Alignments for a candidate for leuC in Shewanella amazonensis SB2B

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Shewanella amazonensis SB2B

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate 6936140 Sama_0337 isopropylmalate isomerase large subunit (RefSeq)

Query= CharProtDB::CH_024771
         (466 letters)



>FitnessBrowser__SB2B:6936140
          Length = 470

 Score =  696 bits (1797), Expect = 0.0
 Identities = 342/463 (73%), Positives = 389/463 (84%)

Query: 1   MAKTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFAT 60
           MAKTLYEK++DAH+V E   E P++Y+DRHLVHEVTSPQAF GL+  GRP+R   KTFAT
Sbjct: 1   MAKTLYEKVWDAHLVVEPAGEAPIIYVDRHLVHEVTSPQAFSGLKMAGRPLRAVEKTFAT 60

Query: 61  MDHNVSTQTKDINACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTLP 120
           MDHN ST++  + A   MAR Q++ L  NC++F V LYD++HP QGIVHVMGPE G+TLP
Sbjct: 61  MDHNTSTKSASLTALSPMARTQVETLADNCRDFNVRLYDIHHPNQGIVHVMGPELGITLP 120

Query: 121 GMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGITA 180
           G  IVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTL+Q +AKTMKIEV+GK A GITA
Sbjct: 121 GTVIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLRQLKAKTMKIEVRGKVADGITA 180

Query: 181 KDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETTF 240
           KDIVLAIIGK G  GGTG+VVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAG+VAPDETTF
Sbjct: 181 KDIVLAIIGKIGMDGGTGYVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGMVAPDETTF 240

Query: 241 NYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVISV 300
            Y++GR  APKG  +  A+A W+ L TD  A FD  V L+A  I+PQ+TWGTNPGQV+++
Sbjct: 241 AYLEGREFAPKGDAWQQALADWRELHTDADAVFDAEVVLEAAAIAPQLTWGTNPGQVVAI 300

Query: 301 NDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAAE 360
           +  +P+PA   +PV R S EKALAY+ L PG P+T++AI+KVFIGSCTNSRIEDLRAAA 
Sbjct: 301 DGVVPNPADETNPVVRTSMEKALAYVDLTPGTPMTDIAINKVFIGSCTNSRIEDLRAAAA 360

Query: 361 IAKGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLNP 420
            AKGRKVA GV A+VVPGSG VK QAEAEGLDKIF+EAGFEWRLPGCSMCLAMN+DRL  
Sbjct: 361 QAKGRKVASGVTAIVVPGSGQVKLQAEAEGLDKIFLEAGFEWRLPGCSMCLAMNDDRLEA 420

Query: 421 GERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIR 463
           G+RCASTSNRNFEGRQGRG RTHLVSPAMAAAAAV GHF DIR
Sbjct: 421 GDRCASTSNRNFEGRQGRGSRTHLVSPAMAAAAAVAGHFVDIR 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: 796
Number of extensions: 21
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: 466
Length of database: 470
Length adjustment: 33
Effective length of query: 433
Effective length of database: 437
Effective search space:   189221
Effective search space used:   189221
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 6936140 Sama_0337 (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.10645.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
     6e-253  825.4   1.8   6.8e-253  825.2   1.8    1.0  1  lcl|FitnessBrowser__SB2B:6936140  Sama_0337 isopropylmalate isomer


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6936140  Sama_0337 isopropylmalate isomerase large subunit (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  825.2   1.8  6.8e-253  6.8e-253       1     464 [.       1     463 [.       1     465 [. 1.00

  Alignments for each domain:
  == domain 1  score: 825.2 bits;  conditional E-value: 6.8e-253
                         TIGR00170   1 maktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesrdveikee 77 
                                       maktlyek++dah+v e  +e++++y+drhlvhevtspqaf gl+ agr++r v+kt+at+dhn st+s  ++++  
  lcl|FitnessBrowser__SB2B:6936140   1 MAKTLYEKVWDAHLVVEPAGEAPIIYVDRHLVHEVTSPQAFSGLKMAGRPLRAVEKTFATMDHNTSTKSASLTALSP 77 
                                       89*************************************************************************** PP

                         TIGR00170  78 kaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalafgigtsevehvla 154
                                       +a+ qv++l  n+++f v+l+d+++ +qgivhv+gpe g+tlpg+ ivcgdshtathgafgalafgigtsevehvla
  lcl|FitnessBrowser__SB2B:6936140  78 MARTQVETLADNCRDFNVRLYDIHHPNQGIVHVMGPELGITLPGTVIVCGDSHTATHGAFGALAFGIGTSEVEHVLA 154
                                       ***************************************************************************** PP

                         TIGR00170 155 tqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeermtvcnmaieagakag 231
                                       tqtl+q +akt+kiev+gk+a+gitakdi+laiigkig+ ggtgyvvef+geairdlsme+rmt+cnmaie+gakag
  lcl|FitnessBrowser__SB2B:6936140 155 TQTLRQLKAKTMKIEVRGKVADGITAKDIVLAIIGKIGMDGGTGYVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAG 231
                                       ***************************************************************************** PP

                         TIGR00170 232 liapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtwgtnpgqvlsvneevpdpk 308
                                       ++apdettf+y+ +r++apkg+ +++a+a w+ l+td +a+fd +v+lea  i+pq+twgtnpgqv+++++ vp+p+
  lcl|FitnessBrowser__SB2B:6936140 232 MVAPDETTFAYLEGREFAPKGDAWQQALADWRELHTDADAVFDAEVVLEAAAIAPQLTWGTNPGQVVAIDGVVPNPA 308
                                       ***************************************************************************** PP

                         TIGR00170 309 sladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvkgkkvadnvklalvvpgsglvkk 385
                                       + ++pv ++s+ekalay+ l+pgt+++di+++kvfigsctnsriedlraaa+ +kg+kva++v  a+vvpgsg+vk 
  lcl|FitnessBrowser__SB2B:6936140 309 DETNPVVRTSMEKALAYVDLTPGTPMTDIAINKVFIGSCTNSRIEDLRAAAAQAKGRKVASGVT-AIVVPGSGQVKL 384
                                       ***************************************************************9.************ PP

                         TIGR00170 386 qaekegldkifleagfewreagcslclgmnndvldeyercastsnrnfegrqgkgarthlvspamaaaaavagkfvd 462
                                       qae+egldkifleagfewr +gcs+cl+mn+d+l++++rcastsnrnfegrqg+g+rthlvspamaaaaavag+fvd
  lcl|FitnessBrowser__SB2B:6936140 385 QAEAEGLDKIFLEAGFEWRLPGCSMCLAMNDDRLEAGDRCASTSNRNFEGRQGRGSRTHLVSPAMAAAAAVAGHFVD 461
                                       ***************************************************************************** PP

                         TIGR00170 463 ir 464
                                       ir
  lcl|FitnessBrowser__SB2B:6936140 462 IR 463
                                       *9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (470 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: 00:00:00.03
# Mc/sec: 6.82
//
[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