GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gtsD in Pseudomonas stutzeri RCH2

Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate GFF1860 Psest_1899 ABC-type sugar transport systems, ATPase components

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



>lcl|FitnessBrowser__psRCH2:GFF1860 Psest_1899 ABC-type sugar
           transport systems, ATPase components
          Length = 390

 Score =  557 bits (1436), Expect = e-163
 Identities = 287/368 (77%), Positives = 317/368 (86%), Gaps = 2/368 (0%)

Query: 1   MATLELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGG 60
           MA+LELRNV K+YG     TLK+I LKID GEFLILVGPSGCGKSTLMNCIAGLE I+GG
Sbjct: 1   MASLELRNVQKSYGNSQIATLKDIALKIDAGEFLILVGPSGCGKSTLMNCIAGLENITGG 60

Query: 61  AILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVS 120
            ILVD  DIS  SPKDRDIAMVFQSYALYPTMSVRDNIAFGLK+RK+P A+I+EEVARV+
Sbjct: 61  EILVDGEDISQASPKDRDIAMVFQSYALYPTMSVRDNIAFGLKMRKVPAAKIEEEVARVA 120

Query: 121 KLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180
           KLLQIE LL RKP QLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTE+KL
Sbjct: 121 KLLQIEPLLERKPSQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEIKL 180

Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPP 240
           MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDG+IQQFGTP +IYNNPANLFVASFIGSPP
Sbjct: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGVIQQFGTPHEIYNNPANLFVASFIGSPP 240

Query: 241 MNFIPLRLQRKDGRLLALLDSGQARCELPLGM-QDAGLEDREVILGIRPEQIILANGEAN 299
           MNF+PLR++++DGR + +L+S Q  CELPL +  D GL DRE+ILGIRPEQI LA   + 
Sbjct: 241 MNFVPLRIRQRDGRWVGVLNSEQGSCELPLPITSDDGLRDRELILGIRPEQIGLAPAGSA 300

Query: 300 GLPTIRAEVQVTEPTGPDTLVFVNLNDTKVCCRLAPDVAPAVGETLTLQFDPAKVLLFDA 359
              ++  +++V EPTGPDTLV   LN  K CCRLAPD AP VGETL LQFDP + LLFDA
Sbjct: 301 DF-SLAVDIEVVEPTGPDTLVVFTLNQVKACCRLAPDQAPRVGETLNLQFDPRRALLFDA 359

Query: 360 KTGERLGV 367
           +TGERLGV
Sbjct: 360 QTGERLGV 367


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: 519
Number of extensions: 11
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: 390
Length adjustment: 30
Effective length of query: 356
Effective length of database: 360
Effective search space:   128160
Effective search space used:   128160
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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