Alignments for a candidate for frcA in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for frcA in Cupriavidus basilensis 4G11

Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate RR42_RS04800 RR42_RS04800 ABC transporter

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>FitnessBrowser__Cup4G11:RR42_RS04800
          Length = 529

 Score =  284 bits (726), Expect = 7e-81
 Identities = 188/515 (36%), Positives = 275/515 (53%), Gaps = 28/515 (5%)

Query: 7   TSTKAPLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTAD 66
           T +  P LAL +I K +PGV A   V L    GE+HA++GENGAGKSTLMKI+ GA   D
Sbjct: 2   TLSTTPRLALAHISKRYPGVTANDDVSLVVAPGEIHAVLGENGAGKSTLMKIIFGAVKPD 61

Query: 67  PGGECHIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGD 126
             G+ H +G R  I  P  AR+LG+A+++Q  SL   L+VAENI LG  L R    A G 
Sbjct: 62  -AGDMHFNGARAAIHNPHDARNLGIAMVFQHFSLFDTLTVAENIALG--LPRGSKTAAGS 118

Query: 127 ---------MVRACAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEP 177
                    +      T  R G    P  +V +LS+ +RQ VEI RA+  + ++L++DEP
Sbjct: 119 PHAGTNMKQLAEQIRETALRYGLPLEPNRHVHTLSVGERQRVEIVRALLAKPQLLILDEP 178

Query: 178 TTPLSTHETDRLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHL 237
           T+ L+      LF  +RQL  EG +ILYISH++ EI EL    TV+R G   G  D    
Sbjct: 179 TSVLTPQAVQTLFITLRQLAAEGTSILYISHKLDEIRELCHSATVMRMGRVTGVCDPRQE 238

Query: 238 SQAALVKMMVGRDLSGFYTKTHGQAVEREVMLSVRDV------ADGRRVKGCSFDLRAGE 291
           S A+L ++M+G +      +   Q       L+VR++      A    + G S DLRAGE
Sbjct: 239 SAASLSRLMIGGEPP---REARVQTEPGVCRLAVRELSLPRSHAFATELAGISLDLRAGE 295

Query: 292 VLGLAGLVGAGRTELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYL 351
           ++G+AG+ G G+ EL   + G D R   +    +    G L        RQ   AG+A++
Sbjct: 296 IVGIAGVSGNGQQELLAALSGEDVRAARDAITLDNKPVGKL------DARQRRRAGLAFV 349

Query: 352 TEDRKLQGLFLDQSVHENINLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVN 411
            E+R  +G     S+  NI L   +   +  G ++  AA       I  L ++ +     
Sbjct: 350 PEERLGRGAVPGMSLAANILLSHQSAPYVQRGMISPKAAAGLAQAVIARLRVKASGPHAL 409

Query: 412 VGALSGGNQQKVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMIS 471
             +LSGGN QK ++ R +E  P+VLI+ +PT GVD+GA ++I+  + AL  +G A+L++S
Sbjct: 410 AKSLSGGNLQKFIVGREIESGPKVLIVAQPTWGVDVGAAAQIHNELLALKATGCALLVVS 469

Query: 472 SELPEVVGLCDRVLVMREGTLAGEVRPAGSAAETQ 506
            EL E+  +CDR+ V+ +G L+  + P   A   Q
Sbjct: 470 EELDELFAICDRLHVIAKGRLSPSI-PTRDATREQ 503



 Score = 78.2 bits (191), Expect = 7e-19
 Identities = 69/232 (29%), Positives = 107/232 (46%), Gaps = 29/232 (12%)

Query: 290 GEVLGLAGLVGAGRTELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIA 349
           GE+  + G  GAG++ L +++FGA     G++       +          P  A + GIA
Sbjct: 34  GEIHAVLGENGAGKSTLMKIIFGAVKPDAGDMHFNGARAA-------IHNPHDARNLGIA 86

Query: 350 YLTEDRKLQGLFLDQSVHENINLIVAARDALGLGRLNRTAA--------RRRTTEAIDTL 401
            + +   L   F   +V ENI        ALGL R ++TAA         ++  E I   
Sbjct: 87  MVFQHFSL---FDTLTVAENI--------ALGLPRGSKTAAGSPHAGTNMKQLAEQIRET 135

Query: 402 GIRVA---HAQVNVGALSGGNQQKVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLIN 458
            +R         +V  LS G +Q+V + R L  +P++LILDEPT  +   A   ++  + 
Sbjct: 136 ALRYGLPLEPNRHVHTLSVGERQRVEIVRALLAKPQLLILDEPTSVLTPQAVQTLFITLR 195

Query: 459 ALAQSGVAILMISSELPEVVGLCDRVLVMREGTLAGEVRPAGSAAETQERII 510
            LA  G +IL IS +L E+  LC    VMR G + G   P   +A +  R++
Sbjct: 196 QLAAEGTSILYISHKLDEIRELCHSATVMRMGRVTGVCDPRQESAASLSRLM 247


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: 662
Number of extensions: 40
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 540
Length of database: 529
Length adjustment: 35
Effective length of query: 505
Effective length of database: 494
Effective search space:   249470
Effective search space used:   249470
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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources