GapMind for catabolism of small carbon sources

 

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

Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate 5208388 Shew_0900 acyl-CoA dehydrogenase domain-containing protein (RefSeq)

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



>FitnessBrowser__PV4:5208388
          Length = 391

 Score =  559 bits (1441), Expect = e-164
 Identities = 276/391 (70%), Positives = 317/391 (81%), Gaps = 1/391 (0%)

Query: 2   VGKASFNWIDPLLLDQQLTEEERMVRDSAYQFAQDKLAPRVLEAFRHEQTDPAIFREMGE 61
           + +  F+W DPL  D  L+E+ERM+RD  + +AQ+KL  RVL A R+E  D  I  E+GE
Sbjct: 1   MARVKFDWQDPLQFDALLSEDERMIRDMVHDYAQEKLMTRVLMANRNEHFDREIMNELGE 60

Query: 62  VGLLGATIPEQYGGSGLNYVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQK 121
           +GLLGAT+PE YG +  NYV YGL+ARE+ER+DSGYRS MSVQSSLVM PI  +G E Q+
Sbjct: 61  LGLLGATLPEAYGCANANYVSYGLVAREIERVDSGYRSAMSVQSSLVMHPIYAYGNEQQR 120

Query: 122 QKYLPKLASGEWIGCFGLTEPNHGSDPGSMITRARKVDGGYRLTGSKMWITNSPIADVFV 181
           QKYLPKLA+GEW+GCFGLTEP+ GSDPG M TRA ++DGGYRL G+KMWITNSPIADVFV
Sbjct: 121 QKYLPKLATGEWVGCFGLTEPDVGSDPGGMKTRAERIDGGYRLNGAKMWITNSPIADVFV 180

Query: 182 VWAKDDAGDIRGFVLEKGWQGLSAPAIHGKVGLRASITGEIVMDNVFVPEENIFPDVRGL 241
           VWAK D G IRGF+LEKG +GLSAP I GK  LRASITGEIVMDNV V EE + P+V GL
Sbjct: 181 VWAKLD-GVIRGFILEKGMKGLSAPKIEGKFSLRASITGEIVMDNVEVGEEALLPNVEGL 239

Query: 242 KGPFTCLNSARYGISWGALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTEI 301
           KGPF CLN ARYGI+WGALGAAE CWH ARQY+LDR QF RPLAA QLIQKKLADMQTEI
Sbjct: 240 KGPFGCLNKARYGIAWGALGAAEFCWHAARQYSLDRIQFNRPLAATQLIQKKLADMQTEI 299

Query: 302 TLALQGCLRLGRMKDEGTAAVEITSIMKRNSCGKALDIARMARDMLGGNGISDEFGVARH 361
           T  L  CL+ GR+ D+    VE  S++KRNSCGKAL+IAR +RDM GGNGISDEF V RH
Sbjct: 300 TTGLFACLQAGRLMDQDALPVEAISLIKRNSCGKALEIARTSRDMHGGNGISDEFHVIRH 359

Query: 362 LVNLEVVNTYEGTHDVHALILGRAQTGIQAF 392
           ++NLE VNTYEGTHD+HALILGRAQTGIQAF
Sbjct: 360 VMNLEAVNTYEGTHDIHALILGRAQTGIQAF 390


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: 510
Number of extensions: 14
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: 391
Length adjustment: 31
Effective length of query: 362
Effective length of database: 360
Effective search space:   130320
Effective search space used:   130320
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