Alignments for a candidate for leuB in Thermovibrio ammonificans HB-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuB in Thermovibrio ammonificans HB-1

Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate WP_013537107.1 THEAM_RS01805 3-isopropylmalate dehydrogenase

Query= BRENDA::Q9SA14
         (404 letters)



>NCBI__GCF_000185805.1:WP_013537107.1
          Length = 359

 Score =  390 bits (1001), Expect = e-113
 Identities = 200/357 (56%), Positives = 254/357 (71%), Gaps = 2/357 (0%)

Query: 42  KRYNITLLPGDGIGPEVISVAKNVLQKAGFLQGLEFDFQEMPFGGAALDLVGVPLPEETS 101
           +++ I +LPGDGIGPE++  A  V++ A    G   +      GGAA+D  GVP PEET 
Sbjct: 2   RKFKIAVLPGDGIGPEIVKQAVKVMEAAAEKFGFGLELNYGLIGGAAIDETGVPFPEETK 61

Query: 102 TAAKQSDAILLGAIGGYKWDKNEKHLRPEMGLLNIRRDLNVFANLRPATVLPQLVDASTL 161
                SDA+LLGA+GG KWD     +RPE  LL +R+ LN FANLRPA +  +L+DASTL
Sbjct: 62  ELILSSDAVLLGAVGGPKWDNLPFEIRPERALLGMRKLLNAFANLRPARLYDELIDASTL 121

Query: 162 KKEVAQGVDMMIVRELTGGIYFGEPRGITINENGEEVGFNTEIYAAHEIDRIARVAFETA 221
           K EV +GVD+M++RELT GIYFG P+GI + +  E VG NT  Y  HE++RIA+VAFE A
Sbjct: 122 KPEVVRGVDIMVIRELTSGIYFGIPKGIFV-DGDERVGINTLRYYEHEVERIAKVAFEVA 180

Query: 222 RKRRGKLCSVDKANVLDASILWRKRVTALASEYPDVELSHMYVDNAAMQLVRDPKQFDTI 281
           RKR  K+ SVDKANVL+A++LWR+ V  +   YPDVEL HMYVDNAAMQ++R PKQFD I
Sbjct: 181 RKRNKKVTSVDKANVLEATVLWREVVERVHENYPDVELQHMYVDNAAMQIIRWPKQFDVI 240

Query: 282 VTNNIFGDILSDEASMITGSIGMLPSASLGESGPGLFEPIHGSAPDIAGQDKANPLATIL 341
           VT N+FGDILSD  +M+TGS+GMLPSAS+G    GL+EPIHGSAPDIAGQ+ ANP+ATI 
Sbjct: 241 VTTNMFGDILSDACAMLTGSLGMLPSASIG-GKIGLYEPIHGSAPDIAGQNIANPIATIN 299

Query: 342 SAAMLLKYGLGEEKAAKMIEDAVVDALNKGFRTGDIYSPGNKLVGCKEMGEEVLKSV 398
           SA M+  Y     +  + I+ AV   L KG+RT DIYS G KLV  +EMG+ + + +
Sbjct: 300 SAGMMFTYSFDMPEVEEAIDKAVRAVLAKGYRTRDIYSEGTKLVSTEEMGDLIAEEL 356


Lambda     K      H
   0.317    0.136    0.389 

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: 424
Number of extensions: 11
Number of successful extensions: 3
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: 404
Length of database: 359
Length adjustment: 30
Effective length of query: 374
Effective length of database: 329
Effective search space:   123046
Effective search space used:   123046
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_013537107.1 THEAM_RS01805 (3-isopropylmalate dehydrogenase)
to HMM TIGR00169 (leuB: 3-isopropylmalate dehydrogenase (EC 1.1.1.85))

# 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/TIGR00169.hmm
# target sequence database:        /tmp/gapView.7206.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00169  [M=349]
Accession:   TIGR00169
Description: leuB: 3-isopropylmalate dehydrogenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.6e-162  525.7   0.0     3e-162  525.5   0.0    1.0  1  lcl|NCBI__GCF_000185805.1:WP_013537107.1  THEAM_RS01805 3-isopropylmalate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000185805.1:WP_013537107.1  THEAM_RS01805 3-isopropylmalate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  525.5   0.0    3e-162    3e-162       1     348 [.       5     351 ..       5     352 .. 0.99

  Alignments for each domain:
  == domain 1  score: 525.5 bits;  conditional E-value: 3e-162
                                 TIGR00169   1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlg 69 
                                               kiavLpGDgiGpe+v++a+kv++a +e+f++ le ++ liGGaaid+tg P+peet +   ++davLlg
  lcl|NCBI__GCF_000185805.1:WP_013537107.1   5 KIAVLPGDGIGPEIVKQAVKVMEAAAEKFGFGLELNYGLIGGAAIDETGVPFPEETKELILSSDAVLLG 73 
                                               79******************************************************************* PP

                                 TIGR00169  70 avGGpkWdnlprdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiY 138
                                               avGGpkWdnlp ++rPe++LL +rk l+ fanLrPa+l+++L+++s+lk+e+v+gvD++v+reLt+GiY
  lcl|NCBI__GCF_000185805.1:WP_013537107.1  74 AVGGPKWDNLPFEIRPERALLGMRKLLNAFANLRPARLYDELIDASTLKPEVVRGVDIMVIRELTSGIY 142
                                               ********************************************************************* PP

                                 TIGR00169 139 fGepkereeaeeekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiak 207
                                               fG pk+++ +++e+ +++t +Y+++e+eria+vafe+arkr+kkvtsvDkanvLe++ lWr++ve +++
  lcl|NCBI__GCF_000185805.1:WP_013537107.1 143 FGIPKGIFVDGDERVGINTLRYYEHEVERIAKVAFEVARKRNKKVTSVDKANVLEATVLWREVVERVHE 211
                                               ********************************************************************* PP

                                 TIGR00169 208 eyPdvelehlyiDnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslsskglalfepv 276
                                               +yPdvel+h+y+Dnaamq+++ P+q+dv+vt n+fGDilsD ++++tGslG+LPsas++  + +l+ep+
  lcl|NCBI__GCF_000185805.1:WP_013537107.1 212 NYPDVELQHMYVDNAAMQIIRWPKQFDVIVTTNMFGDILSDACAMLTGSLGMLPSASIG-GKIGLYEPI 279
                                               ***********************************************************.6789***** PP

                                 TIGR00169 277 hgsapdiagkgianpiaailsaalllryslnleeaaeaieaavkkvleegkrtedlaseattavstkev 345
                                               hgsapdiag++ianpia+i sa ++  ys++++e +eai++av+ vl++g+rt+d++se+t+ vst+e+
  lcl|NCBI__GCF_000185805.1:WP_013537107.1 280 HGSAPDIAGQNIANPIATINSAGMMFTYSFDMPEVEEAIDKAVRAVLAKGYRTRDIYSEGTKLVSTEEM 348
                                               ********************************************************************* PP

                                 TIGR00169 346 eee 348
                                               ++ 
  lcl|NCBI__GCF_000185805.1:WP_013537107.1 349 GDL 351
                                               986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (359 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 0.00s 00:00:00.00 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