Alignments for a candidate for ech in Pseudomonas benzenivorans DSM 8628

GapMind for catabolism of small carbon sources

Alignments for a candidate for ech in Pseudomonas benzenivorans DSM 8628

Align fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized)
to candidate WP_090447062.1 BLS63_RS17605 3-hydroxyacyl-CoA dehydrogenase

Query= CharProtDB::CH_003230
         (714 letters)



>NCBI__GCF_900100495.1:WP_090447062.1
          Length = 714

 Score =  392 bits (1006), Expect = e-113
 Identities = 269/721 (37%), Positives = 378/721 (52%), Gaps = 25/721 (3%)

Query: 3   MTSAFTLNVRLDNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKE-LRGVVFVSAK 61
           MT A       D I V+TID+PG+  NT+ A++   +  ++++L   K+ + GV+  SAK
Sbjct: 1   MTDAIRYEKGQDAIVVLTIDMPGQSANTMNAQYREAMGQVVERLEAEKDSIAGVIVTSAK 60

Query: 62  PDNFIAGADINMIGNCKTAQEAEALARQGQQLMAEIHALPI---QVIAAIHGACLGGGLE 118
              F AG D+N +     A +A+A  R   ++  ++  L      V+AAI+GA LGGG E
Sbjct: 61  K-TFFAGGDLNELIKVSKA-DADAFYRMILKIKGQLRRLECLGKPVVAAINGAALGGGWE 118

Query: 119 LALACHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQLRAKQ 178
           + LACH R+  D     LGLPEV LGLLPG GG  R+ RL+G+  AL  +  GK++R + 
Sbjct: 119 ICLACHHRIALDSSSVQLGLPEVTLGLLPGGGGVVRMVRLLGLEKALPYLAEGKKVRPEA 178

Query: 179 ALKLGLVDDVVPHS--ILLEAAVELAKKERPSSRPLPVRERILAGPLGRALLFKMVG--- 233
           ALK GL+D++      +L +A   +A    P         +I  G      + +M+    
Sbjct: 179 ALKAGLIDELASDKDDLLAKARAWIAANPAPRQPWDLPGYKIPGGTPSSPNVAQMLAIAP 238

Query: 234 KKTEHKTQGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQALRSIFFAST 293
                KT+G +PA E+IL     G      +    EAR F EL     ++ +   F+   
Sbjct: 239 SVLRDKTKGCFPAPEKILCAAVEGAQVDFDTAQLIEARYFTELTTGQVAKNMIGTFWFQL 298

Query: 294 DVKKDPGSDAP---PAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGINHALK 350
           +     GS      P     VG+LG G+MG GIAYV+A  AGI V +KDI+ +       
Sbjct: 299 NEINAGGSRPQGFAPYLTKKVGVLGAGMMGAGIAYVSAL-AGIEVVLKDISLEAAEKGKS 357

Query: 351 YSWDQLEGKVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLELKQQMVAEV 410
           YS   LE KV R  + A +RD  LA I+ T     FA  DLIIEAVFE+ +LK  + A  
Sbjct: 358 YSAKLLEKKVGRGQMSAEKRDAILARIATTDKDADFAGCDLIIEAVFEDRDLKANVTAAA 417

Query: 411 EQNCAAHTIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTSAQTI 470
           E+   A  + ASNTS+LPI  +A    + ++ IGLHFFSPV+KMPLVEII    TS +T+
Sbjct: 418 ERAALAEAVIASNTSTLPITGLANAVQKQDRFIGLHFFSPVDKMPLVEIIRGERTSDETL 477

Query: 471 ATTVKLAKKQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVKFGFPV 530
           A       +  KTPIVV D  GF+ +R+   + NE I ML +G     I+    K G PV
Sbjct: 478 ARGFDYVMQIKKTPIVVNDSRGFFTSRVFGTFTNEGIAMLGEGVSAALIENEARKAGMPV 537

Query: 531 GPIQLLDEVGIDTGTKI-IPVLEAAYGERFSAPAN----VVSSILND-DRKGRKNGRGFY 584
           GP+ + DEV +     I    L+    E  S P +    V+ S+L +  R G+  G GFY
Sbjct: 538 GPLAISDEVSLSLMQHIRQQTLKDLAEEGKSLPEHPAFAVIESMLGEYKRPGKAAGGGFY 597

Query: 585 LYGQKGRKSKKQVDPAIYPLIGTQGQGRISAPQVAERCVMLMLNEAVRCVDEQVIRSVRD 644
            Y   G   KK + P +      +   +I    V +R + +   E VRCV+E V+ S  D
Sbjct: 598 EYPAGG---KKYLWPELKSRF-EKADRQIPQEDVRDRILFIQAIETVRCVEEGVLNSTAD 653

Query: 645 GDIGAVFGIGFPPFLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVEMGARGES 704
            +IG++FGIGF  + GG  ++I+  G  + VA  Q LA QYG RF P   L+E  A+GES
Sbjct: 654 ANIGSIFGIGFAAWTGGALQFINQYGIQDFVARAQYLAEQYGERFLPPALLLEKAAKGES 713

Query: 705 F 705
           F
Sbjct: 714 F 714


Lambda     K      H
   0.319    0.137    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: 1020
Number of extensions: 38
Number of successful extensions: 7
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: 714
Length of database: 714
Length adjustment: 39
Effective length of query: 675
Effective length of database: 675
Effective search space:   455625
Effective search space used:   455625
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 (21.8 bits)
S2: 55 (25.8 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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

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 catabolism of small carbon sources