GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctA in Cupriavidus basilensis 4G11

Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate RR42_RS33745 RR42_RS33745 C4-dicarboxylate transporter

Query= TCDB::Q848I3
         (444 letters)



>FitnessBrowser__Cup4G11:RR42_RS33745
          Length = 452

 Score =  491 bits (1263), Expect = e-143
 Identities = 248/437 (56%), Positives = 327/437 (74%), Gaps = 2/437 (0%)

Query: 4   RQPLYKSLYFQVIVAIAIGILLGHFYPQTGVALKPLGDGFIKLIKMVIAPIIFCTVVSGI 63
           ++ L  SLY QV++A+A GILLG F P  G ALKPLGD FI+LIKMV APIIF TVV GI
Sbjct: 2   KRRLISSLYVQVLIAVAAGILLGIFMPHIGSALKPLGDIFIRLIKMVFAPIIFATVVLGI 61

Query: 64  AGMQNMKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGNGMHIDVSTLDASKVAAYV 123
           A M++MK +G+ G  ALLYFE++ST ALL+G++VVNVVQPG+GM++D +TLD   +AAY 
Sbjct: 62  AKMESMKDLGRVGWRALLYFEVLSTFALLLGVIVVNVVQPGHGMNVDPATLDTKSIAAYT 121

Query: 124 TAGKDQSIVGFILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPVLDFIDRF 183
              K + I+ F+LN++P +I+ A A  DILQ+L+FSV  G AL  LG  GKP +  +D F
Sbjct: 122 AQVKHEGIMDFLLNLVPMSIMDALAKNDILQILVFSVFMGVALAHLGERGKPFVAALDSF 181

Query: 184 AHVMFNIINMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITCVLFVLVVLGAI 243
           A+ MF I+ MIM++AP+ A GAM+FT+G YG GS+  LG+L+   Y TC LFVL+VLGAI
Sbjct: 182 ANAMFAIVGMIMRVAPVAAFGAMSFTVGKYGFGSIASLGKLVATMYGTCALFVLIVLGAI 241

Query: 244 CRAHGFSVLKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIPTGYSFN 303
           CR  GF +   ++YI++E+L VLGTSSSES +P+++ K+E +G  K VVGLV+P G +FN
Sbjct: 242 CRICGFGLFNFLKYIKDEILTVLGTSSSESVIPQLMRKLENVGVSKPVVGLVVPAGLTFN 301

Query: 304 LDGTSIYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIVLAATLSAV 363
            DG  IY TMAA+FIAQAT+T + +T Q  +L VLLL+SKG+AG+TGSGFI LAATL+++
Sbjct: 302 PDGQCIYYTMAAIFIAQATNTPLTLTDQFVVLGVLLLTSKGSAGITGSGFITLAATLASL 361

Query: 364 GHLPVAGLALILGIDRFMSEARALTNLVGNAVATVVVAKWVKELDEDQLQAELASGGRAI 423
           G +PVAG+ L+LG+DRFMSEARA+TN +GNAVAT+ +AKWV  LDED++Q  L   G   
Sbjct: 362 GKIPVAGMVLLLGVDRFMSEARAITNTIGNAVATMAIAKWVGALDEDRVQRVL--NGEVD 419

Query: 424 SDTREEDDLGVAEGPTP 440
            +  E+   GVA  P P
Sbjct: 420 PEDLEQLYEGVAPEPIP 436


Lambda     K      H
   0.326    0.142    0.402 

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: 586
Number of extensions: 22
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: 444
Length of database: 452
Length adjustment: 33
Effective length of query: 411
Effective length of database: 419
Effective search space:   172209
Effective search space used:   172209
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (24.3 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