GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Desulfovibrio vulgaris Miyazaki F

Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate 8500849 DvMF_1587 ABC transporter related (RefSeq)

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897
         (386 letters)



>FitnessBrowser__Miya:8500849
          Length = 366

 Score =  207 bits (526), Expect = 5e-58
 Identities = 127/308 (41%), Positives = 178/308 (57%), Gaps = 20/308 (6%)

Query: 1   MATLELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGG 60
           MA + L  + K YG      L  + L ++ GE   L+GPSGCGK+ L+  IAG ET   G
Sbjct: 1   MADITLAGIGKAYGAHA--VLDGLSLTVNHGECFTLLGPSGCGKTVLLRLIAGFETPDAG 58

Query: 61  AILVDDADISG------MSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDE 114
            I +    +S       + P  RD+ +VFQ YA++P MSV DNI + LK+  +P AE   
Sbjct: 59  TISIGGEPVSDAVTGDCVPPDARDLGVVFQDYAVWPHMSVADNIGYPLKLAGLPAAERTR 118

Query: 115 EVARVSKLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEM 174
           +V    +++ +  L +R P QLSGGQQQRVA+ RAL  RP + L DEPL NLDA LR EM
Sbjct: 119 QVLETVEMVNLTGLENRMPSQLSGGQQQRVALARALVGRPSLMLLDEPLCNLDANLREEM 178

Query: 175 RTEMKLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKD-GIIQQFGTPKDIYNNPANLFVA 233
           R E+K + + L  T +YVTHDQ  A+ + D++A+M   G I+Q GTP +I+  PA+ FV 
Sbjct: 179 RFEIKELQRTLGITILYVTHDQEIALAISDRLAIMDHAGAIRQVGTPWEIFERPADEFVF 238

Query: 234 SFIGSPPMNFIPLRLQRKDGRLLALLDSGQARCELPLGMQDAGLEDREVILGIRPEQIIL 293
            F+G    NF+P R      R +A+L +G  +  +P G+ D   E    + G RP  + L
Sbjct: 239 RFMG--VANFLPAR-----RRGMAMLAAGGEQ-PVPWGLPDGDAE--HWMAGFRPSDVRL 288

Query: 294 ANGEANGL 301
           A  + +GL
Sbjct: 289 AR-QGDGL 295


Lambda     K      H
   0.319    0.138    0.393 

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: 370
Number of extensions: 17
Number of successful extensions: 3
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: 386
Length of database: 366
Length adjustment: 30
Effective length of query: 356
Effective length of database: 336
Effective search space:   119616
Effective search space used:   119616
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 (21.7 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