GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PfGW456L13_1897 in Pseudomonas simiae WCS417

Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate GFF2270 PS417_11575 spermidine/putrescine ABC transporter ATPase

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



>FitnessBrowser__WCS417:GFF2270
          Length = 342

 Score =  226 bits (575), Expect = 1e-63
 Identities = 130/301 (43%), Positives = 182/301 (60%), Gaps = 21/301 (6%)

Query: 1   MATLELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGG 60
           MA L+L  ++K YG    D +   +L ++ GEF+ L+GPSGCGK+T +  IAG   +SGG
Sbjct: 1   MAFLQLNALSKRYGA--VDAVVATDLAVEKGEFVSLLGPSGCGKTTTLQMIAGFVDVSGG 58

Query: 61  AILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVS 120
            IL+D  DI+   P  R + +VFQSYAL+P MSVRDN+AFGLK+RK+P AEI  +V  V 
Sbjct: 59  QILLDGRDITHAKPASRGLGVVFQSYALFPHMSVRDNVAFGLKMRKVPAAEIASKVKTVL 118

Query: 121 KLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180
           +L+++     R P +LSGGQ+QRVA+ RAL   P + L DEPLSNLDA LR EM+ E++ 
Sbjct: 119 ELVRLAPHADRYPRELSGGQRQRVALARALVIEPPVLLLDEPLSNLDANLREEMQFEIRR 178

Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPP 240
           +   +  TT+ VTHDQ EA+++ D+V VM+ G + Q   P  +Y +P   F++ F+G   
Sbjct: 179 IQCAVGITTLMVTHDQAEALSISDRVVVMQAGRVTQIDAPYKLYEHPRTRFISDFVGK-- 236

Query: 241 MNFIPLRLQRKDGRLLALLDSGQARCELPLGMQDAGLEDREVILGIRPEQIILANGEANG 300
            N +P            LL S Q R E           D E+ L +RPE+I L +  +  
Sbjct: 237 ANLLPGDYD--------LLGSPQVRHE---------SGDGELTLSLRPEKIQLVDAGSGR 279

Query: 301 L 301
           L
Sbjct: 280 L 280


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: 315
Number of extensions: 13
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 386
Length of database: 342
Length adjustment: 29
Effective length of query: 357
Effective length of database: 313
Effective search space:   111741
Effective search space used:   111741
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: 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