Alignments for a candidate for leuC in Trichormus variabilis ATCC 29413

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Trichormus variabilis ATCC 29413

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized, see rationale)
to candidate WP_011320659.1 AVA_RS20110 3-isopropylmalate dehydratase large subunit

Query= uniprot:A0A1X9Z7T5
         (470 letters)



>NCBI__GCF_000204075.1:WP_011320659.1
          Length = 467

 Score =  494 bits (1273), Expect = e-144
 Identities = 247/467 (52%), Positives = 322/467 (68%), Gaps = 2/467 (0%)

Query: 1   MSK-TLVEKIWDAHVVKSEEGFPDILYIDTHLIHEVTSPQAFDGLRKRGLPVFRPKQTVA 59
           MSK TL +K+WD H V +       L+I  HL+HEVTSPQAF  LR+RGL V  P++TVA
Sbjct: 1   MSKGTLFDKVWDLHTVGTLPSGLTQLFIGLHLVHEVTSPQAFAMLRERGLKVLFPERTVA 60

Query: 60  TADHNVPTLNQLLPIKEELSRYQVDMLTKNCAEFGVELYGLGHPFQGIVHVIGPELGITL 119
           T DH VPT NQ  P  + L+   +  L +NC E  +  Y +G   QGIVHVI PELG+T 
Sbjct: 61  TVDHIVPTENQARPFVDRLAEEMIQALEQNCQENNITFYNIGSGNQGIVHVIAPELGLTQ 120

Query: 120 PGKTMVCGDSHTSTHGAFGAIAFGIGTSQVEQVFATQCLLQSKPKTMKIEVNGELGKGVG 179
           PG T+ CGDSHTS+HGAFGAIAFGIGTSQV  V A+Q L  SK K  KIEVNG L  GV 
Sbjct: 121 PGMTIACGDSHTSSHGAFGAIAFGIGTSQVRDVLASQTLSLSKLKVRKIEVNGTLNPGVY 180

Query: 180 AKDIILYIIAKISAAGGTGYFIEYAGSAIEALSMEARMTICNMSIEMGARGGLIAPDQTT 239
           AKD+IL+II  +   GG GY  EYAG+  E ++ME RMT+CNM+IE GAR G + PDQ T
Sbjct: 181 AKDVILHIIRTLGVKGGVGYAYEYAGTTFEQMNMEERMTVCNMAIEGGARCGYVNPDQVT 240

Query: 240 FDYIKGREFAPAGEEWDKALAYWKTLYSDADAKFDSVLTFDAADIAPMITYGTNPGMGMG 299
           +DY++GR+FAP G +W+KA+A+W+++ SDADA++D V+ F+AADI P +T+G  PG G+G
Sbjct: 241 YDYLQGRDFAPQGADWEKAVAWWESIKSDADAEYDDVIVFNAADIPPTVTWGITPGQGIG 300

Query: 300 IQEHIPATGAQPEKEKLSYQKALDYMGFDDDSSLIGKPVDYVFIGSCTNSRIEDLREVAD 359
           + + IP      E+++   ++A  YM       + G  +D  FIGSCTN R+ DL+E A 
Sbjct: 301 VNQLIPQPEELLEEDRFVAEEAYRYMDLYPGQPIKGTKIDVCFIGSCTNGRLSDLQEAAK 360

Query: 360 FVKDKRKADNVTVWIVPGSKQVEQQAKNEGLDKIFEAAGFQLREPGCSACLGMNEDKIPA 419
             K +  A+ V  ++VPGS++V++ A+ EGLDKIFEAAGF+ REPGCS CL MN DK+  
Sbjct: 361 IAKGRHVAEGVKAFVVPGSERVKKAAEAEGLDKIFEAAGFEWREPGCSMCLAMNPDKLEG 420

Query: 420 GKYCVSTSNRNFEGRQGQ-NARTLLASPLTAAAAAVTGKITDVRDLL 465
            +   S+SNRNF+GRQG  + RTLL SP   A AA+ G++ DVR+LL
Sbjct: 421 RQISASSSNRNFKGRQGSASGRTLLMSPAMVATAAIQGEVADVRELL 467


Lambda     K      H
   0.317    0.135    0.399 

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: 613
Number of extensions: 24
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: 470
Length of database: 467
Length adjustment: 33
Effective length of query: 437
Effective length of database: 434
Effective search space:   189658
Effective search space used:   189658
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: 51 (24.3 bits)

Align candidate WP_011320659.1 AVA_RS20110 (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.2008395.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.6e-192  625.5   0.0   2.9e-192  625.3   0.0    1.0  1  NCBI__GCF_000204075.1:WP_011320659.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000204075.1:WP_011320659.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  625.3   0.0  2.9e-192  2.9e-192       4     466 .]       5     466 ..       1     466 [. 0.99

  Alignments for each domain:
  == domain 1  score: 625.3 bits;  conditional E-value: 2.9e-192
                             TIGR00170   4 tlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesrdveike 76 
                                           tl++k++d h v    ++ + l+i +hlvhevtspqaf  lr++g kv  +++t+at+dh ++te++    ++
  NCBI__GCF_000204075.1:WP_011320659.1   5 TLFDKVWDLHTVGTLPSGLTQLFIGLHLVHEVTSPQAFAMLRERGLKVLFPERTVATVDHIVPTENQARPFVD 77 
                                           9************************************************************************ PP

                             TIGR00170  77 ekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalafgigtsev 149
                                             a   +++le+n++e  + ++++ s +qgivhv+ pe glt pg+ti cgdsht++hgafga+afgigts+v
  NCBI__GCF_000204075.1:WP_011320659.1  78 RLAEEMIQALEQNCQENNITFYNIGSGNQGIVHVIAPELGLTQPGMTIACGDSHTSSHGAFGAIAFGIGTSQV 150
                                           ************************************************************************* PP

                             TIGR00170 150 ehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeermtvcnm 222
                                             vla+qtl  ++ k  kiev+g+l++g+ akd+il ii  +gv+gg gy  e+ag +++++ meermtvcnm
  NCBI__GCF_000204075.1:WP_011320659.1 151 RDVLASQTLSLSKLKVRKIEVNGTLNPGVYAKDVILHIIRTLGVKGGVGYAYEYAGTTFEQMNMEERMTVCNM 223
                                           ************************************************************************* PP

                             TIGR00170 223 aieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtwgtnpg 295
                                           aie ga+ g ++pd++t++y+++r +ap+g+++ekava w ++k+d +a++d v++++a di p+vtwg++pg
  NCBI__GCF_000204075.1:WP_011320659.1 224 AIEGGARCGYVNPDQVTYDYLQGRDFAPQGADWEKAVAWWESIKSDADAEYDDVIVFNAADIPPTVTWGITPG 296
                                           ************************************************************************* PP

                             TIGR00170 296 qvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvkgkkva 368
                                           q + vn+ +p+p++l ++ ++  ae a++y+ l pg+++k  k+d  figsctn+r+ dl++aa+++kg++va
  NCBI__GCF_000204075.1:WP_011320659.1 297 QGIGVNQLIPQPEELLEE-DRFVAEEAYRYMDLYPGQPIKGTKIDVCFIGSCTNGRLSDLQEAAKIAKGRHVA 368
                                           ***************876.7999************************************************** PP

                             TIGR00170 369 dnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmnndvldeyercastsnrnfegrqgk.g 440
                                           ++vk a+vvpgs+ vkk ae+egldkif +agfewre+gcs+cl+mn+d+l+  +  as+snrnf+grqg  +
  NCBI__GCF_000204075.1:WP_011320659.1 369 EGVK-AFVVPGSERVKKAAEAEGLDKIFEAAGFEWREPGCSMCLAMNPDKLEGRQISASSSNRNFKGRQGSaS 440
                                           ****.*****************************************************************726 PP

                             TIGR00170 441 arthlvspamaaaaavagkfvdirel 466
                                           +rt l+spam a+aa++g+ +d+rel
  NCBI__GCF_000204075.1:WP_011320659.1 441 GRTLLMSPAMVATAAIQGEVADVREL 466
                                           8***********************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (467 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 0.02s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 8.88
//
[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