesis

Alignments for a candidate for hcs in Azorhizobium caulinodans ORS 571

Align homocitrate synthase (EC 2.3.3.14) (characterized)
to candidate WP_043879531.1 AZC_RS17440 homocitrate synthase

Query= BRENDA::A0A0S6UXF5
         (400 letters)



>NCBI__GCF_000010525.1:WP_043879531.1
          Length = 399

 Score =  421 bits (1081), Expect = e-122
 Identities = 226/375 (60%), Positives = 269/375 (71%)

Query: 23  RSVVLNDTTLRDGEQAPGVAFTTAEKLSIARALASAGVTEIEAGTPAMGHDEVSAIRAIV 82
           R+  LNDTTLRDGEQAPGVAFT  EK+ IA ALA+AGV EIEAGTPAMG +EV  IR+IV
Sbjct: 14  RTAFLNDTTLRDGEQAPGVAFTRKEKIEIAAALAAAGVPEIEAGTPAMGDEEVETIRSIV 73

Query: 83  EADLPATAIGWCRMRTSDVDAAIEAGVSMVNVSIPASDVQIAAKLSGGRPAALEQVRRVV 142
             +LP   + WCRM   D+ AA+ AGV +VNVSIP SD Q+A KL   R  AL +V  VV
Sbjct: 74  SLNLPTRVMAWCRMSEDDLMAAVAAGVKIVNVSIPTSDRQLAGKLGKDRAWALGRVAEVV 133

Query: 143 GYARDSGLDVAVGGEDSSRADVDFLVELIATAKAAGARRFRIADTLSVLDPDAAFALLTA 202
             AR  G +VAVGGEDSSRAD DFL  L  TAKAAGA R R+ADTL VLDP   +AL+  
Sbjct: 134 TLARRLGFEVAVGGEDSSRADPDFLCRLAETAKAAGAFRLRLADTLGVLDPFGTYALVRR 193

Query: 203 LRATTDLELEFHGHDDLGLATANTLAAIKAGATHASVTVIGLGERAGNAPLEEVAVALKQ 262
           + ATTD+ELEFH HDDLGLATANTLAA+  GA HASVTV GLGERAGNA LEEVA+AL+Q
Sbjct: 194 VAATTDIELEFHAHDDLGLATANTLAAVMGGARHASVTVAGLGERAGNAALEEVAIALRQ 253

Query: 263 LYGRETGVVLSELKHVASVVAAAAARAIPLNKAIVGEHVFTHESGIHVDGLLKDQRTYQA 322
               ETG+  + LK +A +V  AAAR +P  KAIVG  VFTHESGIHV GLLKD+ TY+A
Sbjct: 254 TARAETGIAPAALKPLAELVCGAAARPVPRGKAIVGADVFTHESGIHVSGLLKDRATYEA 313

Query: 323 LDPHLLGRSNRIVIGKHSGLAAITALLAELQLSASADEAKSVLARVRQHAVEHKGAVGRE 382
           L+P L GR + +V+GKHSGLAA+   LA+  ++  A   +++L RVR  AV  K  V RE
Sbjct: 314 LNPELFGRGHTVVLGKHSGLAAVEKALADEGITVDAVRGRAILDRVRAFAVRTKENVSRE 373

Query: 383 TVTSIWREVRERSLL 397
           T+   +++    S L
Sbjct: 374 TLLRFYQDSFTESAL 388


Lambda     K      H
   0.317    0.130    0.362 

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: 450
Number of extensions: 16
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: 400
Length of database: 399
Length adjustment: 31
Effective length of query: 369
Effective length of database: 368
Effective search space:   135792
Effective search space used:   135792
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: 50 (23.9 bits)

Align candidate WP_043879531.1 AZC_RS17440 (homocitrate synthase)
to HMM TIGR02660 (nifV: homocitrate synthase (EC 2.3.3.14))

# 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/TIGR02660.hmm
# target sequence database:        /tmp/gapView.606632.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02660  [M=365]
Accession:   TIGR02660
Description: nifV_homocitr: homocitrate 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.5e-155  503.2   6.9   2.9e-155  503.0   6.9    1.0  1  NCBI__GCF_000010525.1:WP_043879531.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000010525.1:WP_043879531.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  503.0   6.9  2.9e-155  2.9e-155       3     365 .]      17     379 ..      15     379 .. 0.99

  Alignments for each domain:
  == domain 1  score: 503.0 bits;  conditional E-value: 2.9e-155
                             TIGR02660   3 linDttLRDGEqaagvaFsaeEKlaiAkaLdeaGvdelEvGipamgeeEraairaiaalglkarllaWcRlra 75 
                                           ++nDttLRDGEqa+gvaF+++EK++iA+aL++aGv+e+E+G+pamg+eE+++ir i++l+l++r++aWcR+++
  NCBI__GCF_000010525.1:WP_043879531.1  17 FLNDTTLRDGEQAPGVAFTRKEKIEIAAALAAAGVPEIEAGTPAMGDEEVETIRSIVSLNLPTRVMAWCRMSE 89 
                                           69*********************************************************************** PP

                             TIGR02660  76 edieaaaevGvkavdlsvpvsdlqleaklkkdrawvleelkelvslakeeglkvsvgaeDasRadeeflvela 148
                                            d+ aa+++Gvk v++s+p+sd+ql+ kl kdraw+l +++e+v+la++ g +v+vg+eD+sRad++fl +la
  NCBI__GCF_000010525.1:WP_043879531.1  90 DDLMAAVAAGVKIVNVSIPTSDRQLAGKLGKDRAWALGRVAEVVTLARRLGFEVAVGGEDSSRADPDFLCRLA 162
                                           ************************************************************************* PP

                             TIGR02660 149 evakeagakRlRfaDtvgvldPfstyelvkalraalelelElHaHnDlGlAtAntlaavkaGassvsvtvlGl 221
                                           e+ak+aga RlR+aDt+gvldPf+ty+lv+++ a++++elE+HaH+DlGlAtAntlaav++Ga+++svtv Gl
  NCBI__GCF_000010525.1:WP_043879531.1 163 ETAKAAGAFRLRLADTLGVLDPFGTYALVRRVAATTDIELEFHAHDDLGLATANTLAAVMGGARHASVTVAGL 235
                                           ************************************************************************* PP

                             TIGR02660 222 GERAGnAaleevalalkellgldtgidlselkelsqlvakasgraleaqkavvGesvFaHEsGiHvdgllkde 294
                                           GERAGnAaleeva+al++++  +tgi   +lk l++lv  a++r+++  ka+vG++vF+HEsGiHv+gllkd+
  NCBI__GCF_000010525.1:WP_043879531.1 236 GERAGNAALEEVAIALRQTARAETGIAPAALKPLAELVCGAAARPVPRGKAIVGADVFTHESGIHVSGLLKDR 308
                                           ************************************************************************* PP

                             TIGR02660 295 atYesldPeevGrerelviGKHsgraaviealkelgleleeeeaeelleavravaerlKrsleeeelaalv 365
                                           atYe+l+Pe++Gr + +v+GKHsg aav +al++ g+++++ + +++l++vra+a r+K ++++e+l +++
  NCBI__GCF_000010525.1:WP_043879531.1 309 ATYEALNPELFGRGHTVVLGKHSGLAAVEKALADEGITVDAVRGRAILDRVRAFAVRTKENVSRETLLRFY 379
                                           *****************************************************************998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (399 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 16.09
//
[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