GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuA in Phaeobacter inhibens BS107

Align isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate GFF3369 PGA1_c34220 acyl-CoA dehydrogenase AcdA

Query= BRENDA::P26440
         (426 letters)



>FitnessBrowser__Phaeo:GFF3369
          Length = 387

 Score =  216 bits (550), Expect = 1e-60
 Identities = 138/380 (36%), Positives = 198/380 (52%), Gaps = 8/380 (2%)

Query: 44  GLSEEQRQLRQTMAKFLQEHLAPKAQEIDRSNEF--KNLREFWKQLGNLGVLGITAPVQY 101
           GLSEEQ  +  T   F+ + L P   E++RS     + +RE   +    G+     P + 
Sbjct: 4   GLSEEQSMIVDTTRAFVTKELYPHELEVERSGHLPMELVREIQAKAIEAGLYAANMPEEV 63

Query: 102 GGSGLGYLEHVLVMEEISRASGAVGLSYGAHSNLCINQLVRNGNEAQKEKYLPKLISGEY 161
           GG+GL  L  +L  +E+ RA+ A+  +  A  +     ++  G E QKEKYL   I GE 
Sbjct: 64  GGAGLDTLTWLLYEKELGRANYALHWTCVARPS----NILLAGTEEQKEKYLYPCIRGEK 119

Query: 162 IGALAMSEPNAGSDVVSMKLKAEKKGNHYILNGNKFWITNGPDADVLIVYAKTDLAAVPA 221
              LAM+EP AGSD+  M   A + G+ +ILNG K +I++   AD  IV+  T     P 
Sbjct: 120 WDCLAMTEPGAGSDLRGMTATARQDGDEFILNGTKHFISHADIADFAIVFMATGEEDTPR 179

Query: 222 S--RGITAFIVEKGMPGFSTSKKLDKLGMRGSNTCELIFEDCKIPAANILGHENKGVYVL 279
              + ITAF V+KG PGF+       +  RG     L F+DC++P +++LG  +KG  V 
Sbjct: 180 GPKKKITAFFVDKGTPGFTIRDGYRNVSHRGYTNAVLEFDDCRLPKSSVLGEVDKGFDVA 239

Query: 280 MSGLDLERLVLAGGPLGLMQAVLDHTIPYLHVREAFGQKIGHFQLMQGKMADMYTRLMAC 339
            + L   RL +A   LG  +  LDH I Y   R  FGQ+IG FQ +  K+ADM T L A 
Sbjct: 240 NTWLGATRLQVAATCLGRAERALDHAISYAAERRQFGQQIGKFQGVSFKLADMATELKAA 299

Query: 340 RQYVYNVAKACDEGHCTAKDCAGVILYSAECATQVALDGIQCFGGNGYINDFPMGRFLRD 399
               +  A   D+G  T  D +   L + E    VA + IQ  GG G +++ P+ R  RD
Sbjct: 300 NLLTWEAAWKFDQGSVTEADMSMAKLKATEMLAMVADEAIQIHGGMGLMDELPLERIWRD 359

Query: 400 AKLYEIGAGTSEVRRLVIGR 419
           A++  I  GTSE++R +I R
Sbjct: 360 ARVERIWEGTSEIQRHIISR 379


Lambda     K      H
   0.321    0.137    0.410 

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: 423
Number of extensions: 21
Number of successful extensions: 4
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: 426
Length of database: 387
Length adjustment: 31
Effective length of query: 395
Effective length of database: 356
Effective search space:   140620
Effective search space used:   140620
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