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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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