GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acdH in Marinobacter adhaerens HP15

Align Branched-chain acyl-CoA dehydrogenase (EC 1.3.99.12) (characterized)
to candidate GFF928 HP15_907 acyl-CoA dehydrogenase domain protein

Query= reanno::ANA3:7025618
         (385 letters)



>lcl|FitnessBrowser__Marino:GFF928 HP15_907 acyl-CoA dehydrogenase
           domain protein
          Length = 388

 Score =  540 bits (1391), Expect = e-158
 Identities = 261/387 (67%), Positives = 319/387 (82%), Gaps = 2/387 (0%)

Query: 1   MDFNFNEDQRQFADLARQFAADELAPFAAKWDEEHHFPKDVIQKAGELGFCSLYSPESEG 60
           MDFN  EDQ  F + AR FA   +AP AAKWD EH FP D++++AGE+GF  +Y+PE+ G
Sbjct: 1   MDFNLTEDQLAFREAARAFAEKSMAPHAAKWDNEHIFPVDMMKEAGEMGFMGMYTPEALG 60

Query: 61  GMGLSRLDASIIFEELSKGCTATTAMLTIHNMATWMVTTWGTDTLRQAWSEPLTTGQMLA 120
           GMGLSRLD S+I EEL+  C +T A +TIHNMATWMV ++ +D L+Q     L +G+ LA
Sbjct: 61  GMGLSRLDTSVIVEELAAACPSTAAFITIHNMATWMVASFASDDLKQEIVPKLASGEWLA 120

Query: 121 SYCLTEPGAGSDAASLQTKAVREGDEYVVSGSKMFISGAGSTELLVVMCRTG--QAGPKG 178
           SYCLTEPGAGSDAASL+TKAVR+GD YV++GSK+FISGAG+T++LV+M RTG   +G KG
Sbjct: 121 SYCLTEPGAGSDAASLRTKAVRDGDSYVINGSKVFISGAGATDILVLMARTGAPDSGYKG 180

Query: 179 ISAIAIPADSEGIIYGKAEDKMGWNAQPTRLVTFDNVRVPVANLLGEEGQGFTFAMKGLD 238
           IS   IPAD++GI YGK E+KMGW++QPTR+++ +NVR+P +N +G+EG GF  AMKGLD
Sbjct: 181 ISTFVIPADADGISYGKNEEKMGWHSQPTRMISLENVRIPASNRVGDEGDGFAIAMKGLD 240

Query: 239 GGRINIATCSVGTAQAALERATQYMNERQQFGKPLAAFQALQFKLADMATELVAARQMVR 298
           GGR+NIATCS+G AQAAL RA  YM+ER+QFGKPLAAFQALQFKLADMAT LVAARQMVR
Sbjct: 241 GGRLNIATCSLGGAQAALLRARNYMHEREQFGKPLAAFQALQFKLADMATNLVAARQMVR 300

Query: 299 LAAFKLDSGDPEATAYCAMAKRFATDVGFQVCDAALQIHGGYGYIREYPLERHFRDVRVH 358
           L AFKLD+ DPEAT +CAMAKRFATD  F+V + ALQ+HGGYGYIREYPLER+ RD+RVH
Sbjct: 301 LGAFKLDNADPEATLHCAMAKRFATDACFEVVNEALQLHGGYGYIREYPLERYLRDLRVH 360

Query: 359 QILEGTNEIMRLIIARRLLDENAGQIL 385
           QILEGTNEIMRLI+ARRLLD+   + +
Sbjct: 361 QILEGTNEIMRLIVARRLLDDGVAEAI 387


Lambda     K      H
   0.320    0.134    0.396 

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: 450
Number of extensions: 10
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: 385
Length of database: 388
Length adjustment: 30
Effective length of query: 355
Effective length of database: 358
Effective search space:   127090
Effective search space used:   127090
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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