GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Pseudomonas fluorescens FW300-N2E2

Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate Pf6N2E2_1146 Butyryl-CoA dehydrogenase (EC 1.3.99.2)

Query= metacyc::G1G01-166-MONOMER
         (393 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1146
          Length = 375

 Score =  211 bits (538), Expect = 2e-59
 Identities = 129/370 (34%), Positives = 191/370 (51%), Gaps = 5/370 (1%)

Query: 20  TEEERMVRDSAYQFAQDKLAPRVLEAFRHEQTDPAIFREMGEVGLLGATIPEQYGGSGLN 79
           TEE+  +RD A QFA+++L P   E  R  +       EM E+G  G  +PEQ+GG    
Sbjct: 4   TEEQTQIRDMARQFAEERLKPFAAEWDREHRFPREAIDEMAELGFFGMLVPEQWGGCDTG 63

Query: 80  YVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQKQKYLPKLASGEWIGCFGL 139
           Y+ Y +   E+   D    ++MSV +S+  VPI +FG + QK K+L  LASG  +G F L
Sbjct: 64  YLAYAMTLEEIAAGDGACSTIMSVHNSVGCVPILKFGNDEQKAKFLTPLASGAMLGAFAL 123

Query: 140 TEPNHGSDPGSMITRARKVDGGYRLTGSKMWITNSPIADVFVVWAKDDAG----DIRGFV 195
           TEP  GSD  S+ TRAR     Y L G K +IT+   A V +V+A  D       I  F+
Sbjct: 124 TEPQAGSDASSLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFI 183

Query: 196 LEKGWQGLSAPAIHGKVGLRASITGEIVMDNVFVPEEN-IFPDVRGLKGPFTCLNSARYG 254
           +     G S   +  K+G  AS T +I+ +++ VP  N +  +  G K     L   R G
Sbjct: 184 VPTDSPGYSVARVEDKLGQHASDTCQILFEDLKVPVGNRLGEEGEGYKIALANLEGGRVG 243

Query: 255 ISWGALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTEITLALQGCLRLGRM 314
           I+  A+G A A +  AR Y  +R  FG+P+  +Q +  +LADM T+I +A Q       +
Sbjct: 244 IAAQAVGMARAAFEAARDYARERSSFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAAL 303

Query: 315 KDEGTAAVEITSIMKRNSCGKALDIARMARDMLGGNGISDEFGVARHLVNLEVVNTYEGT 374
           +D G  A+   S+ K  +   A  +  MA   LGG G  ++F + R   ++ V   YEGT
Sbjct: 304 RDSGQPALVEASMAKLFASEMAEKVCSMALQTLGGYGYLNDFPLERIYRDVRVCQIYEGT 363

Query: 375 HDVHALILGR 384
            D+  +++ R
Sbjct: 364 SDIQRMVISR 373


Lambda     K      H
   0.320    0.137    0.413 

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: 326
Number of extensions: 9
Number of successful extensions: 2
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: 393
Length of database: 375
Length adjustment: 30
Effective length of query: 363
Effective length of database: 345
Effective search space:   125235
Effective search space used:   125235
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