Alignments for a candidate for gcdH in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for gcdH in Phaeobacter inhibens BS107

Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate GFF1551 PGA1_c15710 acyl-CoA dehydrogenase

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



>FitnessBrowser__Phaeo:GFF1551
          Length = 406

 Score =  584 bits (1506), Expect = e-171
 Identities = 290/389 (74%), Positives = 325/389 (83%), Gaps = 2/389 (0%)

Query: 7   FNWIDPLLLDQQLTEEERMVRDSAYQFAQDKLAPRVLEAFRHEQTDPAIFREMGEVGLLG 66
           FNW DPL LD QL+E+ERM+  SA  +AQ+KL PRVL A+ +E+TDP IFREMGE+GLLG
Sbjct: 18  FNWDDPLRLDDQLSEDERMIAASARSYAQEKLQPRVLNAYENEETDPEIFREMGEMGLLG 77

Query: 67  ATIPEQYGGSGLNYVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQKQKYLP 126
            TIPEQYGG G  YV YGL+AREVER+DSGYRSMMSVQSSLVM PI  +G+E Q+QKYLP
Sbjct: 78  TTIPEQYGGLGAGYVSYGLVAREVERVDSGYRSMMSVQSSLVMYPIYAYGSEEQRQKYLP 137

Query: 127 KLASGEWIGCFGLTEPNHGSDPGSMITRARKVDGGYRLTGSKMWITNSPIADVFVVWAKD 186
           KL+SGEWIGCFGLTEP+ GSDP  M TRA K DGGYRLTGSKMWI+N+PIADVFVVWAK 
Sbjct: 138 KLSSGEWIGCFGLTEPDAGSDPAGMKTRAEKTDGGYRLTGSKMWISNAPIADVFVVWAKS 197

Query: 187 DA--GDIRGFVLEKGWQGLSAPAIHGKVGLRASITGEIVMDNVFVPEENIFPDVRGLKGP 244
           +A  G IRGFVLEKG +GLSAP I  K  LRASITGEIVMD V V ++ + P V GLKGP
Sbjct: 198 EAHGGKIRGFVLEKGMKGLSAPKIANKASLRASITGEIVMDGVEVGDDALLPHVEGLKGP 257

Query: 245 FTCLNSARYGISWGALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTEITLA 304
           F CLN ARYGISWGA+GAAEACWH ARQY LDR+QFGRPLA  QL Q KLA+MQTEITL 
Sbjct: 258 FGCLNRARYGISWGAMGAAEACWHAARQYGLDRKQFGRPLANTQLFQLKLANMQTEITLG 317

Query: 305 LQGCLRLGRMKDEGTAAVEITSIMKRNSCGKALDIARMARDMLGGNGISDEFGVARHLVN 364
           LQ  LR+GR+ DE  AA E+ SI+KRN+CGKAL+IAR ARDM GGNGIS EFGV RH+VN
Sbjct: 318 LQASLRVGRLMDEANAAPEMISIVKRNNCGKALEIARHARDMHGGNGISLEFGVIRHMVN 377

Query: 365 LEVVNTYEGTHDVHALILGRAQTGIQAFY 393
           LE VNTYEGTHDVHALILGRAQTG+QAF+
Sbjct: 378 LETVNTYEGTHDVHALILGRAQTGLQAFF 406


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: 574
Number of extensions: 19
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: 406
Length adjustment: 31
Effective length of query: 362
Effective length of database: 375
Effective search space:   135750
Effective search space used:   135750
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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, or view the source code.

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