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

GapMind for Amino acid biosynthesis

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

Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate 5211055 Shew_3471 3-isopropylmalate dehydrogenase (RefSeq)

Query= BRENDA::D2YZL2
         (364 letters)



>FitnessBrowser__PV4:5211055
          Length = 364

 Score =  647 bits (1669), Expect = 0.0
 Identities = 318/362 (87%), Positives = 343/362 (94%)

Query: 1   MSYQIAVLAGDGIGPEVMAEARKVLAAVEKRFDLSIEYSEYDVGGAAIDNHGCPLPEATL 60
           MSYQ+AVLAGDGIGPEVMAEARKVL AVE+RF L IEYSEYDVGGAAID+HGCPLPE+TL
Sbjct: 1   MSYQVAVLAGDGIGPEVMAEARKVLKAVEERFSLDIEYSEYDVGGAAIDHHGCPLPESTL 60

Query: 61  KGCEAADAVLFGSVGGPKWEHLPPNDQPERGALLPLRGHFELFCNMRPAKLHPGLEHMSP 120
           KGCE ADA+LFGSVGGPKWEHLPPNDQPERGALLPLRGHFELFCNMRPAKLH GLEHMSP
Sbjct: 61  KGCEEADAILFGSVGGPKWEHLPPNDQPERGALLPLRGHFELFCNMRPAKLHVGLEHMSP 120

Query: 121 LRSDISEKGFDILCVRELTGGIYFGKPKGRQGEGENEEAFDTMRYSRKEIRRIAKIAFES 180
           LRSDIS +GFD+LCVRELTGGIYFGKPKGRQGEGE EEAFDTMRYSR+E+RRIAKIAFE+
Sbjct: 121 LRSDISAQGFDVLCVRELTGGIYFGKPKGRQGEGEQEEAFDTMRYSRREVRRIAKIAFEA 180

Query: 181 AQGRRKKVTSVDKANVLACSVLWREVVEEVAKDYPDVELEHIYIDNATMQLLRRPNEFDV 240
           A+GRRKKVTSVDKANVLACSVLWREVVEEVAK++PDV LEHIYIDNATMQLLRRP +FDV
Sbjct: 181 ARGRRKKVTSVDKANVLACSVLWREVVEEVAKEFPDVALEHIYIDNATMQLLRRPFDFDV 240

Query: 241 MLCSNLFGDIVSDEIAMLTGSMGLLASISMNSQGFGMYEPAGGSAPDIAGQGIANPVAQI 300
           MLCSNLFGDI+SDEIAMLTGSMGLL+S+S+NS GFG+YEPAGGSAPDIAGQGIANP+AQI
Sbjct: 241 MLCSNLFGDIISDEIAMLTGSMGLLSSVSLNSDGFGLYEPAGGSAPDIAGQGIANPIAQI 300

Query: 301 LSAALLLRHSLKLEDAALAIEAAVSKALSDGYLTCELLPASERSQAKSTSQMGDYIAQAI 360
           LSAALLLRHSLK E AA AIE AV+KALSDGYLT ELLPA +R +AKST +MGDYIAQA+
Sbjct: 301 LSAALLLRHSLKEEAAAKAIEDAVAKALSDGYLTGELLPADQRDKAKSTREMGDYIAQAV 360

Query: 361 AE 362
            E
Sbjct: 361 RE 362


Lambda     K      H
   0.317    0.135    0.390 

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: 609
Number of extensions: 17
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 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate 5211055 Shew_3471 (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.8007.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   1.9e-160  519.6   0.0   2.1e-160  519.4   0.0    1.0  1  lcl|FitnessBrowser__PV4:5211055  Shew_3471 3-isopropylmalate dehy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5211055  Shew_3471 3-isopropylmalate dehydrogenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  519.4   0.0  2.1e-160  2.1e-160       1     347 [.       4     354 ..       4     356 .. 0.97

  Alignments for each domain:
  == domain 1  score: 519.4 bits;  conditional E-value: 2.1e-160
                        TIGR00169   1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlgavGGpkWdn 78 
                                      ++avL+GDgiGpev+aea kvLkaveerf l++e++e+++GGaaid++g Plpe tlk+c+eada+L+g+vGGpkW++
  lcl|FitnessBrowser__PV4:5211055   4 QVAVLAGDGIGPEVMAEARKVLKAVEERFSLDIEYSEYDVGGAAIDHHGCPLPESTLKGCEEADAILFGSVGGPKWEH 81 
                                      59**************************************************************************** PP

                        TIGR00169  79 lprdvrPek.gLLklrkeldlfanLrPaklfksLeklsplkeeiv.kgvDlvvvreLtgGiYfGepkereeaeeekka 154
                                      lp++ +Pe+ +LL+lr +++lf+n+rPakl+ +Le++spl+++i  +g+D+++vreLtgGiYfG+pk+r++++e+++a
  lcl|FitnessBrowser__PV4:5211055  82 LPPNDQPERgALLPLRGHFELFCNMRPAKLHVGLEHMSPLRSDISaQGFDVLCVRELTGGIYFGKPKGRQGEGEQEEA 159
                                      *********88*********************************77******************************** PP

                        TIGR00169 155 ldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiakeyPdvelehlyiDnaamqLvksPeq 232
                                      +dt++Y+++e++ria++afe+ar rrkkvtsvDkanvL+ s lWr++vee+ake+Pdv+leh+yiDna+mqL+++P  
  lcl|FitnessBrowser__PV4:5211055 160 FDTMRYSRREVRRIAKIAFEAARGRRKKVTSVDKANVLACSVLWREVVEEVAKEFPDVALEHIYIDNATMQLLRRPFD 237
                                      ****************************************************************************** PP

                        TIGR00169 233 ldvvvtsnlfGDilsDeasvitGslGlLPsaslsskglalfepvhgsapdiagkgianpiaailsaalllryslnlee 310
                                      +dv+++snlfGDi+sDe +++tGs+GlL s sl+s+g++l+ep++gsapdiag+gianpia+ilsaalllr+sl+ e 
  lcl|FitnessBrowser__PV4:5211055 238 FDVMLCSNLFGDIISDEIAMLTGSMGLLSSVSLNSDGFGLYEPAGGSAPDIAGQGIANPIAQILSAALLLRHSLKEEA 315
                                      ****************************************************************************** PP

                        TIGR00169 311 aaeaieaavkkvleegkrtedla..seattavstkevee 347
                                      aa+aie+av+k+l++g+ t +l   ++  +a st+e+++
  lcl|FitnessBrowser__PV4:5211055 316 AAKAIEDAVAKALSDGYLTGELLpaDQRDKAKSTREMGD 354
                                      ******************999861144456667777766 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 10.57
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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