Alignments for a candidate for hcs in Bradyrhizobium sp. BTAi1

GapMind for Amino acid biosynthesis

Alignments for a candidate for hcs in Bradyrhizobium sp. BTAi1

Align homocitrate synthase (EC 2.3.3.14) (characterized)
to candidate WP_012045776.1 BBTA_RS27445 homocitrate synthase

Query= BRENDA::A0A1Y6KBA1
         (416 letters)



>NCBI__GCF_000015165.1:WP_012045776.1
          Length = 379

 Score =  691 bits (1782), Expect = 0.0
 Identities = 363/379 (95%), Positives = 368/379 (97%)

Query: 38  MPRVILNDTTLRDGEQAPGVAFALSEKVAIARALARAGVPEIEAGTPAMGADEISAIRAI 97
           MPRVILNDTTLRDGEQAPGVAFAL+EKVAIARALARAGVPEIEAGTPAMGADEI+AIRAI
Sbjct: 1   MPRVILNDTTLRDGEQAPGVAFALAEKVAIARALARAGVPEIEAGTPAMGADEIAAIRAI 60

Query: 98  VEAGLPATIIGWCRMREADVDAAIAAGVSMVNVSIPTSDVQIAAKLGGGRSVALELLKRV 157
           V+A LPATIIGWCRMREADVDAAIAAGVSMVNVSIPTSDVQIAAKLGG RS ALELLKRV
Sbjct: 61  VDARLPATIIGWCRMREADVDAAIAAGVSMVNVSIPTSDVQIAAKLGGDRSAALELLKRV 120

Query: 158 VSYARSRGLGVAVGGEDSSRADVGFLAEVIATAKALGARRFRVADTLSVLDPDATSALVG 217
           V+YAR RGL VAVGGEDSSRADVGFLAEVIATAKALGARRFRVADTLSVLDPDAT ALV 
Sbjct: 121 VTYARQRGLDVAVGGEDSSRADVGFLAEVIATAKALGARRFRVADTLSVLDPDATFALVN 180

Query: 218 ALRATTDLEIEFHGHDDLGLATANTLAAIKAGATHASVTVIGLGERAGNAPLEEVAVALR 277
           ALRATTDLEIEFHGHDDLGLATANTLAA+KAGATHASVTVIGLGERAGNAPLEEVAVALR
Sbjct: 181 ALRATTDLEIEFHGHDDLGLATANTLAAVKAGATHASVTVIGLGERAGNAPLEEVAVALR 240

Query: 278 QLYRRETGIVLAELDHVANVVAAAAARAIPLNKAIVGEHVFTHESGIHVDGLLKDQRTYQ 337
           QLYRRETGIVLAELD VANVVAAAAARAIPLNKAIVGEHVFTHESGIHVDGLLKDQRTYQ
Sbjct: 241 QLYRRETGIVLAELDRVANVVAAAAARAIPLNKAIVGEHVFTHESGIHVDGLLKDQRTYQ 300

Query: 338 ALDPMLFGRSNRIVIGKHSGLSAITSLLSDLRLPASADQAQRILARVRKHAVAHKGPVPK 397
           ALDPMLFGRSNRIVIGKHSGLSAITSLLSDLRLP SADQAQRILARVRKHAV HKGPVPK
Sbjct: 301 ALDPMLFGRSNRIVIGKHSGLSAITSLLSDLRLPVSADQAQRILARVRKHAVVHKGPVPK 360

Query: 398 EAVAAIWREVCDHPHASFA 416
           EAVAAIWREVCDHP ASFA
Sbjct: 361 EAVAAIWREVCDHPLASFA 379


Lambda     K      H
   0.317    0.132    0.369 

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: 619
Number of extensions: 14
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: 416
Length of database: 379
Length adjustment: 31
Effective length of query: 385
Effective length of database: 348
Effective search space:   133980
Effective search space used:   133980
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_012045776.1 BBTA_RS27445 (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.25195.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.2e-157  508.7  10.7   5.8e-157  508.6  10.7    1.0  1  lcl|NCBI__GCF_000015165.1:WP_012045776.1  BBTA_RS27445 homocitrate synthas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015165.1:WP_012045776.1  BBTA_RS27445 homocitrate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  508.6  10.7  5.8e-157  5.8e-157       2     364 ..       4     366 ..       3     367 .. 0.99

  Alignments for each domain:
  == domain 1  score: 508.6 bits;  conditional E-value: 5.8e-157
                                 TIGR02660   2 vlinDttLRDGEqaagvaFsaeEKlaiAkaLdeaGvdelEvGipamgeeEraairaiaalglkarllaW 70 
                                               v++nDttLRDGEqa+gvaF+ +EK+aiA+aL++aGv+e+E+G+pamg++E+aairai+++ l+a+++ W
  lcl|NCBI__GCF_000015165.1:WP_012045776.1   4 VILNDTTLRDGEQAPGVAFALAEKVAIARALARAGVPEIEAGTPAMGADEIAAIRAIVDARLPATIIGW 72 
                                               89******************************************************************* PP

                                 TIGR02660  71 cRlraedieaaaevGvkavdlsvpvsdlqleaklkkdrawvleelkelvslakeeglkvsvgaeDasRa 139
                                               cR+r++d++aa ++Gv++v++s+p+sd+q++akl  dr+++le lk++v++a+++gl+v+vg+eD+sRa
  lcl|NCBI__GCF_000015165.1:WP_012045776.1  73 CRMREADVDAAIAAGVSMVNVSIPTSDVQIAAKLGGDRSAALELLKRVVTYARQRGLDVAVGGEDSSRA 141
                                               ********************************************************************* PP

                                 TIGR02660 140 deeflvelaevakeagakRlRfaDtvgvldPfstyelvkalraalelelElHaHnDlGlAtAntlaavk 208
                                               d  fl+e++++ak+ ga+R+R+aDt++vldP +t++lv+alra+++le+E+H+H+DlGlAtAntlaavk
  lcl|NCBI__GCF_000015165.1:WP_012045776.1 142 DVGFLAEVIATAKALGARRFRVADTLSVLDPDATFALVNALRATTDLEIEFHGHDDLGLATANTLAAVK 210
                                               ********************************************************************* PP

                                 TIGR02660 209 aGassvsvtvlGlGERAGnAaleevalalkellgldtgidlselkelsqlvakasgraleaqkavvGes 277
                                               aGa+++svtv+GlGERAGnA+leeva+al++l+ ++tgi l el +++++va+a++ra++ +ka+vGe+
  lcl|NCBI__GCF_000015165.1:WP_012045776.1 211 AGATHASVTVIGLGERAGNAPLEEVAVALRQLYRRETGIVLAELDRVANVVAAAAARAIPLNKAIVGEH 279
                                               ********************************************************************* PP

                                 TIGR02660 278 vFaHEsGiHvdgllkdeatYesldPeevGrerelviGKHsgraaviealkelgleleeeeaeelleavr 346
                                               vF+HEsGiHvdgllkd++tY++ldP ++Gr++++viGKHsg +a+++ l++l l++++++a+++l++vr
  lcl|NCBI__GCF_000015165.1:WP_012045776.1 280 VFTHESGIHVDGLLKDQRTYQALDPMLFGRSNRIVIGKHSGLSAITSLLSDLRLPVSADQAQRILARVR 348
                                               ********************************************************************* PP

                                 TIGR02660 347 avaerlKrsleeeelaal 364
                                               ++a  +K ++ +e +aa+
  lcl|NCBI__GCF_000015165.1:WP_012045776.1 349 KHAVVHKGPVPKEAVAAI 366
                                               *********999988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (379 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: 00:00:00.01
# Mc/sec: 11.49
//
[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