GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcC in Acidovorax sp. GW101-3H11

Align Ribose ABC transport system, permease protein RbsC (characterized, see rationale)
to candidate Ac3H11_2880 Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)

Query= uniprot:A0A0C4Y7K0
         (337 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2880
          Length = 350

 Score =  173 bits (438), Expect = 7e-48
 Identities = 117/347 (33%), Positives = 185/347 (53%), Gaps = 25/347 (7%)

Query: 3   ESITRPAASTGAPLPAGTLGRLTTQERLRALGMLPVLVLLCIGFSVLTENFAGWQNLSII 62
           E+   P A       A   G      +L  LG +  LVLLCI  ++L  NFA + N+  +
Sbjct: 11  ENAAAPQAGGSRHAAAAATGASAWWGKLHGLGPVIGLVLLCIAGTLLNSNFATYDNVMNV 70

Query: 63  AQQASINMVLAAGMTFVILTGGIDLSVGSILSISA--VVAMLVSLMPQLG------MLSV 114
             + +   ++A GM FVI++GGIDLSVGS+ ++ A  V+  + ++ P LG      ++ +
Sbjct: 71  LTRTAFIGIIAVGMCFVIISGGIDLSVGSMAALIAGSVILFMNAMAPVLGSPMAAVVVGM 130

Query: 115 PAALLCGLLFGIVNGALVAFMKLPPFIVTLGTLTAVR---------GLARLVGNDSTIYN 165
             A++ G +FG+V+G L+   ++ PFIVTLGTL   R         G   L  + S IY+
Sbjct: 131 LLAVVLGAVFGLVHGLLITKGRIEPFIVTLGTLGIFRAYLTYFSNGGAITLENDLSDIYS 190

Query: 166 PDIGFAFIGNGEVLGVPWLVIIAFAVVAVSWFVLRRTVLGLQIYAVGGNAEAARLSGIKV 225
           P      +    +LGVP  V I   V  V   +L RT  G  + A+G N + A+ + + V
Sbjct: 191 P------VYYANLLGVPIPVWIFLLVAIVGGVILNRTAYGRYVQAIGSNEQVAQYAAVDV 244

Query: 226 WVVLLFVYAVSGLLAGLGGVMSSARLYAANGLQLGQSYELDAIAAVILGGTSFVGGTGSI 285
             + +  Y + G+  G+  ++   RL +A+    G  +EL+AIAAVI+GGT   GG GSI
Sbjct: 245 HKIKILTYMLLGVCVGIATLLYVPRLGSASP-TTGLLWELEAIAAVIVGGTVLKGGAGSI 303

Query: 286 VGTLVGALIIAVLSNGLVLLGVSDIW-QYIIKGLVIIGAVALDSYRR 331
            GT+VGA++++V+SN L L  +  ++    ++G VII    +   +R
Sbjct: 304 TGTVVGAILLSVISNILNLTSIISVYLNAAVQGFVIIAVAFMQRGKR 350


Lambda     K      H
   0.325    0.141    0.409 

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: 399
Number of extensions: 21
Number of successful extensions: 4
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: 337
Length of database: 350
Length adjustment: 29
Effective length of query: 308
Effective length of database: 321
Effective search space:    98868
Effective search space used:    98868
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 49 (23.5 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