Aligments for a candidate for leuB in Shewanella sp. ANA-3

GapMind for Amino acid biosynthesis

Aligments for a candidate for leuB in Shewanella sp. ANA-3

Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate 7026627 Shewana3_3760 3-isopropylmalate dehydrogenase (RefSeq)

Query= BRENDA::Q8E9N3
         (364 letters)



>lcl|FitnessBrowser__ANA3:7026627 Shewana3_3760 3-isopropylmalate
           dehydrogenase (RefSeq)
          Length = 364

 Score =  711 bits (1834), Expect = 0.0
 Identities = 358/364 (98%), Positives = 364/364 (100%)

Query: 1   MSYQIAVLAGDGIGPEVMAEARKVLKAVEARFGLNIEYTEYDVGGIAIDNHGCPLPEATL 60
           MSYQIAVLAGDGIGPEVMAEARKVLKAVEARFGLNIEY+EYDVGGIAIDNHGCPLPEATL
Sbjct: 1   MSYQIAVLAGDGIGPEVMAEARKVLKAVEARFGLNIEYSEYDVGGIAIDNHGCPLPEATL 60

Query: 61  KGCEAADAILFGSVGGPKWEKLPPNEQPERGALLPLRGHFELFCNLRPAKLHDGLEHMSP 120
           KGCEAADAILFGSVGGPKWEKLPPNEQPERGALLPLRGHFELFCNLRPAKLHDGLEHMSP
Sbjct: 61  KGCEAADAILFGSVGGPKWEKLPPNEQPERGALLPLRGHFELFCNLRPAKLHDGLEHMSP 120

Query: 121 LRSDISARGFDVLCVRELTGGIYFGKPKGRQGEGESEEAFDTMRYSRREISRIARIAFEA 180
           LRSDISARGFDVLCVRELTGGIYFGKPKGRQGEGESEEAFDTMRYSRREI+RIARIAFEA
Sbjct: 121 LRSDISARGFDVLCVRELTGGIYFGKPKGRQGEGESEEAFDTMRYSRREIARIARIAFEA 180

Query: 181 ARGRRKKVTSVDKANVLACSVLWRQVVEEVAVDFPDVELEHIYIDNATMQLLRRPDEFDV 240
           ARGRRKKVTSVDKANVLACSVLWRQVVEEVAVDFPDVELEHIYIDNATMQLLRRPDEFDV
Sbjct: 181 ARGRRKKVTSVDKANVLACSVLWRQVVEEVAVDFPDVELEHIYIDNATMQLLRRPDEFDV 240

Query: 241 MLCSNLFGDILSDEIAMLTGSMGLLSSASMNSTGFGLFEPAGGSAPDIAGKGIANPIAQI 300
           MLCSNLFGDILSDEIAMLTGSMGLLSSASMNSTGFGLFEPAGGSAPDIAGKGIANPIAQI
Sbjct: 241 MLCSNLFGDILSDEIAMLTGSMGLLSSASMNSTGFGLFEPAGGSAPDIAGKGIANPIAQI 300

Query: 301 LSAALMLRHSLKQEEAASAIERAVTKALNSGYLTGELLSSDQRHKAKTTVQMGDFIADAV 360
           LSAALMLRHSLKQEEAASAIERAV+KALNSGYLTGELLSSDQRHKAK+TV+MG+FIADAV
Sbjct: 301 LSAALMLRHSLKQEEAASAIERAVSKALNSGYLTGELLSSDQRHKAKSTVEMGNFIADAV 360

Query: 361 KAGV 364
           KAGV
Sbjct: 361 KAGV 364


Lambda     K      H
   0.318    0.136    0.393 

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: 572
Number of extensions: 15
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: 364
Length of database: 364
Length adjustment: 29
Effective length of query: 335
Effective length of database: 335
Effective search space:   112225
Effective search space used:   112225
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate 7026627 Shewana3_3760 (3-isopropylmalate dehydrogenase (RefSeq))
to HMM TIGR00169 (leuB: 3-isopropylmalate dehydrogenase (EC 1.1.1.85))

# 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/TIGR00169.hmm
# target sequence database:        /tmp/gapView.22952.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00169  [M=349]
Accession:   TIGR00169
Description: leuB: 3-isopropylmalate dehydrogenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.2e-162  526.0   0.0   2.4e-162  525.8   0.0    1.0  1  lcl|FitnessBrowser__ANA3:7026627  Shewana3_3760 3-isopropylmalate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7026627  Shewana3_3760 3-isopropylmalate dehydrogenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  525.8   0.0  2.4e-162  2.4e-162       1     342 [.       4     347 ..       4     356 .. 0.97

  Alignments for each domain:
  == domain 1  score: 525.8 bits;  conditional E-value: 2.4e-162
                         TIGR00169   1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlgavGGpkWd 77 
                                       +iavL+GDgiGpev+aea kvLkave rf+l++e++e+++GG aid++g Plpe+tlk+c++ada+L+g+vGGpkW+
  lcl|FitnessBrowser__ANA3:7026627   4 QIAVLAGDGIGPEVMAEARKVLKAVEARFGLNIEYSEYDVGGIAIDNHGCPLPEATLKGCEAADAILFGSVGGPKWE 80 
                                       69*************************************************************************** PP

                         TIGR00169  78 nlprdvrPek.gLLklrkeldlfanLrPaklfksLeklsplkeeiv.kgvDlvvvreLtgGiYfGepkereeaeeek 152
                                       +lp++ +Pe+ +LL+lr +++lf+nLrPakl+++Le++spl+++i  +g+D+++vreLtgGiYfG+pk+r++++e++
  lcl|FitnessBrowser__ANA3:7026627  81 KLPPNEQPERgALLPLRGHFELFCNLRPAKLHDGLEHMSPLRSDISaRGFDVLCVRELTGGIYFGKPKGRQGEGESE 157
                                       **********88*********************************77****************************** PP

                         TIGR00169 153 kaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiakeyPdvelehlyiDnaamqLvks 229
                                       +a+dt++Y+++ei riar+afe+ar rrkkvtsvDkanvL+ s lWr++vee+a ++Pdveleh+yiDna+mqL+++
  lcl|FitnessBrowser__ANA3:7026627 158 EAFDTMRYSRREIARIARIAFEAARGRRKKVTSVDKANVLACSVLWRQVVEEVAVDFPDVELEHIYIDNATMQLLRR 234
                                       ***************************************************************************** PP

                         TIGR00169 230 PeqldvvvtsnlfGDilsDeasvitGslGlLPsaslsskglalfepvhgsapdiagkgianpiaailsaalllrysl 306
                                       P+++dv+++snlfGDilsDe +++tGs+GlL sas++s+g++lfep++gsapdiagkgianpia+ilsaal+lr+sl
  lcl|FitnessBrowser__ANA3:7026627 235 PDEFDVMLCSNLFGDILSDEIAMLTGSMGLLSSASMNSTGFGLFEPAGGSAPDIAGKGIANPIAQILSAALMLRHSL 311
                                       ***************************************************************************** PP

                         TIGR00169 307 nleeaaeaieaavkkvleegkrtedlaseattavst 342
                                       ++eeaa+aie+av+k+l++g+ t +l s++  + ++
  lcl|FitnessBrowser__ANA3:7026627 312 KQEEAASAIERAVSKALNSGYLTGELLSSDQRHKAK 347
                                       ************************999887544433 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (364 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 7.89
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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