Alignments for a candidate for frcA in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for frcA in Azospirillum brasilense Sp245

Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate AZOBR_RS06950 AZOBR_RS06950 ABC transporter

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>FitnessBrowser__azobra:AZOBR_RS06950
          Length = 520

 Score =  281 bits (719), Expect = 4e-80
 Identities = 194/506 (38%), Positives = 278/506 (54%), Gaps = 27/506 (5%)

Query: 3   DMSDTSTKAPLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGA 62
           D    S+    L LR I K FPG  A  +V+L    GE+HAL+GENGAGKSTL+KI+ G 
Sbjct: 2   DSPSVSSPPHRLELRGITKRFPGCLANDQVDLVLRPGEIHALLGENGAGKSTLVKIIYGV 61

Query: 63  YTADPGGECHIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLV 122
             AD  G    +G    I  P  AR LG+ +++Q  SL   L+VAENI LG  L + G +
Sbjct: 62  LHAD-AGRIQWNGHDTHIPDPAGARRLGIGMVFQHFSLFDTLTVAENISLG--LDQPGPI 118

Query: 123 ARGDMVRA-CAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPL 181
              D + A  A    R G    P  +V +LS+ +RQ VEI R +  + ++L+MDEPT+ L
Sbjct: 119 ---DALSARIAEVSERYGLSLDPRRHVHNLSVGERQRVEIVRCLLQDPKLLIMDEPTSVL 175

Query: 182 STHETDRLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAA 241
           +  E  RLF  +R+L  EG  ILYISH++ EI  L D  TVLR G  VG+ D    +  +
Sbjct: 176 TPQEATRLFETLRRLAAEGCTILYISHKLEEIRALCDTATVLRGGRVVGSCDPRRETARS 235

Query: 242 LVKMMVGRDLSGFYTKTHGQAVEREVML----SVRDVADGRRVKGCSFDLRAGEVLGLAG 297
           L +MM+G +LS       G+A   ++ +    +  D      +K  SF++RAGE+LG+AG
Sbjct: 236 LAEMMIGTELSTPERLPQGEAGAAKLQVRHLSTTSDNPFATNLKDVSFEVRAGEILGIAG 295

Query: 298 LVGAGRTELARLVFGADARTRGEVRIANPAGSGGLVTLPAG--GPRQAIDAGIAYLTEDR 355
           + G G+ EL        A   GE  + +PA S  +   PAG  GPR+    G+A++ E+R
Sbjct: 296 VAGNGQAELM-------AALSGEALVPDPA-SVAIEGRPAGHLGPRERRLLGLAFVPEER 347

Query: 356 KLQGLFLDQSVHENINLIVAARDAL---GLGRLNRTAARRRTTEAIDTLGIRVAHAQVNV 412
             +G   + S+ EN  L   AR+ L   GL    R  AR      I    +     +   
Sbjct: 348 LGRGAVPELSLSENALLSGYAREPLVRSGLVHFGR--ARSYAERIIGAFNVVTHGHRAEA 405

Query: 413 GALSGGNQQKVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISS 472
            +LSGGN QK ++ R +  +PR+L++ +PT GVD GA + I+R +  LA++G A+L+IS 
Sbjct: 406 RSLSGGNLQKFIIGREILQKPRLLVVGQPTWGVDAGAAAAIHRALIDLARAGAAVLVISQ 465

Query: 473 ELPEVVGLCDRVLVMREGTLAGEVRP 498
           +L E+  L DR+ V+  G L+ E RP
Sbjct: 466 DLDELFVLSDRIAVLFHGHLS-ESRP 490



 Score = 74.7 bits (182), Expect = 8e-18
 Identities = 65/235 (27%), Positives = 104/235 (44%), Gaps = 21/235 (8%)

Query: 287 LRAGEVLGLAGLVGAGRTELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDA 346
           LR GE+  L G  GAG++ L ++++G      G ++     G    +  PAG  R  I  
Sbjct: 35  LRPGEIHALLGENGAGKSTLVKIIYGVLHADAGRIQWN---GHDTHIPDPAGARRLGIGM 91

Query: 347 GIAYLTEDRKLQGLFLDQSVHENINLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVA 406
              + +       LF   +V ENI+L +     +        A   R  E  +  G+ + 
Sbjct: 92  VFQHFS-------LFDTLTVAENISLGLDQPGPID-------ALSARIAEVSERYGLSLD 137

Query: 407 HAQVNVGALSGGNQQKVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVA 466
             + +V  LS G +Q+V + R L   P++LI+DEPT  +     + ++  +  LA  G  
Sbjct: 138 PRR-HVHNLSVGERQRVEIVRCLLQDPKLLIMDEPTSVLTPQEATRLFETLRRLAAEGCT 196

Query: 467 ILMISSELPEVVGLCDRVLVMREGTLAGEVRPAGSAAETQERIIALATGAAAAAP 521
           IL IS +L E+  LCD   V+R G + G   P     ET   +  +  G   + P
Sbjct: 197 ILYISHKLEEIRALCDTATVLRGGRVVGSCDP---RRETARSLAEMMIGTELSTP 248



 Score = 67.4 bits (163), Expect = 1e-15
 Identities = 72/251 (28%), Positives = 106/251 (42%), Gaps = 16/251 (6%)

Query: 11  APLLALRNICKTF--PGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPG 68
           A  L +R++  T   P    L+ V     AGE+  + G  G G++ LM  LSG       
Sbjct: 258 AAKLQVRHLSTTSDNPFATNLKDVSFEVRAGEILGIAGVAGNGQAELMAALSGEALVPDP 317

Query: 69  GECHIDGQRVQIDGPQSARDLGVAVIYQEL---SLAPNLSVAENI----YLGRALQRRGL 121
               I+G+     GP+  R LG+A + +E       P LS++EN     Y    L R GL
Sbjct: 318 ASVAIEGRPAGHLGPRERRLLGLAFVPEERLGRGAVPELSLSENALLSGYAREPLVRSGL 377

Query: 122 VARGDMVRACAPTLARLGA----DFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEP 177
           V  G   RA +     +GA         A   SLS    Q   I R +  + R+LV+ +P
Sbjct: 378 VHFG---RARSYAERIIGAFNVVTHGHRAEARSLSGGNLQKFIIGREILQKPRLLVVGQP 434

Query: 178 TTPLSTHETDRLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHL 237
           T  +       +   +  L   G A+L IS  + E+  L+DR+ VL  G    +    H 
Sbjct: 435 TWGVDAGAAAAIHRALIDLARAGAAVLVISQDLDELFVLSDRIAVLFHGHLSESRPTHHT 494

Query: 238 SQAALVKMMVG 248
           S   +  +M G
Sbjct: 495 SVEEIGLLMGG 505


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: 687
Number of extensions: 27
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 4
Number of HSP's successfully gapped: 3
Length of query: 540
Length of database: 520
Length adjustment: 35
Effective length of query: 505
Effective length of database: 485
Effective search space:   244925
Effective search space used:   244925
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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Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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