GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PfGW456L13_1897 in Paucidesulfovibrio gracilis DSM 16080

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

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



>NCBI__GCF_900167125.1:WP_078717009.1
          Length = 370

 Score =  224 bits (572), Expect = 2e-63
 Identities = 124/279 (44%), Positives = 175/279 (62%), Gaps = 9/279 (3%)

Query: 21  LKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGGAILVDDADISGMSPKDRDIA 80
           L ++ L I  GEFL ++GPSGCGK+TL+  +AG E+ S G I++D   +  + P  R + 
Sbjct: 23  LHDVCLDIRHGEFLTILGPSGCGKTTLLRLLAGFESPSSGEIILDGRSMRDVPPDGRRVN 82

Query: 81  MVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVSKLLQIEHLLSRKPGQLSGGQ 140
            VFQSYAL+P MSV DN+AFGL++  +P  EI E VA+  +++ +     R+P  LSGGQ
Sbjct: 83  TVFQSYALFPHMSVFDNVAFGLRMSGIPKVEIGERVAKALRMVGLAGQAGRRPTSLSGGQ 142

Query: 141 QQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQRLKTTTVYVTHDQIEAM 200
           QQRVA+ RA+  RP + L DEPLS LD KLRV+MRTE+K + + +  T ++VTHDQ EA 
Sbjct: 143 QQRVAIARAVVNRPLVLLLDEPLSALDYKLRVQMRTELKQLRREMGITFIFVTHDQEEAF 202

Query: 201 TLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPPMNFIPLRLQRKDGRLLALLD 260
           ++ D+V VM +G + Q GTP ++Y  P N+FVA F+G    N       + DG +L  L 
Sbjct: 203 SMSDRVVVMNEGCVAQVGTPVEVYEQPVNMFVARFVGE--TNVFEGVAGQSDGGILQALV 260

Query: 261 SGQARCELP--LGMQDAGLEDREVILGIRPEQIILANGE 297
            G+  CEL    G Q     DR  +L +RPE +++   E
Sbjct: 261 EGRT-CELSSHRGFQPG---DRIRVL-LRPEDLLVEREE 294


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: 374
Number of extensions: 9
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: 386
Length of database: 370
Length adjustment: 30
Effective length of query: 356
Effective length of database: 340
Effective search space:   121040
Effective search space used:   121040
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 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