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_RS31210 AZOBR_RS31210 sugar ABC transporter ATP-binding protein

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>FitnessBrowser__azobra:AZOBR_RS31210
          Length = 516

 Score =  362 bits (930), Expect = e-104
 Identities = 219/526 (41%), Positives = 304/526 (57%), Gaps = 17/526 (3%)

Query: 1   MSDMSDTSTKAPLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILS 60
           M+D + T++  PLLA+R + K F GV+AL  V+ T   GE+HAL+GENGAGKSTL+K L+
Sbjct: 1   MTDPTPTASP-PLLAIRGLSKAFLGVQALDGVDFTVRHGEIHALLGENGAGKSTLIKTLT 59

Query: 61  GAYTADPGGECHIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRG 120
           G Y  D  G   ++G+ +   G + A+ L +  +YQE++L PNLSVAEN++LGR   R G
Sbjct: 60  GVYQRD-AGTVTLEGRAIAPRGVEEAQRLHIGTVYQEVNLLPNLSVAENLFLGRQPMRFG 118

Query: 121 LVARGDMVRACAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTP 180
           LV RG M R     L   G      A +   S+A +Q+V IARAV   A++L++DEPT  
Sbjct: 119 LVDRGAMRRRARAVLIPYGLTLDVTAPLGRFSVATQQIVAIARAVDMSAKVLILDEPTAS 178

Query: 181 LSTHETDRLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQA 240
           L   E   LF ++R LR  G+ I++++H + ++  L DR+TVLR+G  VG    A L + 
Sbjct: 179 LDAQEVAVLFKVMRTLRSRGIGIVFVTHFLDQVYALCDRITVLRNGRLVGERRTAELPRL 238

Query: 241 ALVKMMVGRDLSGFYTKTHGQAVE-----REVMLSVRDVADGRRVKGCSFDLRAGEVLGL 295
            LV MM+GR+L     +    A +     R  ++  R     R V+    D+R GEV+GL
Sbjct: 239 DLVAMMLGRELEAVAHRIAPPADDAEEDARPPLVRFRGYGKARSVEPFDLDIRPGEVVGL 298

Query: 296 AGLVGAGRTELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDR 355
           AGL+G+GRTE ARLVFG D   RGE  +   A       +   GPR AI  G  +  EDR
Sbjct: 299 AGLLGSGRTETARLVFGMDRADRGEAAVDGQA-------VRLRGPRDAIRLGFGFCPEDR 351

Query: 356 KLQGLFLDQSVHENINLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGAL 415
           K +G+    SV ENI L + AR    L  + R          I  L IR  HA+  +  L
Sbjct: 352 KKEGIVGALSVRENIILALQARQG-WLRPIPRCRQEEIADRFIRLLDIRTPHAEQPIQLL 410

Query: 416 SGGNQQKVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELP 475
           SGGNQQK +L+R L  +PR+LILDEPTRG+D+GA +EI RLI  L   G+A+L++SSEL 
Sbjct: 411 SGGNQQKALLARWLATEPRLLILDEPTRGIDVGAHAEIIRLIERLCADGMALLVVSSELE 470

Query: 476 EVVGLCDRVLVMREGTLAGEVRPAGSAAETQERIIALATGAAAAAP 521
           E+V    RV+V+R+     E+R  G        + A+A+ +    P
Sbjct: 471 EIVAYSRRVVVLRDRRHVAELR--GGEVAVDRIVAAIASESVPEEP 514


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: 690
Number of extensions: 37
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: 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 Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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