GapMind for catabolism of small carbon sources

 

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

Align ABC transporter permease (characterized, see rationale)
to candidate Ac3H11_1841 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)

Query= uniprot:A0A166R405
         (325 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1841
          Length = 892

 Score =  401 bits (1030), Expect = e-116
 Identities = 203/305 (66%), Positives = 254/305 (83%)

Query: 17  LGTYLGLAGALLAMVALFSVLSSHFLSYDTFSTLANQIPDLMVLAVGMTFVLIIGGIDLS 76
           LGTYLGL   L  MVALFS LS +F S +TF T+AN+IP L V+AVGMTFVLII GIDLS
Sbjct: 586 LGTYLGLLAVLAGMVALFSSLSEYFWSAETFITIANEIPALAVMAVGMTFVLIIAGIDLS 645

Query: 77  VGSVLALAASAVSVAILGWGWSVLPAALLGMAVAALAGTITGSITVAWRIPSFIVSLGVL 136
           VGSV+ALAA+  + AIL WGW+V  AA L +A   + GTITG+I+VAWR+PSFIVSLG+L
Sbjct: 646 VGSVMALAAATSAAAILQWGWTVPAAAALALATGLVCGTITGAISVAWRLPSFIVSLGML 705

Query: 137 EMARGLAYQMTGSRTAYIGDAFAWLSNPIAFGISPSFIIALLIIFIAQAVLTRTVFGRYL 196
           E  RG AY +T SRT Y+GDA +WLS P   GIS +F++A++++ +AQ VL+RTVFGR +
Sbjct: 706 EAVRGSAYVVTDSRTQYVGDAISWLSAPFFGGISFAFLLAVVLVVVAQLVLSRTVFGRCV 765

Query: 197 IGIGTNEEAVRLAGINPKPYKILVFSLMGLLAGIAALFQISRLEAADPNAGSGLELQVIA 256
           +GIGTNEEA+RLAG++P+P +++VF++ GLLAG+A L Q +RLEAADPNAG+G+ELQVIA
Sbjct: 766 VGIGTNEEAMRLAGVDPRPIRVIVFAMTGLLAGLAGLMQSARLEAADPNAGTGMELQVIA 825

Query: 257 AVVIGGTSLMGGRGSVISTFFGVLIISVLAAGLAQIGATEPTKRIITGAVIVVAVVLDTY 316
           AVVIGGTSLMGGRGSV++T FGVLII+VL AGLAQ+GA+EP+KRIITG VIV AV++DT 
Sbjct: 826 AVVIGGTSLMGGRGSVVNTAFGVLIIAVLEAGLAQVGASEPSKRIITGFVIVAAVIVDTL 885

Query: 317 RSQRA 321
           R +RA
Sbjct: 886 RQRRA 890


Lambda     K      H
   0.325    0.139    0.393 

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: 617
Number of extensions: 19
Number of successful extensions: 1
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: 325
Length of database: 892
Length adjustment: 35
Effective length of query: 290
Effective length of database: 857
Effective search space:   248530
Effective search space used:   248530
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: 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