GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PfGW456L13_1897 in Marinobacter adhaerens HP15

Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate GFF960 HP15_939 spermidine/putrescine ABC transporter ATPase subunit

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



>FitnessBrowser__Marino:GFF960
          Length = 372

 Score =  216 bits (550), Expect = 8e-61
 Identities = 123/298 (41%), Positives = 181/298 (60%), Gaps = 6/298 (2%)

Query: 4   LELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGGAIL 63
           L +R ++K++   L   + N+ L I  GE   L+G SG GKSTL+  +AG ET + G+I+
Sbjct: 15  LSIRGISKSFDGTL--AVDNVNLDIHKGEIFALLGGSGSGKSTLLRMLAGFETPNAGSIM 72

Query: 64  VDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVSKLL 123
           +D  D++ + P  R   M+FQSYAL+P M+V  NIA GLK  K+P +EI + VA + KL+
Sbjct: 73  LDGQDVTALPPFLRPTNMMFQSYALFPHMTVEQNIAMGLKQDKLPKSEIRDRVAAMLKLV 132

Query: 124 QIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQ 183
           ++E    RKP QLSGGQQQRVA+ R+LA+RPK+ L DEP+  LD KLR EM+ E+  + +
Sbjct: 133 KMEPYARRKPQQLSGGQQQRVALARSLAKRPKLLLLDEPMGALDKKLRTEMQLELVEILE 192

Query: 184 RLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPPMNF 243
            +  T + VTHDQ EAMT+  ++A+M  G I Q G+P DIY +P +   A FIGS  +N 
Sbjct: 193 NVGATCLMVTHDQEEAMTMASRIAIMAQGRIAQIGSPIDIYESPNSRMTAEFIGS--VNI 250

Query: 244 IPLRLQRKDGRLLALL-DSGQARCELPLGMQDAGLEDREVILGIRPEQIILANGEANG 300
               ++  +   + L  D   A   +  G+     E    ++ +RPE+I L   + +G
Sbjct: 251 FEAHIREDEADSVTLTSDLLDAPVFIDRGVTTPA-ESTATLVALRPEKIYLTPDKPDG 307


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: 338
Number of extensions: 16
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: 372
Length adjustment: 30
Effective length of query: 356
Effective length of database: 342
Effective search space:   121752
Effective search space used:   121752
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:

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