GapMind for catabolism of small carbon sources

 

Aligments for a candidate for SM_b21106 in Desulfovibrio vulgaris Miyazaki F

Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate 8500849 DvMF_1587 ABC transporter related (RefSeq)

Query= reanno::Smeli:SM_b21106
         (365 letters)



>lcl|FitnessBrowser__Miya:8500849 DvMF_1587 ABC transporter related
           (RefSeq)
          Length = 366

 Score =  231 bits (590), Expect = 2e-65
 Identities = 134/291 (46%), Positives = 179/291 (61%), Gaps = 12/291 (4%)

Query: 1   MAPVTLKKLVKRYGALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAI 60
           MA +TL  + K YGA  V+ G+ L V   E   L+GPSGCGK+  LR+IAG E    G I
Sbjct: 1   MADITLAGIGKAYGAHAVLDGLSLTVNHGECFTLLGPSGCGKTVLLRLIAGFETPDAGTI 60

Query: 61  EIGGRKVND------LPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRV 114
            IGG  V+D      +PP AR++ +VFQ YA++PHM+VA+N+G+ LK+AG PA E   +V
Sbjct: 61  SIGGEPVSDAVTGDCVPPDARDLGVVFQDYAVWPHMSVADNIGYPLKLAGLPAAERTRQV 120

Query: 115 AEAAAILDLAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRT 174
            E   +++L  L  R PSQLSGGQ+QRVA+ RA+V +P + L DEPL NLDA LR ++R 
Sbjct: 121 LETVEMVNLTGLENRMPSQLSGGQQQRVALARALVGRPSLMLLDEPLCNLDANLREEMRF 180

Query: 175 EIKKLHARMQATMIYVTHDQVEAMTLSDRIVIM-RDGHIEQVGTPEDVFRRPATKFVAGF 233
           EIK+L   +  T++YVTHDQ  A+ +SDR+ IM   G I QVGTP ++F RPA +FV  F
Sbjct: 181 EIKELQRTLGITILYVTHDQEIALAISDRLAIMDHAGAIRQVGTPWEIFERPADEFVFRF 240

Query: 234 IGSPPMNMEEAVLTDGKLAFASGATLPLPPRFRSLVREGQKVTFGLRPDDV 284
           +G    N   A    G    A+G   P+P        + +    G RP DV
Sbjct: 241 MG--VANFLPA-RRRGMAMLAAGGEQPVPWGLPD--GDAEHWMAGFRPSDV 286


Lambda     K      H
   0.320    0.137    0.397 

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: 380
Number of extensions: 19
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: 365
Length of database: 366
Length adjustment: 30
Effective length of query: 335
Effective length of database: 336
Effective search space:   112560
Effective search space used:   112560
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: 49 (23.5 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 paper from 2022 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