Alignments for a candidate for hcs in Beijerinckia indica ATCC 9039

GapMind for Amino acid biosynthesis

Alignments for a candidate for hcs in Beijerinckia indica ATCC 9039

Align homocitrate synthase (EC 2.3.3.14) (characterized)
to candidate WP_012383496.1 BIND_RS02470 homocitrate synthase

Query= BRENDA::A0A0S6UXF5
         (400 letters)



>NCBI__GCF_000019845.1:WP_012383496.1
          Length = 400

 Score =  449 bits (1154), Expect = e-131
 Identities = 232/371 (62%), Positives = 281/371 (75%)

Query: 25  VVLNDTTLRDGEQAPGVAFTTAEKLSIARALASAGVTEIEAGTPAMGHDEVSAIRAIVEA 84
           ++LNDTTLRDGEQAPGVAF+  EK++IARALA AGV EIEAGTPAMG  E++AI A+V  
Sbjct: 17  IILNDTTLRDGEQAPGVAFSPEEKIAIARALALAGVPEIEAGTPAMGEREIAAINAVVAE 76

Query: 85  DLPATAIGWCRMRTSDVDAAIEAGVSMVNVSIPASDVQIAAKLSGGRPAALEQVRRVVGY 144
            LP+  I WCRM   D+DAA+ +GV M+N+S+P SD+Q+ AK   GR  A E + R + Y
Sbjct: 77  GLPSKIIAWCRMVPQDIDAAVASGVGMINLSLPVSDIQLKAKFGAGRAYARELIGRFIPY 136

Query: 145 ARDSGLDVAVGGEDSSRADVDFLVELIATAKAAGARRFRIADTLSVLDPDAAFALLTALR 204
           ARD GL+VA+G ED+SRADVDFL+E+     + G RR R ADTL VLDP   FA++  LR
Sbjct: 137 ARDKGLEVALGCEDASRADVDFLLEVAELGASLGVRRMRFADTLGVLDPFMTFAMIERLR 196

Query: 205 ATTDLELEFHGHDDLGLATANTLAAIKAGATHASVTVIGLGERAGNAPLEEVAVALKQLY 264
             +DLE+E H HDDLGLATANTLAA++AGATHASVTV+GLGERAGNAPLEEVAVA++ LY
Sbjct: 197 QASDLEIEIHAHDDLGLATANTLAALRAGATHASVTVVGLGERAGNAPLEEVAVAVEALY 256

Query: 265 GRETGVVLSELKHVASVVAAAAARAIPLNKAIVGEHVFTHESGIHVDGLLKDQRTYQALD 324
           G  TGV L+ L  VA VV  AA R+IP  KAIVGE VFTHESGIHVDGLLKD   YQALD
Sbjct: 257 GFTTGVDLTALAQVAQVVTNAAGRSIPEAKAIVGEAVFTHESGIHVDGLLKDLHCYQALD 316

Query: 325 PHLLGRSNRIVIGKHSGLAAITALLAELQLSASADEAKSVLARVRQHAVEHKGAVGRETV 384
           P LLGRS+ +V+GKHSGL A+T  LAE  LS SADEAK VLAR++ +A + K +V  + +
Sbjct: 317 PALLGRSHHVVLGKHSGLRAVTNALAEQGLSVSADEAKFVLARIKLYAEQEKASVPGDIL 376

Query: 385 TSIWREVRERS 395
              +RE +  S
Sbjct: 377 LDFYREAKVAS 387


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: 419
Number of extensions: 9
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: 400
Length adjustment: 31
Effective length of query: 369
Effective length of database: 369
Effective search space:   136161
Effective search space used:   136161
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_012383496.1 BIND_RS02470 (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.2634.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-154  500.8   2.2   1.6e-154  500.6   2.2    1.0  1  lcl|NCBI__GCF_000019845.1:WP_012383496.1  BIND_RS02470 homocitrate synthas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000019845.1:WP_012383496.1  BIND_RS02470 homocitrate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  500.6   2.2  1.6e-154  1.6e-154       2     359 ..      17     374 ..      16     380 .. 0.99

  Alignments for each domain:
  == domain 1  score: 500.6 bits;  conditional E-value: 1.6e-154
                                 TIGR02660   2 vlinDttLRDGEqaagvaFsaeEKlaiAkaLdeaGvdelEvGipamgeeEraairaiaalglkarllaW 70 
                                               +++nDttLRDGEqa+gvaFs eEK+aiA+aL+ aGv+e+E+G+pamge E+aai+a++a+gl+++++aW
  lcl|NCBI__GCF_000019845.1:WP_012383496.1  17 IILNDTTLRDGEQAPGVAFSPEEKIAIARALALAGVPEIEAGTPAMGEREIAAINAVVAEGLPSKIIAW 85 
                                               79******************************************************************* PP

                                 TIGR02660  71 cRlraedieaaaevGvkavdlsvpvsdlqleaklkkdrawvleelkelvslakeeglkvsvgaeDasRa 139
                                               cR+  +di+aa++ Gv +++ls+pvsd+ql+ak+   ra ++e + +++ +a+++gl+v++g+eDasRa
  lcl|NCBI__GCF_000019845.1:WP_012383496.1  86 CRMVPQDIDAAVASGVGMINLSLPVSDIQLKAKFGAGRAYARELIGRFIPYARDKGLEVALGCEDASRA 154
                                               ********************************************************************* PP

                                 TIGR02660 140 deeflvelaevakeagakRlRfaDtvgvldPfstyelvkalraalelelElHaHnDlGlAtAntlaavk 208
                                               d +fl e+ae  +  g++R+RfaDt+gvldPf t++++++lr+a++le+E+HaH+DlGlAtAntlaa++
  lcl|NCBI__GCF_000019845.1:WP_012383496.1 155 DVDFLLEVAELGASLGVRRMRFADTLGVLDPFMTFAMIERLRQASDLEIEIHAHDDLGLATANTLAALR 223
                                               ********************************************************************* PP

                                 TIGR02660 209 aGassvsvtvlGlGERAGnAaleevalalkellgldtgidlselkelsqlvakasgraleaqkavvGes 277
                                               aGa+++svtv+GlGERAGnA+leeva+a++ l+g+ tg+dl++l +++q+v++a+gr++++ ka+vGe+
  lcl|NCBI__GCF_000019845.1:WP_012383496.1 224 AGATHASVTVVGLGERAGNAPLEEVAVAVEALYGFTTGVDLTALAQVAQVVTNAAGRSIPEAKAIVGEA 292
                                               ********************************************************************* PP

                                 TIGR02660 278 vFaHEsGiHvdgllkdeatYesldPeevGrerelviGKHsgraaviealkelgleleeeeaeelleavr 346
                                               vF+HEsGiHvdgllkd + Y++ldP+++Gr++++v+GKHsg +av++al+e gl+++++ea+ +l++++
  lcl|NCBI__GCF_000019845.1:WP_012383496.1 293 VFTHESGIHVDGLLKDLHCYQALDPALLGRSHHVVLGKHSGLRAVTNALAEQGLSVSADEAKFVLARIK 361
                                               ********************************************************************* PP

                                 TIGR02660 347 avaerlKrsleee 359
                                                +ae+ K s+  +
  lcl|NCBI__GCF_000019845.1:WP_012383496.1 362 LYAEQEKASVPGD 374
                                               *******988655 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (400 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 6.93
//
[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