GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Miya:8500849
          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:

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