Alignments for a candidate for leuC in Shewanella loihica PV-4

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Shewanella loihica PV-4

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate 5211054 Shew_3470 isopropylmalate isomerase large subunit (RefSeq)

Query= CharProtDB::CH_024771
         (466 letters)



>FitnessBrowser__PV4:5211054
          Length = 466

 Score =  683 bits (1762), Expect = 0.0
 Identities = 332/463 (71%), Positives = 390/463 (84%)

Query: 1   MAKTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFAT 60
           MAKTLYEK++D+H+V   E E PL+Y+DRHLVHEVTSPQAF GL+  GR +R P KTFAT
Sbjct: 1   MAKTLYEKVWDSHIVAAPEGEAPLIYVDRHLVHEVTSPQAFSGLKVAGRKLRAPEKTFAT 60

Query: 61  MDHNVSTQTKDINACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTLP 120
           MDHN ST++  ++A   MAR Q++ L +NCKEFGV LYD++H  QGIVHVMGPE G+TLP
Sbjct: 61  MDHNTSTKSASLDALSPMARTQVETLAQNCKEFGVRLYDIHHKNQGIVHVMGPELGITLP 120

Query: 121 GMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGITA 180
           G  IVCGDSHTATHGAFGALAFGIGTSEVEHV+ATQTL+Q +AKTMKIEV+G  A GITA
Sbjct: 121 GTVIVCGDSHTATHGAFGALAFGIGTSEVEHVMATQTLRQLKAKTMKIEVRGLVADGITA 180

Query: 181 KDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETTF 240
           KDIVLAIIGK G  GGTG+VVEFCGEAI  LSMEGRMT+CNMAIEMGAKAG++APD+TT 
Sbjct: 181 KDIVLAIIGKIGMDGGTGYVVEFCGEAIAALSMEGRMTVCNMAIEMGAKAGMIAPDQTTI 240

Query: 241 NYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVISV 300
           +Y++GR  APKG+ +  AVA WK L++DE A FD  V L+A +I+PQ+TWGTNPGQV+++
Sbjct: 241 DYLEGREFAPKGEAWQQAVAAWKALKSDEDAMFDAHVVLEASDIAPQLTWGTNPGQVVAI 300

Query: 301 NDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAAE 360
           +  +P+P    +P  +AS EKAL Y+ L PG  +T+V+I+KVFIGSCTNSRIEDLR+AA+
Sbjct: 301 DQCVPNPEDETNPTVKASIEKALDYVALTPGTQMTDVSINKVFIGSCTNSRIEDLRSAAQ 360

Query: 361 IAKGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLNP 420
            AKGRKVA GV A+VVPGSG VK QAEAEGLDKIFI+AGFEWRLPGCSMCLAMN+DRL  
Sbjct: 361 QAKGRKVAAGVTAIVVPGSGLVKEQAEAEGLDKIFIDAGFEWRLPGCSMCLAMNDDRLEA 420

Query: 421 GERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIR 463
           G+RCASTSNRNFEGRQGRG RTHLVSPAMAAAAA+ GHF DIR
Sbjct: 421 GDRCASTSNRNFEGRQGRGSRTHLVSPAMAAAAAIAGHFVDIR 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: 783
Number of extensions: 19
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: 466
Length adjustment: 33
Effective length of query: 433
Effective length of database: 433
Effective search space:   187489
Effective search space used:   187489
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 5211054 Shew_3470 (isopropylmalate isomerase large subunit (RefSeq))
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.11230.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-255  833.2   3.3   2.9e-255  833.0   3.3    1.0  1  lcl|FitnessBrowser__PV4:5211054  Shew_3470 isopropylmalate isomer


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5211054  Shew_3470 isopropylmalate isomerase large subunit (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  833.0   3.3  2.9e-255  2.9e-255       1     465 [.       1     464 [.       1     465 [. 1.00

  Alignments for each domain:
  == domain 1  score: 833.0 bits;  conditional E-value: 2.9e-255
                        TIGR00170   1 maktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesrdveikeek 78 
                                      maktlyek++d+h+v   e+e++l+y+drhlvhevtspqaf gl++agrk+r ++kt+at+dhn st+s  ++++  +
  lcl|FitnessBrowser__PV4:5211054   1 MAKTLYEKVWDSHIVAAPEGEAPLIYVDRHLVHEVTSPQAFSGLKVAGRKLRAPEKTFATMDHNTSTKSASLDALSPM 78 
                                      89**************************************************************************** PP

                        TIGR00170  79 aklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalafgigtsevehvlatq 156
                                      a+ qv++l +n+kefgv+l+d+++++qgivhv+gpe g+tlpg+ ivcgdshtathgafgalafgigtsevehv+atq
  lcl|FitnessBrowser__PV4:5211054  79 ARTQVETLAQNCKEFGVRLYDIHHKNQGIVHVMGPELGITLPGTVIVCGDSHTATHGAFGALAFGIGTSEVEHVMATQ 156
                                      ****************************************************************************** PP

                        TIGR00170 157 tlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeermtvcnmaieagakaglia 234
                                      tl+q +akt+kiev+g +a+gitakdi+laiigkig+ ggtgyvvef+geai +lsme+rmtvcnmaie+gakag+ia
  lcl|FitnessBrowser__PV4:5211054 157 TLRQLKAKTMKIEVRGLVADGITAKDIVLAIIGKIGMDGGTGYVVEFCGEAIAALSMEGRMTVCNMAIEMGAKAGMIA 234
                                      ****************************************************************************** PP

                        TIGR00170 235 pdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtwgtnpgqvlsvneevpdpkslad 312
                                      pd+tt++y+ +r++apkg+ +++ava wk+lk+de+a fd +v+lea+di+pq+twgtnpgqv+++++ vp+p++ ++
  lcl|FitnessBrowser__PV4:5211054 235 PDQTTIDYLEGREFAPKGEAWQQAVAAWKALKSDEDAMFDAHVVLEASDIAPQLTWGTNPGQVVAIDQCVPNPEDETN 312
                                      ****************************************************************************** PP

                        TIGR00170 313 pvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvkgkkvadnvklalvvpgsglvkkqaeke 390
                                      p  kas+ekal+y+ l+pgt+++d+ ++kvfigsctnsriedlr+aa+ +kg+kva +v  a+vvpgsglvk+qae+e
  lcl|FitnessBrowser__PV4:5211054 313 PTVKASIEKALDYVALTPGTQMTDVSINKVFIGSCTNSRIEDLRSAAQQAKGRKVAAGVT-AIVVPGSGLVKEQAEAE 389
                                      ***********************************************************9.***************** PP

                        TIGR00170 391 gldkifleagfewreagcslclgmnndvldeyercastsnrnfegrqgkgarthlvspamaaaaavagkfvdire 465
                                      gldkif++agfewr +gcs+cl+mn+d+l++++rcastsnrnfegrqg+g+rthlvspamaaaaa+ag+fvdir+
  lcl|FitnessBrowser__PV4:5211054 390 GLDKIFIDAGFEWRLPGCSMCLAMNDDRLEAGDRCASTSNRNFEGRQGRGSRTHLVSPAMAAAAAIAGHFVDIRK 464
                                      *************************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (466 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: 7.77
//
[ok]

This GapMind analysis is from Apr 09 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