GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__BFirm:BPHYT_RS28215
          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:

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