GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS17020 in Halomonas xinjiangensis TRM 0175

Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate WP_043527041.1 JH15_RS03500 sn-glycerol-3-phosphate import ATP-binding protein UgpC

Query= uniprot:D8IPI1
         (406 letters)



>NCBI__GCF_000759345.1:WP_043527041.1
          Length = 354

 Score =  308 bits (788), Expect = 2e-88
 Identities = 175/365 (47%), Positives = 231/365 (63%), Gaps = 22/365 (6%)

Query: 1   MADIHCQALAKHYAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGT 60
           MA I    L K YAG    +  +DL I DGEFVVL+GPSGCGKST+LRM+AGLE I+ GT
Sbjct: 1   MASIQLTGLKKTYAGNVEAVKGIDLEIADGEFVVLVGPSGCGKSTLLRMVAGLETITDGT 60

Query: 61  LRIGGTVVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAA 120
           L+I   VVNDL   ER++AMVFQNYALYPHM+V+ N+A+GL+       EI+RRV + AA
Sbjct: 61  LKIDDRVVNDLEPAERDIAMVFQNYALYPHMTVFGNLAYGLKNRGVKREEIERRVHDAAA 120

Query: 121 LLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRL 180
           +L +E  LERKPR +SGGQ+QR A+ RA+++ PS FLFDEPLSNLDAKLR Q+R +IK+L
Sbjct: 121 MLEIEPFLERKPRKLSGGQRQRVAMGRALVREPSAFLFDEPLSNLDAKLRVQMRVEIKQL 180

Query: 181 HQRLRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAM 240
            +RL+TT++YVTHDQLEA+TL DR++++  G I Q G+P E+Y  P ++F A FIG+PAM
Sbjct: 181 QRRLKTTSLYVTHDQLEALTLGDRLVVLNGGSIEQVGTPMEVYEKPASMFVATFIGSPAM 240

Query: 241 NFLSGTVQRQDGQLFIETAHQRWALTGERFSRLRHAMAVK--LAVRPDHVRIAGEREPAA 298
           N L     R+ G   +                L H  A    + +RPD +RI    E   
Sbjct: 241 NMLPVAYLRERGANGL----------------LDHLAADTDVIGIRPDDLRIEAPDED-- 282

Query: 299 SLTCPVSVELVEILGADA-LLTTRCGDQTLTALVPADRLP-QPGATLTLALDQHELHVFD 356
            L    +VEL E  GA++ L  +  G    T +  + R P   G T+   +    LH F+
Sbjct: 283 HLVVTGTVELFEAAGAESHLYVSLEGSDQPTVIRTSARPPVAEGETMRFHVLPSALHPFN 342

Query: 357 VESGE 361
             SG+
Sbjct: 343 QASGK 347


Lambda     K      H
   0.321    0.137    0.403 

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: 398
Number of extensions: 12
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: 406
Length of database: 354
Length adjustment: 30
Effective length of query: 376
Effective length of database: 324
Effective search space:   121824
Effective search space used:   121824
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 (21.8 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