GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Halomonas xinjiangensis TRM 0175

Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate WP_043527041.1 JH15_RS03500 sn-glycerol-3-phosphate import ATP-binding protein UgpC

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



>NCBI__GCF_000759345.1:WP_043527041.1
          Length = 354

 Score =  309 bits (792), Expect = 7e-89
 Identities = 171/366 (46%), Positives = 242/366 (66%), Gaps = 20/366 (5%)

Query: 1   MATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGG 60
           MA+++L  + KTY AG  + +K I+L I +GEF++LVGPSGCGKSTL+  +AGLETIT G
Sbjct: 1   MASIQLTGLKKTY-AGNVEAVKGIDLEIADGEFVVLVGPSGCGKSTLLRMVAGLETITDG 59

Query: 61  AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVA 120
            + I D+ V+ + P +RDIAMVFQ+YALYP M+V  N+ +GLK R + + +I+  V   A
Sbjct: 60  TLKIDDRVVNDLEPAERDIAMVFQNYALYPHMTVFGNLAYGLKNRGVKREEIERRVHDAA 119

Query: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180
            +L+IE  L RKP +LSGGQ+QRVAMGRAL R P  +LFDEPLSNLDAKLRV+MR E+K 
Sbjct: 120 AMLEIEPFLERKPRKLSGGQRQRVAMGRALVREPSAFLFDEPLSNLDAKLRVQMRVEIKQ 179

Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPP 240
           + +RLKTT++YVTHDQ+EA+TLGD++ V+  G I+Q GTP E+Y  PA+ FVA+FIGSP 
Sbjct: 180 LQRRLKTTSLYVTHDQLEALTLGDRLVVLNGGSIEQVGTPMEVYEKPASMFVATFIGSPA 239

Query: 241 MNFVPLRLQRKDGRLVALLDSGQARCELALNTTEAGLEDRDVILGLRPEQIMLAAGEGDS 300
           MN +P+   R+ G    LLD       LA +T          ++G+RP+ + + A + D 
Sbjct: 240 MNMLPVAYLRERG-ANGLLD------HLAADTD---------VIGIRPDDLRIEAPDEDH 283

Query: 301 ASSIRAEVQVTEPTGPDTLVFVQLNDTKVCCRLAPDVAPQVGETLTLQFD--PSKVLLFD 358
              +   V++ E  G ++ ++V L  +     +     P V E  T++F   PS +  F+
Sbjct: 284 L-VVTGTVELFEAAGAESHLYVSLEGSDQPTVIRTSARPPVAEGETMRFHVLPSALHPFN 342

Query: 359 ANTGER 364
             +G+R
Sbjct: 343 QASGKR 348


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: 366
Number of extensions: 10
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: 354
Length adjustment: 30
Effective length of query: 356
Effective length of database: 324
Effective search space:   115344
Effective search space used:   115344
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: 49 (23.5 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