Alignments for a candidate for leuC in Thiomicrospira cyclica ALM1

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Thiomicrospira cyclica ALM1

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate WP_013835169.1 THICY_RS03150 3-isopropylmalate dehydratase large subunit

Query= CharProtDB::CH_024771
         (466 letters)



>NCBI__GCF_000214825.1:WP_013835169.1
          Length = 471

 Score =  588 bits (1517), Expect = e-172
 Identities = 298/468 (63%), Positives = 355/468 (75%), Gaps = 4/468 (0%)

Query: 2   AKTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFATM 61
           AKTLY+KL+D HVV + E+ T L+YIDR L+HEVTSPQAF+GLR  GR   +     AT 
Sbjct: 3   AKTLYDKLWDEHVVRQEEDGTALIYIDRQLLHEVTSPQAFEGLRLAGRTPWRISANLATA 62

Query: 62  DHNVSTQTKDINACG---EMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVT 118
           DHNV T   +  A G    ++RIQ+Q L +N +EFG+  + + H  QGIVHV+GPE G T
Sbjct: 63  DHNVPTTPVEGGAAGIVDPISRIQVQTLHRNTQEFGITEFGMGHIRQGIVHVVGPENGAT 122

Query: 119 LPGMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGI 178
           LPGMTIVCGDSHT+THGA GALA GIGTSEVEHVLATQ L Q + K M I V G+  PG+
Sbjct: 123 LPGMTIVCGDSHTSTHGALGALAHGIGTSEVEHVLATQCLIQKKNKNMLIRVDGQLQPGV 182

Query: 179 TAKDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDET 238
            AKD+VLAIIG+ G+AGGTG+ +EF G+ +RD+S+EGRM++CNM+IE GA+AGLVA DE 
Sbjct: 183 GAKDVVLAIIGEIGTAGGTGYTIEFGGQVLRDMSIEGRMSICNMSIEAGARAGLVAVDEK 242

Query: 239 TFNYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVI 298
           T  YVKGR  +P G  +D AV +W+TL +DEGA FD VV L    I PQV+WGT+P  V+
Sbjct: 243 TIEYVKGRPFSPTGAHWDAAVKHWQTLHSDEGAHFDKVVVLDGSAIQPQVSWGTSPEMVV 302

Query: 299 SVNDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAA 358
            VNDN+PDPA  ADPV+  S  +AL YMGL   IP+ ++ +D VFIGSCTNSRIEDLRAA
Sbjct: 303 GVNDNVPDPAIEADPVKSNSMRRALEYMGLSANIPIKDIQLDYVFIGSCTNSRIEDLRAA 362

Query: 359 AEIAKGRKVAPGV-QALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDR 417
           A I  G+KVA  + QALVVPGSG VK QAEAEGLDKIF++AGFEWR PGCSMCLAMN DR
Sbjct: 363 AAIVNGKKVAANIEQALVVPGSGLVKQQAEAEGLDKIFMDAGFEWRNPGCSMCLAMNADR 422

Query: 418 LNPGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNI 465
           L   + CASTSNRNFEGRQG GGRTHLVSP MAAAAAV G F D+R +
Sbjct: 423 LPAKKHCASTSNRNFEGRQGAGGRTHLVSPIMAAAAAVAGRFVDVREL 470


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: 726
Number of extensions: 21
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: 466
Length of database: 471
Length adjustment: 33
Effective length of query: 433
Effective length of database: 438
Effective search space:   189654
Effective search space used:   189654
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_013835169.1 THICY_RS03150 (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.308372.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.2e-235  768.4   0.7   1.4e-235  768.2   0.7    1.0  1  NCBI__GCF_000214825.1:WP_013835169.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000214825.1:WP_013835169.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  768.2   0.7  1.4e-235  1.4e-235       2     466 .]       3     470 ..       2     470 .. 0.99

  Alignments for each domain:
  == domain 1  score: 768.2 bits;  conditional E-value: 1.4e-235
                             TIGR00170   2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesr...d 71 
                                           aktly+kl+d+hvv+++e++t l+yidr l+hevtspqafeglr agr   r++  lat dhn++t+      
  NCBI__GCF_000214825.1:WP_013835169.1   3 AKTLYDKLWDEHVVRQEEDGTALIYIDRQLLHEVTSPQAFEGLRLAGRTPWRISANLATADHNVPTTPVeggA 75 
                                           89***************************************************************98764556 PP

                             TIGR00170  72 veikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalafgi 144
                                             i++  +++qv++l++n++efg+  f++ + +qgivhvvgpe+g tlpg+tivcgdsht+thga+gala gi
  NCBI__GCF_000214825.1:WP_013835169.1  76 AGIVDPISRIQVQTLHRNTQEFGITEFGMGHIRQGIVHVVGPENGATLPGMTIVCGDSHTSTHGALGALAHGI 148
                                           8899********************************************************************* PP

                             TIGR00170 145 gtsevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeerm 217
                                           gtsevehvlatq l+q+++k++ i+v+g+l++g+ akd++laiig ig+aggtgy +ef g+++rd+s+e+rm
  NCBI__GCF_000214825.1:WP_013835169.1 149 GTSEVEHVLATQCLIQKKNKNMLIRVDGQLQPGVGAKDVVLAIIGEIGTAGGTGYTIEFGGQVLRDMSIEGRM 221
                                           ************************************************************************* PP

                             TIGR00170 218 tvcnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtw 290
                                           ++cnm+ieaga+agl+a de t+eyvk+r+++p g++++ av++w+tl++dega+fdkvv+l+++ i pqv+w
  NCBI__GCF_000214825.1:WP_013835169.1 222 SICNMSIEAGARAGLVAVDEKTIEYVKGRPFSPTGAHWDAAVKHWQTLHSDEGAHFDKVVVLDGSAIQPQVSW 294
                                           ************************************************************************* PP

                             TIGR00170 291 gtnpgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvk 363
                                           gt+p++v+ vn++vpdp+  adpv+ +s+ +al+y+gl +++++kdi++d vfigsctnsriedlraaa++v+
  NCBI__GCF_000214825.1:WP_013835169.1 295 GTSPEMVVGVNDNVPDPAIEADPVKSNSMRRALEYMGLSANIPIKDIQLDYVFIGSCTNSRIEDLRAAAAIVN 367
                                           ************************************************************************* PP

                             TIGR00170 364 gkkvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmnndvldeyercastsnrnfegr 436
                                           gkkva n+++alvvpgsglvk+qae+egldkif++agfewr++gcs+cl+mn d+l++ + castsnrnfegr
  NCBI__GCF_000214825.1:WP_013835169.1 368 GKKVAANIEQALVVPGSGLVKQQAEAEGLDKIFMDAGFEWRNPGCSMCLAMNADRLPAKKHCASTSNRNFEGR 440
                                           ************************************************************************* PP

                             TIGR00170 437 qgkgarthlvspamaaaaavagkfvdirel 466
                                           qg+g+rthlvsp maaaaavag+fvd+rel
  NCBI__GCF_000214825.1:WP_013835169.1 441 QGAGGRTHLVSPIMAAAAAVAGRFVDVREL 470
                                           ****************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (471 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: 00:00:00.01
# Mc/sec: 14.75
//
[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 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