Alignments for a candidate for leuC in Stenotrophomonas chelatiphaga DSM 21508

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Stenotrophomonas chelatiphaga DSM 21508

Align 3-isopropylmalate dehydratase large subunit; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase; EC 4.2.1.33 (characterized)
to candidate WP_057509303.1 ABB28_RS14500 3-isopropylmalate dehydratase large subunit

Query= SwissProt::Q7TXH6
         (473 letters)



>NCBI__GCF_001431535.1:WP_057509303.1
          Length = 472

 Score =  514 bits (1325), Expect = e-150
 Identities = 264/472 (55%), Positives = 321/472 (68%), Gaps = 11/472 (2%)

Query: 5   TGEPRTLAEKIWDDHIVVSGGGCAPDLIYIDLHLVHEVTSPQAFDGLRLAGRRVRRPELT 64
           T  P TL +K+WD H+VV     AP ++YIDLHL+HEVTSPQAF  LR  G   RRP+ T
Sbjct: 2   TPAPSTLYDKLWDAHVVVPESDSAPAVLYIDLHLIHEVTSPQAFTELRERGLSPRRPDRT 61

Query: 65  LATEDHNVPTV----DIDQPIADPVSRTQVETLRRNCAEFGIRLHSMGDIEQGIVHVVGP 120
             T DH+ PT+    D   P A   S  QV  L  NCAE+G+ L  M   ++GIVHV+ P
Sbjct: 62  KGTMDHSTPTLPARADGSLPYASAASEAQVAMLASNCAEYGVELFDMASADRGIVHVIAP 121

Query: 121 QLGLTQPGMTIVCGDSHTSTHGAFGALAMGIGTSEVEHVLATQTLPLRPFKTMAVNVDGR 180
           + G T PGMTIVCGDSHTSTHGAFG+LA GIGTSEV HVLATQ L  R  KTMA+ VDG 
Sbjct: 122 EQGFTLPGMTIVCGDSHTSTHGAFGSLAFGIGTSEVGHVLATQCLLQRKAKTMAITVDGV 181

Query: 181 LPDGVSAKDIILALIAKIGTGGGQGHVIEYRGSAIESLSMEGRMTICNMSIEAGARAGMV 240
           LP GV AKD++L +I  IG  GG GHV+E+RGS I ++ ME RMT+CNMSIEAGARAGMV
Sbjct: 182 LPAGVGAKDVVLHIIGVIGVNGGTGHVLEFRGSTIAAMDMEQRMTLCNMSIEAGARAGMV 241

Query: 241 APDETTYAFLRGRPHAPTGAQWDTALVYWQRLRTDVGAVFDTEVYLDAASLSPFVTWGTN 300
           APD+ T+ ++   P  P GA +D A+  W +LR+D GA FD EV +DAA + P +TWGT+
Sbjct: 242 APDQVTFDWVAATPRGPKGADFDAAVGRWTQLRSDDGARFDAEVTIDAADIRPTLTWGTH 301

Query: 301 PGQGVPLAAAVPDPQLMTDDAERQAAEKALAYMDLRPGTAMREIAVDAVFVGSCTNGRIE 360
           PG  + + A +P        A   AA+K L YM L  G  ++   VD VFVGSCTNGR+ 
Sbjct: 302 PGTAIAVDAPIP-------AANDAAAQKGLDYMQLHAGDTLQGTPVDVVFVGSCTNGRLS 354

Query: 361 DLRVVAEVLRGRKVADGVRMLIVPGSMRVRAQAEAEGLGEIFTDAGAQWRQAGCSMCLGM 420
           D+R VA+VL GR+VAD VRML+VPGS  V+ QAEAEG+  I   AGA+WR+ GCSMC+ M
Sbjct: 355 DMREVAQVLHGRQVADRVRMLVVPGSEIVKRQAEAEGIDAIVRAAGAEWREPGCSMCIAM 414

Query: 421 NPDQLASGERCAATSNRNFEGRQGAGGRTHLVSPAVAAATAVRGTLSSPADL 472
           N D +A G+   +TSNRNFEGRQG G RT L SP  AA  AV G +S   DL
Sbjct: 415 NGDLVAPGQLAVSTSNRNFEGRQGPGSRTLLASPMTAAWAAVNGRVSDTRDL 466


Lambda     K      H
   0.319    0.135    0.402 

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: 718
Number of extensions: 29
Number of successful extensions: 4
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: 473
Length of database: 472
Length adjustment: 33
Effective length of query: 440
Effective length of database: 439
Effective search space:   193160
Effective search space used:   193160
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: 51 (24.3 bits)

Align candidate WP_057509303.1 ABB28_RS14500 (3-isopropylmalate dehydratase large subunit)
to HMM TIGR00170 (leuC: 3-isopropylmalate dehydratase, large subunit (EC 4.2.1.33))

# 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/TIGR00170.hmm
# target sequence database:        /tmp/gapView.16156.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00170  [M=466]
Accession:   TIGR00170
Description: leuC: 3-isopropylmalate dehydratase, large subunit
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   9.2e-197  640.1   0.1   1.1e-196  639.9   0.1    1.0  1  lcl|NCBI__GCF_001431535.1:WP_057509303.1  ABB28_RS14500 3-isopropylmalate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_057509303.1  ABB28_RS14500 3-isopropylmalate dehydratase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  639.9   0.1  1.1e-196  1.1e-196       2     466 .]       5     466 ..       4     466 .. 0.97

  Alignments for each domain:
  == domain 1  score: 639.9 bits;  conditional E-value: 1.1e-196
                                 TIGR00170   2 aktlyeklfdahvvk.eaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistes 69 
                                               + tly+kl+dahvv  e+++ + +lyid+hl+hevtspqaf  lr++g   rr+d+t +t+dh+ +t  
  lcl|NCBI__GCF_001431535.1:WP_057509303.1   5 PSTLYDKLWDAHVVVpESDSAPAVLYIDLHLIHEVTSPQAFTELRERGLSPRRPDRTKGTMDHSTPTLP 73 
                                               78**********97627788899*******************************************975 PP

                                 TIGR00170  70 r....dveikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtath 134
                                                     +      +  qv  l  n+ e+gv+lfd+ sa++givhv+ pe+g+tlpg+tivcgdsht+th
  lcl|NCBI__GCF_001431535.1:WP_057509303.1  74 AradgSLPYASAASEAQVAMLASNCAEYGVELFDMASADRGIVHVIAPEQGFTLPGMTIVCGDSHTSTH 142
                                               54655577889999******************************************************* PP

                                 TIGR00170 135 gafgalafgigtsevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvef 203
                                               gafg+lafgigtsev hvlatq l q +akt+ i+v+g l  g+ akd++l iig igv+ggtg+v+ef
  lcl|NCBI__GCF_001431535.1:WP_057509303.1 143 GAFGSLAFGIGTSEVGHVLATQCLLQRKAKTMAITVDGVLPAGVGAKDVVLHIIGVIGVNGGTGHVLEF 211
                                               ********************************************************************* PP

                                 TIGR00170 204 ageairdlsmeermtvcnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegak 272
                                                g +i ++ me+rmt+cnm+ieaga+ag++apd++tf++v   +  pkg++f+ av  w  l++d+ga+
  lcl|NCBI__GCF_001431535.1:WP_057509303.1 212 RGSTIAAMDMEQRMTLCNMSIEAGARAGMVAPDQVTFDWVAATPRGPKGADFDAAVGRWTQLRSDDGAR 280
                                               ********************************************************************* PP

                                 TIGR00170 273 fdkvvtleakdispqvtwgtnpgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdk 341
                                               fd +vt++a di p++twgt pg++++v+  +p+ ++       a a+k l+y+ l++g  l+   vd 
  lcl|NCBI__GCF_001431535.1:WP_057509303.1 281 FDAEVTIDAADIRPTLTWGTHPGTAIAVDAPIPAAND-------AAAQKGLDYMQLHAGDTLQGTPVDV 342
                                               *********************************9765.......55789******************** PP

                                 TIGR00170 342 vfigsctnsriedlraaaevvkgkkvadnvklalvvpgsglvkkqaekegldkifleagfewreagcsl 410
                                               vf+gsctn+r+ d+r+ a+v++g++vad v+ +lvvpgs+ vk+qae+eg+d i  +ag+ewre+gcs+
  lcl|NCBI__GCF_001431535.1:WP_057509303.1 343 VFVGSCTNGRLSDMREVAQVLHGRQVADRVR-MLVVPGSEIVKRQAEAEGIDAIVRAAGAEWREPGCSM 410
                                               *******************************.9************************************ PP

                                 TIGR00170 411 clgmnndvldeyercastsnrnfegrqgkgarthlvspamaaaaavagkfvdirel 466
                                               c++mn d + +++   stsnrnfegrqg g+rt l sp  aa aav+g+  d r+l
  lcl|NCBI__GCF_001431535.1:WP_057509303.1 411 CIAMNGDLVAPGQLAVSTSNRNFEGRQGPGSRTLLASPMTAAWAAVNGRVSDTRDL 466
                                               *****************************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (472 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 8.52
//
[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