Alignments for a candidate for leuC in Thioalkalivibrio paradoxus ARh 1

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Thioalkalivibrio paradoxus ARh 1

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate WP_006748151.1 THITH_RS10455 3-isopropylmalate dehydratase large subunit

Query= CharProtDB::CH_024771
         (466 letters)



>NCBI__GCF_000227685.2:WP_006748151.1
          Length = 469

 Score =  587 bits (1512), Expect = e-172
 Identities = 291/460 (63%), Positives = 351/460 (76%), Gaps = 1/460 (0%)

Query: 3   KTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFATMD 62
           +TLY+KL+ AHVV+E E+ T LLYIDRHLVHEVTSPQAF+GLR  GR   +     A  D
Sbjct: 4   QTLYDKLWQAHVVHEEEDGTALLYIDRHLVHEVTSPQAFEGLRLAGRKPWRSDSVLAVPD 63

Query: 63  HNVSTQTKDINACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTLPGM 122
           HNV T+ ++      ++R Q++ L +N  EFG++ + +    QGIVHV+GPEQG TLPGM
Sbjct: 64  HNVPTEHREAGIADPVSRTQVETLERNVGEFGLKFFPMRDLRQGIVHVIGPEQGATLPGM 123

Query: 123 TIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGITAKD 182
           T+VCGDSHT+THGA GALAFGIGTSEVEHVLATQ L Q ++++M + V G+  PG+TAKD
Sbjct: 124 TVVCGDSHTSTHGALGALAFGIGTSEVEHVLATQCLWQKKSRSMLVRVDGELRPGVTAKD 183

Query: 183 IVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETTFNY 242
           +VLAIIG  G+AGGTG+ +EF G AIR LS+EGRMT+CNMAIE GA+AG+VA DE T  Y
Sbjct: 184 VVLAIIGTIGTAGGTGYAIEFGGAAIRSLSVEGRMTVCNMAIEAGARAGMVAVDEKTIEY 243

Query: 243 VKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVISVND 302
           V+GR  AP G+ F+ A   W+ L +D  A FD VV L A  I PQV+WGT+P  V+ V+ 
Sbjct: 244 VRGRPQAPAGELFERAALSWRELVSDPDARFDRVVVLDAATIEPQVSWGTSPEMVVPVSG 303

Query: 303 NIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAAEIA 362
            +PDPA   DPV      KAL YMGL+PG P+  +  DKVFIGSCTNSRIEDLR AA + 
Sbjct: 304 RVPDPALEKDPVRAEGMRKALRYMGLEPGTPIDGIRPDKVFIGSCTNSRIEDLREAAAVV 363

Query: 363 KGRKVAPGVQ-ALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLNPG 421
           +GR+ A  VQ A+VVPGSG VK QAEAEGLD++F++AGFEWR PGCSMCLAMN DRL PG
Sbjct: 364 RGRRKADSVQLAMVVPGSGLVKQQAEAEGLDRVFLDAGFEWREPGCSMCLAMNADRLEPG 423

Query: 422 ERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFAD 461
           ERCASTSNRNFEGRQG+GGRTHLVSPA+AAAAAV GHF D
Sbjct: 424 ERCASTSNRNFEGRQGQGGRTHLVSPALAAAAAVAGHFVD 463


Lambda     K      H
   0.317    0.134    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: 787
Number of extensions: 27
Number of successful extensions: 2
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: 466
Length of database: 469
Length adjustment: 33
Effective length of query: 433
Effective length of database: 436
Effective search space:   188788
Effective search space used:   188788
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_006748151.1 THITH_RS10455 (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.9371.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     7e-235  765.8   0.0   8.4e-235  765.6   0.0    1.0  1  lcl|NCBI__GCF_000227685.2:WP_006748151.1  THITH_RS10455 3-isopropylmalate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000227685.2:WP_006748151.1  THITH_RS10455 3-isopropylmalate dehydratase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  765.6   0.0  8.4e-235  8.4e-235       3     462 ..       4     463 ..       2     467 .. 1.00

  Alignments for each domain:
  == domain 1  score: 765.6 bits;  conditional E-value: 8.4e-235
                                 TIGR00170   3 ktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesrd 71 
                                               +tly+kl++ahvv+e+e++t llyidrhlvhevtspqafeglr agrk  r d+ la  dhn++te r+
  lcl|NCBI__GCF_000227685.2:WP_006748151.1   4 QTLYDKLWQAHVVHEEEDGTALLYIDRHLVHEVTSPQAFEGLRLAGRKPWRSDSVLAVPDHNVPTEHRE 72 
                                               7******************************************************************** PP

                                 TIGR00170  72 veikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgal 140
                                                 i + +++ qv++le+nv efg+k+f +++ +qgivhv+gpe+g tlpg+t+vcgdsht+thga+gal
  lcl|NCBI__GCF_000227685.2:WP_006748151.1  73 AGIADPVSRTQVETLERNVGEFGLKFFPMRDLRQGIVHVIGPEQGATLPGMTVVCGDSHTSTHGALGAL 141
                                               ********************************************************************* PP

                                 TIGR00170 141 afgigtsevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageair 209
                                               afgigtsevehvlatq l+q++++++ ++v+g+l +g+takd++laiig ig+aggtgy +ef g air
  lcl|NCBI__GCF_000227685.2:WP_006748151.1 142 AFGIGTSEVEHVLATQCLWQKKSRSMLVRVDGELRPGVTAKDVVLAIIGTIGTAGGTGYAIEFGGAAIR 210
                                               ********************************************************************* PP

                                 TIGR00170 210 dlsmeermtvcnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvt 278
                                               +ls+e+rmtvcnmaieaga+ag++a de t+eyv++r++ap g+ fe a   w+ l +d++a+fd+vv+
  lcl|NCBI__GCF_000227685.2:WP_006748151.1 211 SLSVEGRMTVCNMAIEAGARAGMVAVDEKTIEYVRGRPQAPAGELFERAALSWRELVSDPDARFDRVVV 279
                                               ********************************************************************* PP

                                 TIGR00170 279 leakdispqvtwgtnpgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsc 347
                                               l+a  i pqv+wgt+p++v++v++ vpdp+   dpv+ +++ kal+y+glepgt+++ i+ dkvfigsc
  lcl|NCBI__GCF_000227685.2:WP_006748151.1 280 LDAATIEPQVSWGTSPEMVVPVSGRVPDPALEKDPVRAEGMRKALRYMGLEPGTPIDGIRPDKVFIGSC 348
                                               ********************************************************************* PP

                                 TIGR00170 348 tnsriedlraaaevvkgkkvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmnn 416
                                               tnsriedlr+aa+vv+g+++ad+v+la+vvpgsglvk+qae+egld++fl+agfewre+gcs+cl+mn 
  lcl|NCBI__GCF_000227685.2:WP_006748151.1 349 TNSRIEDLREAAAVVRGRRKADSVQLAMVVPGSGLVKQQAEAEGLDRVFLDAGFEWREPGCSMCLAMNA 417
                                               ********************************************************************* PP

                                 TIGR00170 417 dvldeyercastsnrnfegrqgkgarthlvspamaaaaavagkfvd 462
                                               d+l+++ercastsnrnfegrqg+g+rthlvspa+aaaaavag+fvd
  lcl|NCBI__GCF_000227685.2:WP_006748151.1 418 DRLEPGERCASTSNRNFEGRQGQGGRTHLVSPALAAAAAVAGHFVD 463
                                               *********************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (469 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 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 9.25
//
[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