GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Pseudomonas litoralis 2SM5

Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate WP_090274680.1 BLU11_RS14815 polyamine ABC transporter ATP-binding protein

Query= reanno::WCS417:GFF4321
         (386 letters)



>NCBI__GCF_900105005.1:WP_090274680.1
          Length = 378

 Score =  215 bits (548), Expect = 1e-60
 Identities = 125/336 (37%), Positives = 197/336 (58%), Gaps = 23/336 (6%)

Query: 4   LELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGGAIM 63
           +++  V+K +   L   + ++ L+I  GE   L+G SG GKSTL+  +AG ET + G ++
Sbjct: 21  VKIERVSKQFDDAL--AVDDVTLTINRGEIFALLGGSGSGKSTLLRILAGFETPSEGRVL 78

Query: 64  IGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVAKLL 123
           +  Q+++ + P  R I M+FQSYAL+P M+V +NI FGLK  K+   +I   VA + KL+
Sbjct: 79  LDGQNITALPPHKRPINMMFQSYALFPHMTVEQNIAFGLKQDKLSNTEISERVAEMLKLV 138

Query: 124 QIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQ 183
            +     RKP QLSGGQ+QRVA+ R+LA+RPK+ L DEP+  LD KLR +M+ E+  + +
Sbjct: 139 HMAKYAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRSQMQLELVEIIE 198

Query: 184 RLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPPMNF 243
           R+  T + VTHDQ EAMT+  ++A+M  G I Q GTP +IY +P N+ VA F+GS     
Sbjct: 199 RVGVTCIMVTHDQEEAMTMAQRIAIMDQGWIVQVGTPMDIYESPVNRHVAEFVGS----- 253

Query: 244 VPLRLQRKDGRLVA------LLDSGQARCELALN---TTEAGLEDRDVILGLRPEQIMLA 294
               +   +G +VA      +++  Q   ++ L    TT A  ED+  I  LRPE++ + 
Sbjct: 254 ----VNIFEGEIVADMDDHVIIECPQLDRQIYLGHGVTTRA--EDKSAIYALRPEKVFVT 307

Query: 295 AGEGDSASS-IRAEVQVTEPTGPDTLVFVQLNDTKV 329
             + +   +    EV      G  ++ +++L+  K+
Sbjct: 308 TEQPEQPYNWAHGEVHDIAYLGGHSVYYIKLDSGKM 343


Lambda     K      H
   0.318    0.135    0.382 

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: 316
Number of extensions: 6
Number of successful extensions: 2
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: 378
Length adjustment: 30
Effective length of query: 356
Effective length of database: 348
Effective search space:   123888
Effective search space used:   123888
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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 24 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