GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Pseudomonas putida KT2440

Align Glutaryl-CoA dehydrogenase, mitochondrial; GCD; EC 1.3.8.6 (characterized)
to candidate PP_3492 PP_3492 short-chain acyl-CoA dehydrogenase

Query= SwissProt::P81140
         (408 letters)



>FitnessBrowser__Putida:PP_3492
          Length = 383

 Score =  176 bits (445), Expect = 1e-48
 Identities = 116/377 (30%), Positives = 186/377 (49%), Gaps = 9/377 (2%)

Query: 28  QLTADEILIRDTFRTYCQEHLMPRIVLANRNEVFHREIISEMGELGVLGPTI-KGYGCAG 86
           +L+ ++I+IRD  R + +  + P      +       ++ +MGELG+LG  + + +G + 
Sbjct: 5   ELSEEQIMIRDMARDFARGEIAPHAQAWEKAGWIDDGVVRKMGELGLLGMVVPEDFGGSY 64

Query: 87  VSSVAYGLLARELERVDSGYRSAMSVQSSLVMHPIYAYGSEEQQQQKYLPRLAKGELLGC 146
              VAY L   E+        + MS+ +S+   P+ AYG+ EQQQQ +LPRLA GE++GC
Sbjct: 65  TDYVAYALAVEEISAGCGATGAMMSIHNSVGCGPLLAYGTAEQQQQ-WLPRLASGEVIGC 123

Query: 147 FGLTEPNHGSDPGSMETRALHNPSNRSYTLNGAKTWITNSPVADLFVVWARCEDNC---- 202
           F LTEP  GS+  ++ TRA     +  + +NGAK +++N+  A L +V+A  +       
Sbjct: 124 FCLTEPQAGSEAHNLRTRA--ELVDGQWVINGAKQFVSNARRAGLAIVFAVTDPELGKKG 181

Query: 203 IRGFLLEKGMRGLSAPKIEGKFSLRASATGMIIMDDVEVPEENVL-PKASSLAVPFGCLN 261
           +  FL+     G    + E K  +RAS T  +  D+  +P  N+L  +   LA+    L 
Sbjct: 182 LSAFLVPTDNPGFKVDRSEHKMGIRASDTCAVTFDNCRIPAANILGERGKGLAIALSNLE 241

Query: 262 NARYGISWGVLGAAEFCLHTARQYTLDRIQFGVPLAKNQLIQRKLADMLTEITLGLHACL 321
             R GI+   LG A      A  Y+ DRIQFG P+ ++Q I   LADM  ++       L
Sbjct: 242 GGRIGIAAQALGIARAAFEAALVYSRDRIQFGKPINEHQSIANLLADMQVQVNAARLLIL 301

Query: 322 QLGRLKDQDKVTPEMVSLLKRNNCGKALDIARQARDMLGGNGISDEYHVIRHAMNLEAVN 381
              RL+   K      S  K      A  +   A  + GG G  ++Y V R+  +     
Sbjct: 302 HAARLRSAGKPCLSEASQAKLFASEMAERVCSMAIQVHGGYGYLEDYPVERYYRDARITQ 361

Query: 382 TYEGTHDIHALILGRAI 398
            YEG+ +I  +++ R +
Sbjct: 362 IYEGSSEIQRMLIAREL 378


Lambda     K      H
   0.319    0.136    0.404 

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: 386
Number of extensions: 19
Number of successful extensions: 5
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: 408
Length of database: 383
Length adjustment: 31
Effective length of query: 377
Effective length of database: 352
Effective search space:   132704
Effective search space used:   132704
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: 50 (23.9 bits)

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

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