Alignments for a candidate for hcs in Allochromatium vinosum DSM 180

GapMind for Amino acid biosynthesis

Alignments for a candidate for hcs in Allochromatium vinosum DSM 180

Align Homocitrate synthase; EC 2.3.3.14 (characterized)
to candidate WP_012970706.1 ALVIN_RS07410 homocitrate synthase

Query= SwissProt::P05342
         (385 letters)



>NCBI__GCF_000025485.1:WP_012970706.1
          Length = 384

 Score =  438 bits (1126), Expect = e-127
 Identities = 227/379 (59%), Positives = 284/379 (74%), Gaps = 5/379 (1%)

Query: 3   SVIIDDTTLRDGEQSAGVAFNADEKIAIARALAELGVPELEIGIPSMGEEEREVMHAIAG 62
           SVII+DTTLRDGEQSAGVAF+ DEK+AIA+ L  LGVPELEIGIP+MGEEERE + A+A 
Sbjct: 7   SVIINDTTLRDGEQSAGVAFSLDEKLAIAQGLDALGVPELEIGIPAMGEEERESIRAVAA 66

Query: 63  LGLSSRLLAWCRLCDVDLAAARSTGVTMVDLSLPVSDLMLHHKLNRDRDWALREVARLVG 122
           LGLS+RL+ W R+   D+   R  GV +VDLS+P+SD  +  KL RDR W L ++ R V 
Sbjct: 67  LGLSARLMVWTRMLADDIVQCRDLGVQLVDLSMPLSDQQIARKLGRDRGWVLAQIERKVR 126

Query: 123 EARMAGLEVCLGCEDASRADLEFVVQVGEVAQAAGARRLRFADTVGVMEPFGMLDRFRFL 182
            A   GLEVC+G EDASRAD EF+ +  E AQAAGARR RFADTVG+M+PFG+ +R   L
Sbjct: 127 LALDLGLEVCVGGEDASRADSEFLWRAAETAQAAGARRFRFADTVGLMDPFGLYERLHAL 186

Query: 183 SRRLDMELEVHAHDDFGLATANTLAAVMGGATHINTTVNGLGERAGNAALEECVLALKNL 242
             R+D+E+E+HAHDD GLATANTLAAV  GATH+NTTV+GLGERAGNAALEE V+ L+++
Sbjct: 187 RARVDLEIEMHAHDDLGLATANTLAAVRAGATHVNTTVHGLGERAGNAALEEVVMGLRHV 246

Query: 243 HGIDTGIDTRGIPAISALVERASGRQVAWQKSVVGAGVFTHEAGIHVDGLLKHRRNYEGL 302
            G+D G+D +   A+S+LV +ASG+ +AW KS+VGAG FTHEAGIHVDGL+K   NY+G+
Sbjct: 247 QGLDCGVDLKRFSALSSLVAQASGKPIAWHKSLVGAGAFTHEAGIHVDGLIKDPLNYQGV 306

Query: 303 NPDELGRSHSLVLGKHSGAHMVRNTYRD-LGIELADWQSQALLGRIRAFSTRTKRRSPQP 361
           +P ELG +H LVLGKHSG H V+  Y + L  EL   Q++ LL  +R F T TK RSP+ 
Sbjct: 307 DPAELGLNHRLVLGKHSGRHAVQRVYAESLCFELDQEQAERLLPLVRRFVTETK-RSPET 365

Query: 362 AELQDFYRQLCEQGNPELA 380
            +L+ F   L E G P+ A
Sbjct: 366 GDLRRF---LAEIGYPQTA 381


Lambda     K      H
   0.320    0.135    0.396 

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: 496
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: 385
Length of database: 384
Length adjustment: 30
Effective length of query: 355
Effective length of database: 354
Effective search space:   125670
Effective search space used:   125670
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_012970706.1 ALVIN_RS07410 (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.16760.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.1e-163  530.7   1.3   1.2e-163  530.5   1.3    1.0  1  lcl|NCBI__GCF_000025485.1:WP_012970706.1  ALVIN_RS07410 homocitrate syntha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000025485.1:WP_012970706.1  ALVIN_RS07410 homocitrate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  530.5   1.3  1.2e-163  1.2e-163       2     364 ..       8     371 ..       7     372 .. 0.99

  Alignments for each domain:
  == domain 1  score: 530.5 bits;  conditional E-value: 1.2e-163
                                 TIGR02660   2 vlinDttLRDGEqaagvaFsaeEKlaiAkaLdeaGvdelEvGipamgeeEraairaiaalglkarllaW 70 
                                               v+inDttLRDGEq+agvaFs +EKlaiA+ Ld++Gv+elE+GipamgeeEr++ira+aalgl+arl++W
  lcl|NCBI__GCF_000025485.1:WP_012970706.1   8 VIINDTTLRDGEQSAGVAFSLDEKLAIAQGLDALGVPELEIGIPAMGEEERESIRAVAALGLSARLMVW 76 
                                               89******************************************************************* PP

                                 TIGR02660  71 cRlraedieaaaevGvkavdlsvpvsdlqleaklkkdrawvleelkelvslakeeglkvsvgaeDasRa 139
                                               +R+ a di + +++Gv+ vdls+p sd+q++ kl +dr wvl+++++ v+la + gl+v+vg+eDasRa
  lcl|NCBI__GCF_000025485.1:WP_012970706.1  77 TRMLADDIVQCRDLGVQLVDLSMPLSDQQIARKLGRDRGWVLAQIERKVRLALDLGLEVCVGGEDASRA 145
                                               ********************************************************************* PP

                                 TIGR02660 140 deeflvelaevakeagakRlRfaDtvgvldPfstyelvkalraalelelElHaHnDlGlAtAntlaavk 208
                                               d+efl + ae+a++aga+R+RfaDtvg++dPf+ ye+++alra+++le+E+HaH+DlGlAtAntlaav+
  lcl|NCBI__GCF_000025485.1:WP_012970706.1 146 DSEFLWRAAETAQAAGARRFRFADTVGLMDPFGLYERLHALRARVDLEIEMHAHDDLGLATANTLAAVR 214
                                               ********************************************************************* PP

                                 TIGR02660 209 aGassvsvtvlGlGERAGnAaleevalalkellgldtgidlselkelsqlvakasgraleaqkavvGes 277
                                               aGa++v++tv GlGERAGnAaleev+++l+++ gld+g+dl+++++ls+lva+asg++++++k++vG+ 
  lcl|NCBI__GCF_000025485.1:WP_012970706.1 215 AGATHVNTTVHGLGERAGNAALEEVVMGLRHVQGLDCGVDLKRFSALSSLVAQASGKPIAWHKSLVGAG 283
                                               ********************************************************************* PP

                                 TIGR02660 278 vFaHEsGiHvdgllkdeatYesldPeevGrerelviGKHsgraaviealke.lgleleeeeaeelleav 345
                                                F+HE+GiHvdgl+kd+ +Y+++dP+e+G +++lv+GKHsgr+av+++++e l  el++e+ae+ll+ v
  lcl|NCBI__GCF_000025485.1:WP_012970706.1 284 AFTHEAGIHVDGLIKDPLNYQGVDPAELGLNHRLVLGKHSGRHAVQRVYAEsLCFELDQEQAERLLPLV 352
                                               ***********************************************99752789************** PP

                                 TIGR02660 346 ravaerlKrsleeeelaal 364
                                               r++++++Krs+e+ +l+++
  lcl|NCBI__GCF_000025485.1:WP_012970706.1 353 RRFVTETKRSPETGDLRRF 371
                                               ***************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (384 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: 12.09
//
[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