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_RS06625 AZOBR_RS06625 heme ABC transporter ATP-binding protein

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>FitnessBrowser__azobra:AZOBR_RS06625
          Length = 511

 Score =  275 bits (703), Expect = 3e-78
 Identities = 191/518 (36%), Positives = 269/518 (51%), Gaps = 22/518 (4%)

Query: 12  PLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGEC 71
           P L  R + K F    A R V L    G +H ++GENGAGKST+M I+ G   AD GG  
Sbjct: 6   PALETRGVNKWFGANHANRDVSLAVPKGTIHGVIGENGAGKSTIMSIVYGYLPAD-GGTI 64

Query: 72  HIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRAC 131
            +DG+ V +  P+ A   G+ +++Q   L    +V EN+ LG      G+     M RA 
Sbjct: 65  LVDGRPVAVRSPRDALAAGIGMVHQHFMLVDPFTVLENVLLGA---EGGVTLAAGMARA- 120

Query: 132 APTLARLGADFSPAAN----VASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETD 187
              L RL  D+    +    V  L +  +Q VEI +A++  A IL++DEPT  L+  ETD
Sbjct: 121 RTELTRLARDYGLEVDLDRPVGELPVGAQQRVEILKALYRGADILILDEPTGVLTPQETD 180

Query: 188 RLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMV 247
            LF ++R LR +G  ++ I+H++ EI EL D VTV+R G  V  +  A  S+  L ++MV
Sbjct: 181 HLFRILRALREQGKTVVIITHKLREIMELTDNVTVMRRGQVVANVATARTSREELAELMV 240

Query: 248 GRDLSGFYTK---THGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRT 304
           GR +     K   T G AV     L VRD A   RVKG    +RAGE++G+AG+ G G++
Sbjct: 241 GRKVLLRVEKVPATPGPAVLEVSGLCVRDGAGVERVKGIGLTVRAGEIVGIAGVSGNGQS 300

Query: 305 ELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQ 364
           EL   + G      G VR+     +       A G R     G+ ++ EDR+  GL    
Sbjct: 301 ELLEALAGMRPPAEGSVRLRGEELTATPDRFTARGLRAL---GVGHVPEDRQRVGLVTGF 357

Query: 365 SVHENINLIVAARDALGLGRL--NRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQK 422
              E   ++    D    GRL  +R A   R    +D   +R    ++     SGGNQQK
Sbjct: 358 EAQE-CAILGHQGDPAFNGRLLMDRRALFDRCASEMDAYDVRPRDPRLPAANFSGGNQQK 416

Query: 423 VMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCD 482
           ++L+R +E  P +L++ +PTRGVDIGA   I+R + AL   G AIL++S EL E+  L D
Sbjct: 417 IVLAREMERNPDLLLVGQPTRGVDIGAIEFIHRRLVALRDQGKAILLVSVELDEIRALSD 476

Query: 483 RVLVMREGTLAGEVRPAGSAAETQERIIALATGAAAAA 520
           R+LVM +G L GEV P     E  ER + L     A A
Sbjct: 477 RILVMFDGRLVGEVAP----GEADERRLGLMMAGVAEA 510


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: 697
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: 511
Length adjustment: 35
Effective length of query: 505
Effective length of database: 476
Effective search space:   240380
Effective search space used:   240380
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