GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlK in Paucidesulfovibrio gracilis DSM 16080

Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate WP_078717009.1 B5D49_RS06865 spermidine/putrescine ABC transporter ATP-binding protein PotA

Query= reanno::BFirm:BPHYT_RS16095
         (369 letters)



>NCBI__GCF_900167125.1:WP_078717009.1
          Length = 370

 Score =  241 bits (616), Expect = 2e-68
 Identities = 127/291 (43%), Positives = 184/291 (63%), Gaps = 4/291 (1%)

Query: 4   VTLRNIRKAYDENEVMRDINLDIADGEFVVFVGPSGCGKSTLMRMIAGLEDISGGDLTID 63
           + L ++ K +D   V+ D+ LDI  GEF+  +GPSGCGK+TL+R++AG E  S G++ +D
Sbjct: 8   IRLEHVAKEFDGETVLHDVCLDIRHGEFLTILGPSGCGKTTLLRLLAGFESPSSGEIILD 67

Query: 64  GMRVNDVAPAKRGIAMVFQSYALYPHMTLYDNMAFGLKLAGTKKPEIDAAVRNAAKILHI 123
           G  + DV P  R +  VFQSYAL+PHM+++DN+AFGL+++G  K EI   V  A +++ +
Sbjct: 68  GRSMRDVPPDGRRVNTVFQSYALFPHMSVFDNVAFGLRMSGIPKVEIGERVAKALRMVGL 127

Query: 124 DHLLDRKPKQLSGGQRQRVAIGRAITRKPKVFLFDEPLSNLDAALRVKMRLEFARLHDEL 183
                R+P  LSGGQ+QRVAI RA+  +P V L DEPLS LD  LRV+MR E  +L  E+
Sbjct: 128 AGQAGRRPTSLSGGQQQRVAIARAVVNRPLVLLLDEPLSALDYKLRVQMRTELKQLRREM 187

Query: 184 KTTMIYVTHDQVEAMTLADKIVVLSAGNLEQVGSPTMLYHAPANRFVAGFIGSPKMNFME 243
             T I+VTHDQ EA +++D++VV++ G + QVG+P  +Y  P N FVA F+G  + N  E
Sbjct: 188 GITFIFVTHDQEEAFSMSDRVVVMNEGCVAQVGTPVEVYEQPVNMFVARFVG--ETNVFE 245

Query: 244 GVVQSVTHDGVTVRYETGETQRVAVEPAAVKQGDKVTVGIRPEHLHVGMAE 294
           GV    +  G+      G T  ++      + GD++ V +RPE L V   E
Sbjct: 246 GVA-GQSDGGILQALVEGRTCELS-SHRGFQPGDRIRVLLRPEDLLVEREE 294


Lambda     K      H
   0.320    0.135    0.384 

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: 337
Number of extensions: 12
Number of successful extensions: 1
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: 369
Length of database: 370
Length adjustment: 30
Effective length of query: 339
Effective length of database: 340
Effective search space:   115260
Effective search space used:   115260
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 Apr 09 2024. 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