GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Burkholderia phytofirmans PsJN

Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate BPHYT_RS16095 BPHYT_RS16095 sugar ABC transporter ATP-binding protein

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



>FitnessBrowser__BFirm:BPHYT_RS16095
          Length = 369

 Score =  296 bits (758), Expect = 6e-85
 Identities = 166/363 (45%), Positives = 230/363 (63%), Gaps = 13/363 (3%)

Query: 1   MATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGG 60
           MA++ LRN+ K Y     + +++I L I +GEF++ VGPSGCGKSTLM  IAGLE I+GG
Sbjct: 1   MASVTLRNIRKAYDEN--EVMRDINLDIADGEFVVFVGPSGCGKSTLMRMIAGLEDISGG 58

Query: 61  AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVA 120
            + I    V+ ++P  R IAMVFQSYALYP M++ +N+ FGLK+    + +IDA V   A
Sbjct: 59  DLTIDGMRVNDVAPAKRGIAMVFQSYALYPHMTLYDNMAFGLKLAGTKKPEIDAAVRNAA 118

Query: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180
           K+L I+HLL+RKP QLSGGQ+QRVA+GRA+ R+PK++LFDEPLSNLDA LRV+MR E   
Sbjct: 119 KILHIDHLLDRKPKQLSGGQRQRVAIGRAITRKPKVFLFDEPLSNLDAALRVKMRLEFAR 178

Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPP 240
           +H  LKTT +YVTHDQ+EAMTL DK+ V+  G ++Q G+P  +Y+ PAN+FVA FIGSP 
Sbjct: 179 LHDELKTTMIYVTHDQVEAMTLADKIVVLSAGNLEQVGSPTMLYHAPANRFVAGFIGSPK 238

Query: 241 MNFVPLRLQ--RKDGRLVALLDSGQARCELALNTTEAGLEDRDVILGLRPEQIMLAAGEG 298
           MNF+   +Q    DG +    ++G+ +  +A+        D+ V +G+RPE + +   E 
Sbjct: 239 MNFMEGVVQSVTHDG-VTVRYETGETQ-RVAVEPAAVKQGDK-VTVGIRPEHLHVGMAE- 294

Query: 299 DSASSIRAEVQVTEPTGPDTLVFVQ--LNDTKVCCRLAPDVAPQVGETLTLQFDPSKVLL 356
                I A     E  G    ++ +  +    +  R+ P      GET  L   P    L
Sbjct: 295 ---DGISARTMAVESLGDAAYLYAESSVAPDGLIARIPPLERHTKGETQKLGATPEHCHL 351

Query: 357 FDA 359
           FD+
Sbjct: 352 FDS 354


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: 392
Number of extensions: 17
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: 369
Length adjustment: 30
Effective length of query: 356
Effective length of database: 339
Effective search space:   120684
Effective search space used:   120684
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 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