GapMind for Amino acid biosynthesis

 

Alignments 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)



>FitnessBrowser__ANA3:7026627
          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.28955.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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 11.88
//
[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:

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:

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:

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:

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