GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Rhizobium freirei PRF 81

Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate WP_086005351.1 RHSP_RS08730 sugar ABC transporter ATP-binding protein

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>NCBI__GCF_000359745.1:WP_086005351.1
          Length = 477

 Score =  355 bits (910), Expect = e-102
 Identities = 205/476 (43%), Positives = 293/476 (61%), Gaps = 11/476 (2%)

Query: 32  VELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECHIDGQRVQIDGPQSARDLGV 91
           + L    G VH L+GENGAGKSTLMKIL+G Y     GE  + G+  Q   P+ AR  G+
Sbjct: 1   MNLKVRRGRVHTLLGENGAGKSTLMKILAGVYKPT-SGEILLAGKAYQPQNPRDARGHGI 59

Query: 92  AVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRACAPTLARLGADFSPAANVASL 151
           ++++QELSL  NLSVA+NI+      R G V    +V      +  LG   +  A V  L
Sbjct: 60  SIVFQELSLCRNLSVAQNIFASHEPSRFGFVRDRVLVAKAEALIEDLGLPVNVHAKVGDL 119

Query: 152 SIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFALIRQLRGEGMAILYISHRMA 211
           SIAQRQLVEIA+ +   A ++++DEPT+ LS  E + LF++I +L+  G AI+YISHRM 
Sbjct: 120 SIAQRQLVEIAKGLSLPADVIILDEPTSSLSDSEAEILFSIIERLKARGKAIIYISHRME 179

Query: 212 EIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRDLSGFYTKTHGQ--AVEREVML 269
           EI  L+D +TV+RDG +V T +++  S   L+ +MVGR++   Y        A     +L
Sbjct: 180 EIMRLSDDITVIRDGEYVTTTEKSETSIDKLIALMVGREMQDIYPPRVAPRPAESTAPVL 239

Query: 270 SVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELARLVFGADARTRGEVRIANPAGS 329
           + +++    +    S D++ GEV+GL GL+G+GR+++ + +FG + R  G++ +      
Sbjct: 240 ATKNLTVPGKFHEVSIDVKPGEVVGLFGLIGSGRSDIMKALFGME-RPEGQIFL-----D 293

Query: 330 GGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHENINLIVAARDALGLGRLNRTA 389
           G  +TL +  P  AI  GIA++TE+RK +GL L  SV  N+N++   + A   G +  +A
Sbjct: 294 GKPLTLAS--PSDAIRHGIAFVTENRKEEGLVLAHSVERNVNMVALKQLAGPFGLMRGSA 351

Query: 390 ARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSRLLEIQPRVLILDEPTRGVDIGA 449
            R      +  L I+ A    + G+LSGGNQQK++L++ L+I+PRVLILDEPTRGVD+GA
Sbjct: 352 ERAAAKAEVLRLAIKAASIDTSTGSLSGGNQQKIVLAKWLQIRPRVLILDEPTRGVDVGA 411

Query: 450 KSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMREGTLAGEVRPAGSAAET 505
           K EIYR+I  LA  G AILM+SSELPEV+GL DRV VM   +LA  +   G   ET
Sbjct: 412 KFEIYRIIRELAAEGAAILMVSSELPEVLGLSDRVAVMHNRSLAAVLDAEGLTPET 467



 Score = 90.5 bits (223), Expect = 1e-22
 Identities = 73/245 (29%), Positives = 117/245 (47%), Gaps = 13/245 (5%)

Query: 11  APLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGE 70
           AP+LA +N+  T PG     +V +    GEV  L G  G+G+S +MK L G     P G+
Sbjct: 236 APVLATKNL--TVPG--KFHEVSIDVKPGEVVGLFGLIGSGRSDIMKALFGMER--PEGQ 289

Query: 71  CHIDGQRVQIDGPQSARDLGVAVIYQ---ELSLAPNLSVAENIYLGRALQRRGL--VARG 125
             +DG+ + +  P  A   G+A + +   E  L    SV  N+ +    Q  G   + RG
Sbjct: 290 IFLDGKPLTLASPSDAIRHGIAFVTENRKEEGLVLAHSVERNVNMVALKQLAGPFGLMRG 349

Query: 126 DMVRACAPT-LARLGADFSPA-ANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLST 183
              RA A   + RL    +    +  SLS   +Q + +A+ +    R+L++DEPT  +  
Sbjct: 350 SAERAAAKAEVLRLAIKAASIDTSTGSLSGGNQQKIVLAKWLQIRPRVLILDEPTRGVDV 409

Query: 184 HETDRLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALV 243
                ++ +IR+L  EG AIL +S  + E+  L+DRV V+ +      LD   L+   ++
Sbjct: 410 GAKFEIYRIIRELAAEGAAILMVSSELPEVLGLSDRVAVMHNRSLAAVLDAEGLTPETVM 469

Query: 244 KMMVG 248
               G
Sbjct: 470 TYAAG 474


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: 619
Number of extensions: 28
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: 477
Length adjustment: 34
Effective length of query: 506
Effective length of database: 443
Effective search space:   224158
Effective search space used:   224158
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 24 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