GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PfGW456L13_1897 in Halomonas xinjiangensis TRM 0175

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

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



>NCBI__GCF_000759345.1:WP_043527041.1
          Length = 354

 Score =  309 bits (791), Expect = 9e-89
 Identities = 168/366 (45%), Positives = 242/366 (66%), Gaps = 20/366 (5%)

Query: 1   MATLELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGG 60
           MA+++L  + KTY  G  + +K I+L+I DGEF++LVGPSGCGKSTL+  +AGLETI+ G
Sbjct: 1   MASIQLTGLKKTYA-GNVEAVKGIDLEIADGEFVVLVGPSGCGKSTLLRMVAGLETITDG 59

Query: 61  AILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVS 120
            + +DD  ++ + P +RDIAMVFQ+YALYP M+V  N+A+GLK R +   EI+  V   +
Sbjct: 60  TLKIDDRVVNDLEPAERDIAMVFQNYALYPHMTVFGNLAYGLKNRGVKREEIERRVHDAA 119

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

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

Query: 241 MNFIPLRLQRKDGRLLALLDSGQARCELPLGMQDAGLEDREVILGIRPEQIILANGEANG 300
           MN +P+   R+ G                 G+ D    D +VI GIRP+ + +   + + 
Sbjct: 240 MNMLPVAYLRERG---------------ANGLLDHLAADTDVI-GIRPDDLRIEAPDEDH 283

Query: 301 LPTIRAEVQVTEPTGPDTLVFVNL--NDTKVCCRLAPDVAPAVGETLTLQFDPAKVLLFD 358
           L  +   V++ E  G ++ ++V+L  +D     R +     A GET+     P+ +  F+
Sbjct: 284 L-VVTGTVELFEAAGAESHLYVSLEGSDQPTVIRTSARPPVAEGETMRFHVLPSALHPFN 342

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


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: 386
Number of extensions: 18
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 ( 7.4 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 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