Alignments for a candidate for hcs in Trichormus variabilis ATCC 29413

GapMind for Amino acid biosynthesis

Alignments for a candidate for hcs in Trichormus variabilis ATCC 29413

Align homocitrate synthase (EC 2.3.3.14) (characterized)
to candidate WP_011320648.1 AVA_RS20055 homocitrate synthase

Query= BRENDA::P58637
         (376 letters)



>NCBI__GCF_000204075.1:WP_011320648.1
          Length = 377

 Score =  582 bits (1499), Expect = e-171
 Identities = 292/375 (77%), Positives = 333/375 (88%)

Query: 1   MNKVLINDTTLRDGEQAAGVAFSVEEKIAIAKFLDAIGVHEIEVGIPAMGKAEQEAIANI 60
           MNKVLINDTTLRDGEQAAGV F++EEK+AIAKFLD IGV E+EVGIPAMG+ E  AI  I
Sbjct: 1   MNKVLINDTTLRDGEQAAGVVFTLEEKVAIAKFLDTIGVPELEVGIPAMGEEEMRAICAI 60

Query: 61  VKLDLSANLLGWNRAVIADIQASIACGLQRVHISIPVSAIQIAVKFHGQWQVVLQKLHDS 120
             L L ANLL WNRAVI+DI+AS+ACG++RVHI+IPVS IQIA KFHGQW+V LQ+L D 
Sbjct: 61  SNLGLKANLLAWNRAVISDIKASVACGMERVHIAIPVSGIQIAAKFHGQWRVSLQRLKDC 120

Query: 121 ISFAVDQGLFVSIGGEDSSRAEESFLLDVVLAAQEWGASRFRFCDTVGILDPFTTHAKVK 180
           ISFAVDQGL+V++GGEDSSRA+E+FLLDV L AQEWGASRFRFCDTVG+LDPFTT+ KVK
Sbjct: 121 ISFAVDQGLWVAVGGEDSSRADENFLLDVALYAQEWGASRFRFCDTVGVLDPFTTYGKVK 180

Query: 181 QLVASLTIPVEMHTHNDFGLATANALAGTKAGALSVNTTVNGLGERAGNAALEEVVMALK 240
            LV++LTIPVE+HTHNDFG+ATANALAG KAGA SVNTTV GLGERAGNAALEEVVMA+K
Sbjct: 181 LLVSALTIPVEVHTHNDFGMATANALAGIKAGAASVNTTVIGLGERAGNAALEEVVMAIK 240

Query: 241 HLYHHDLGIDTRRLLEISQLVASASGHPVPPWKAIVGENTFAHESGIHAHGVLQNPQTYE 300
            +Y  D+GIDT RLLE+SQLVA+ASG  VPPWKAIVGENTFAHESGIHAHGVLQNP TYE
Sbjct: 241 RIYGVDMGIDTPRLLELSQLVAAASGANVPPWKAIVGENTFAHESGIHAHGVLQNPDTYE 300

Query: 301 PFAPEEVGRERRLVVGKHSGRHLLSSILQQHDIILNHEETQFVLDAVRQESVEKKRSLTD 360
           PFAPEEVG ERRLVVGKHSGRH +S++L+QH I LN EETQ VLDAVRQ+SV+KKRSLT 
Sbjct: 301 PFAPEEVGWERRLVVGKHSGRHSVSNLLEQHGIFLNPEETQSVLDAVRQQSVKKKRSLTT 360

Query: 361 QELLHLVQTKQHFRA 375
           +ELL+LV+ +++  A
Sbjct: 361 EELLNLVKEQRYSHA 375


Lambda     K      H
   0.319    0.133    0.383 

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: 505
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: 376
Length of database: 377
Length adjustment: 30
Effective length of query: 346
Effective length of database: 347
Effective search space:   120062
Effective search space used:   120062
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate WP_011320648.1 AVA_RS20055 (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.290185.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.4e-172  559.9   0.6   1.6e-172  559.7   0.6    1.0  1  NCBI__GCF_000204075.1:WP_011320648.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000204075.1:WP_011320648.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  559.7   0.6  1.6e-172  1.6e-172       1     364 [.       3     366 ..       3     367 .. 0.99

  Alignments for each domain:
  == domain 1  score: 559.7 bits;  conditional E-value: 1.6e-172
                             TIGR02660   1 kvlinDttLRDGEqaagvaFsaeEKlaiAkaLdeaGvdelEvGipamgeeEraairaiaalglkarllaWcRl 73 
                                           kvlinDttLRDGEqaagv+F+ eEK+aiAk+Ld++Gv+elEvGipamgeeE++ai+ai++lglka+llaW+R+
  NCBI__GCF_000204075.1:WP_011320648.1   3 KVLINDTTLRDGEQAAGVVFTLEEKVAIAKFLDTIGVPELEVGIPAMGEEEMRAICAISNLGLKANLLAWNRA 75 
                                           589********************************************************************** PP

                             TIGR02660  74 raedieaaaevGvkavdlsvpvsdlqleaklkkdrawvleelkelvslakeeglkvsvgaeDasRadeeflve 146
                                             +di+a++++G+++v++++pvs +q++ak++ ++++ l++lk+++s+a ++gl+v+vg+eD+sRade+fl +
  NCBI__GCF_000204075.1:WP_011320648.1  76 VISDIKASVACGMERVHIAIPVSGIQIAAKFHGQWRVSLQRLKDCISFAVDQGLWVAVGGEDSSRADENFLLD 148
                                           ************************************************************************* PP

                             TIGR02660 147 laevakeagakRlRfaDtvgvldPfstyelvkalraalelelElHaHnDlGlAtAntlaavkaGassvsvtvl 219
                                           +a +a+e+ga+R+Rf+DtvgvldPf+ty +vk l++al++++E+H+HnD+G+AtAn+la++kaGa+sv++tv+
  NCBI__GCF_000204075.1:WP_011320648.1 149 VALYAQEWGASRFRFCDTVGVLDPFTTYGKVKLLVSALTIPVEVHTHNDFGMATANALAGIKAGAASVNTTVI 221
                                           ************************************************************************* PP

                             TIGR02660 220 GlGERAGnAaleevalalkellgldtgidlselkelsqlvakasgraleaqkavvGesvFaHEsGiHvdgllk 292
                                           GlGERAGnAaleev++a+k+++g+d+gid+ +l elsqlva+asg +++++ka+vGe++FaHEsGiH++g+l+
  NCBI__GCF_000204075.1:WP_011320648.1 222 GLGERAGNAALEEVVMAIKRIYGVDMGIDTPRLLELSQLVAAASGANVPPWKAIVGENTFAHESGIHAHGVLQ 294
                                           ************************************************************************* PP

                             TIGR02660 293 deatYesldPeevGrerelviGKHsgraaviealkelgleleeeeaeelleavravaerlKrsleeeelaal 364
                                           +++tYe+++PeevG+er+lv+GKHsgr++v++ l+++g+ l+ ee++++l+avr+++ ++Krsl++eel +l
  NCBI__GCF_000204075.1:WP_011320648.1 295 NPDTYEPFAPEEVGWERRLVVGKHSGRHSVSNLLEQHGIFLNPEETQSVLDAVRQQSVKKKRSLTTEELLNL 366
                                           *********************************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (377 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: 12.30
//
[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