GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcE in Desulfovibrio vulgaris Miyazaki F

Align D-lactate oxidase, FAD binding subunit (EC 1.1.3.15) (characterized)
to candidate 8501126 DvMF_1862 FAD linked oxidase domain protein (RefSeq)

Query= reanno::Phaeo:GFF2924
         (366 letters)



>FitnessBrowser__Miya:8501126
          Length = 461

 Score = 96.3 bits (238), Expect = 1e-24
 Identities = 111/399 (27%), Positives = 162/399 (40%), Gaps = 62/399 (15%)

Query: 19  PLAVSGGGTRGLSTG-------GETLSVAGLNGVTLYEPGALTLVVQAGTSVEEVQALLA 71
           P+ V G GT  LS G       G  +    LN +       L  VV+ G    +  A +A
Sbjct: 66  PITVRGAGTN-LSGGTIPDPREGIVILTNSLNRIIEINEEDLYAVVEPGVVTAKFAAEVA 124

Query: 72  GENQRLAFEPMDHRGLLGTKGTPTIGGVFAANVSGPRRIQCGAARDFLLGVRFVDGRGDV 131
              +R  F P D     G++   T+GG  A N  G R ++ G  +D+++G+ F D  G +
Sbjct: 125 ---KRGLFYPPDP----GSQAVSTLGGNVAENAGGLRGLKYGVTKDYVMGIEFFDVNGGL 177

Query: 132 LSNGGRVMKNVTGYDLVKLMAGSHGTLGVLSEVSLKVLP---CSEACATVTVHVADLTSA 188
           +  G R +K VTGY+L  LM  S GTLGV S + LK++P    S+A   V   V   + A
Sbjct: 178 VKTGSRTVKCVTGYNLAGLMVASEGTLGVFSNIVLKLVPPPQASKAMMAVFDDVNKASEA 237

Query: 189 VAAMSTALGSPY--------------DVTGAAYDPEAGAV-YIRVEGFEASVTYRAEALK 233
           VA +  A   P               D T A    +A A+  I V+G    V   AE ++
Sbjct: 238 VAGIIAAHVVPCTLEFMDQATIRYVDDFTKAGLPRDAQAILLIEVDGHAGQVAEDAEKVE 297

Query: 234 MALGKFG--EVSLALGAGD--ALWEGIRNV--AAFHDRPGDVWRISVKPSDAV-ALAPAL 286
             L K G  E+ +A  A +   LWE  RN   A    +P  V   +  P   + A+  A+
Sbjct: 298 KVLNKVGATEIKVAKDAAEKFKLWEARRNALPALARAKPTTVLEDATVPRSKIPAMVKAI 357

Query: 287 E--------AEGLLFDWGGGLIWALVPAGR-------------DLRFRLTVPGHATLVRA 325
                    + G     G G +   +   R             D  F + +  H TL   
Sbjct: 358 NDIAAKYNISIGTFGHAGDGNLHPTILCDRRDKHEFERVEHAVDEIFDVALSLHGTLSGE 417

Query: 326 SAQTRAELGQFQPQPGPLA-AISGGLRRQFDPRGILNPG 363
                A+    + +        S  ++R  DP+ ILNPG
Sbjct: 418 HGIGMAKSKWMEKETSKATIEFSRNMKRAIDPKYILNPG 456


Lambda     K      H
   0.318    0.136    0.401 

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: 371
Number of extensions: 21
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 366
Length of database: 461
Length adjustment: 31
Effective length of query: 335
Effective length of database: 430
Effective search space:   144050
Effective search space used:   144050
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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