GapMind for catabolism of small carbon sources

 

Aligments for a candidate for frcA in Burkholderia phytofirmans PsJN

Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate BPHYT_RS28215 BPHYT_RS28215 D-ribose transporter ATP binding protein

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS28215 BPHYT_RS28215 D-ribose
           transporter ATP binding protein
          Length = 509

 Score =  386 bits (991), Expect = e-111
 Identities = 233/532 (43%), Positives = 323/532 (60%), Gaps = 25/532 (4%)

Query: 4   MSDTSTKAPLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAY 63
           M   ++  P L LR+  K+F  VRAL   +L  + GEVHAL+GENGAGKST++KIL+G +
Sbjct: 1   MQQPTSAVPRLELRHASKSFGRVRALSDGDLALWPGEVHALLGENGAGKSTVVKILAGVH 60

Query: 64  TADPGGECHIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRA-LQRRGLV 122
             D G E  +DG+  +   P  ARD G+AVIYQE +L  +LS+AENI++GR  + R G +
Sbjct: 61  QPDTG-ELVVDGEARRFATPAEARDAGLAVIYQEPTLFFDLSIAENIFMGRQPVDRIGRI 119

Query: 123 ARGDMVRACAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLS 182
               M R     LA LG D      V  LSIA +Q++EIA+A+   A +L+MDEPT  LS
Sbjct: 120 QYDAMRREVDGLLASLGVDLRADQLVRGLSIADQQVIEIAKALSLNANVLIMDEPTAALS 179

Query: 183 THETDRLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAAL 242
             E +RLF ++R+LR   +AIL+I+HR+ E+  L  RVT++RDG  V       L+  A+
Sbjct: 180 LPEVERLFTIVRKLRERDVAILFITHRLDEVFALTQRVTIMRDGAKVFDGLTTDLNTEAI 239

Query: 243 VKMMVGRDLSGFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAG 302
           V  MVGRDL  FY K   +    EV LSVR +      K  SFD+RAGE++ LAGLVGAG
Sbjct: 240 VAKMVGRDLETFYPKA--ERPPGEVRLSVRGLTRVGVFKDISFDVRAGEIVALAGLVGAG 297

Query: 303 RTELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFL 362
           R+E+AR +FG D    GE+ IA          L AG P  A+ AG+A + EDR+ QGL L
Sbjct: 298 RSEVARAIFGIDPLDSGEIWIAGKR-------LTAGRPAAAVRAGLALVPEDRRQQGLAL 350

Query: 363 DQSVHENINLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQK 422
           + S+  N ++ V  R  +  G ++  +  +   +    L ++       VG LSGGNQQK
Sbjct: 351 ELSIARNASMTVLGR-LVKHGLISARSETQLANQWGTRLRLKAGDPNAPVGTLSGGNQQK 409

Query: 423 VMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCD 482
           V+L + L   P+VLI+DEPTRG+D+GAK+E+Y  +  L + G+A+LMISSELPEV+G+ D
Sbjct: 410 VVLGKWLATGPKVLIIDEPTRGIDVGAKAEVYSALAELVRDGMAVLMISSELPEVLGMAD 469

Query: 483 RVLVMREGTLAGEVRPAGSAAETQERIIALATGAAAAAPAWVDVPLPGAGNA 534
           RVLVM EG ++ ++  A +    +ERI+  A G           P+P  G+A
Sbjct: 470 RVLVMHEGRISADIARADA---DEERIMGAALGQ----------PMPPLGHA 508


Lambda     K      H
   0.320    0.136    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: 723
Number of extensions: 46
Number of successful extensions: 9
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: 540
Length of database: 509
Length adjustment: 35
Effective length of query: 505
Effective length of database: 474
Effective search space:   239370
Effective search space used:   239370
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: 52 (24.6 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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