GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Bradyrhizobium sp. BTAi1

Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate WP_012042345.1 BBTA_RS09915 sugar ABC transporter ATP-binding protein

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>NCBI__GCF_000015165.1:WP_012042345.1
          Length = 516

 Score =  369 bits (946), Expect = e-106
 Identities = 218/529 (41%), Positives = 314/529 (59%), Gaps = 28/529 (5%)

Query: 1   MSDMSDTSTKAP-LLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKIL 59
           MSD S      P LL +R + K+F  ++AL+ V+ T   GE+HAL+GENGAGKSTL+K++
Sbjct: 1   MSDSSAPPAARPSLLEIRGLTKSFGALKALQDVDFTLGEGEIHALLGENGAGKSTLIKVV 60

Query: 60  SGAYTADPGGECHIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRR 119
           +G +  D  G   + G  +     + A + G+A +YQE++L PNLSVA+N+YLGR   R 
Sbjct: 61  TGVFARD-AGTVRLAGDEIAPRSAKDAVEAGIATVYQEVNLLPNLSVAQNLYLGRQPTRF 119

Query: 120 GLVARGDMVRACAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTT 179
           G+V + +M R     L   G D    A +AS S+A + +  IARAV   AR+L++DEPT 
Sbjct: 120 GVVRQAEMRRRAHALLLDYGLDIDVGAPLASYSVAVQHITAIARAVDLSARVLILDEPTA 179

Query: 180 PLSTHETDRLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQ 239
            L  HE + LF ++R+L  +G+ I+++SH + ++ E+ DRVTVLR+G  +GT D   L +
Sbjct: 180 SLDRHEVEILFRVMRKLAADGIGIVFVSHFLDQVYEICDRVTVLRNGRLIGTRDITDLPR 239

Query: 240 AALVKMMVGRDLSGFYTKTHGQAVE-----REVMLSVRDVADGRRVKGCSFDLRAGEVLG 294
             L++MM+GR+L+     TH +A       REV +S +       V     +LR GEV+G
Sbjct: 240 LDLIRMMLGRELA---ETTHERAASQPDTAREVCVSFKGFGKQGYVAPFDLELRRGEVVG 296

Query: 295 LAGLVGAGRTELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTED 354
           LAGL+G+GRTE ARLVFGA+    GE  +A  A       +    PR A   G  Y  E+
Sbjct: 297 LAGLLGSGRTETARLVFGAERADSGEASVAGKA-------VRLNSPRDAAGLGFGYCPEE 349

Query: 355 RKLQGLFLDQSVHENINLIVAARDALGLGRLNRTAARRRTTEA----IDTLGIRVAHAQV 410
           RK +G+  D +V ENI L + AR       L+R  +RR   E     I  L IR    + 
Sbjct: 350 RKTEGIVADLTVRENIVLALQARRG-----LHRPLSRREQDEIAMRYIRMLDIRPPDPER 404

Query: 411 NVGALSGGNQQKVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMI 470
            +G LSGGNQQK +L+R L   P++L+LDEPTRG+D+GA +EI RL+  L + G+A+L+I
Sbjct: 405 PIGLLSGGNQQKALLARWLATSPKLLVLDEPTRGIDVGAHAEIIRLVRDLCEQGLALLVI 464

Query: 471 SSELPEVVGLCDRVLVMREGTLAGEVRPAGSAAETQERIIALATGAAAA 519
           SSEL E+V   +RV+V+R+     E++  G A E    + A+A  A  A
Sbjct: 465 SSELDEIVTYSNRVVVLRDRAHVEELK--GDAVEVSSILAAIAADAPTA 511


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: 667
Number of extensions: 33
Number of successful extensions: 8
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: 516
Length adjustment: 35
Effective length of query: 505
Effective length of database: 481
Effective search space:   242905
Effective search space used:   242905
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 Apr 09 2024. 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