GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctA in Pseudomonas putida KT2440

Align C4-dicarboxylate transport protein 2 (characterized)
to candidate PP_2056 PP_2056 C4-dicarboxylate transport protein

Query= SwissProt::Q9I4F5
         (436 letters)



>FitnessBrowser__Putida:PP_2056
          Length = 435

 Score =  471 bits (1211), Expect = e-137
 Identities = 229/411 (55%), Positives = 308/411 (74%)

Query: 8   KSLYVQVLVAIAIGIALGHWYPETAVAMKPFGDGFVKLIKMAIAPIIFCTVVTGIAGMQS 67
           KSLY Q+L A+ +G+ +GH++ + AVA+KP GD F+KLIKM IAP++FCT+VTGIAGM  
Sbjct: 5   KSLYFQILCAVLLGVVVGHFWAQQAVALKPLGDAFIKLIKMMIAPVVFCTIVTGIAGMTD 64

Query: 68  MKSVGKTGGMALLYFEVVSTVALIIGLVVVNVVQPGAGMHVDPNTLDTSKIAAYAAAGEK 127
            +S+G+     LL F  ++ V+L+IGL  V + +PGAGM++DP TL T+ ++ Y A+  K
Sbjct: 65  KRSLGRLMSKTLLLFLGLTVVSLVIGLAAVYLFKPGAGMNIDPATLSTAGLSQYTASAAK 124

Query: 128 QSTVDFLMNVIPGTVVGAFANGDILQVLFFSVLFGYALHRLGSYGKPVFEFIERVSHVMF 187
            S VDF M++IP T +GAF  G++L VLF +VL G+AL  +G  GKPV + +E  S ++F
Sbjct: 125 LSVVDFFMHIIPDTFIGAFNKGEVLPVLFIAVLSGFALSSMGEKGKPVLDVLESASTMVF 184

Query: 188 NIINVIMKVAPIGAFGAMAFTIGAYGVGSLVQLGQLMLCFYITCILFVLIVLGGIARAHG 247
            I   +M+ APIGAFGA+AFT+G YG+ SL  L +L+   YI C  FVL+VLGGI RAHG
Sbjct: 185 RIFGYLMRFAPIGAFGALAFTVGQYGITSLGALAKLVGTLYIACAFFVLVVLGGICRAHG 244

Query: 248 FSILRFIRYIREELLIVLGTSSSESALPRMIDKMEKLGCNKSVVGLVIPTGYSFNLDGTS 307
           FS+ + +RY REE L+VLGTSS+E  LPRM++K+EKLGC K VVGLV+PTGYSFNLDGT+
Sbjct: 245 FSLWKLLRYFREEFLVVLGTSSTEPVLPRMLEKLEKLGCKKGVVGLVLPTGYSFNLDGTA 304

Query: 308 IYLTMAAVFIAQATDTPMDITHQITLLLVLLIASKGAAGVTGSGFIVLAATLSAVGHLPV 367
           IYL++AAVFIAQA +  + +   +T+L ++L++SKGAAGVTGSGF+ LA+TL+ +  +P+
Sbjct: 305 IYLSLAAVFIAQACNIDLSLGQVVTMLAIMLLSSKGAAGVTGSGFVALASTLTVIHDIPL 364

Query: 368 AGLALILGIDRFMSEARALTNLVGNGVATVVVSKWCKQLDEGTLQRELAGE 418
           AGLAL++G+DRFMSEARALT+L  N VATVVVS      D  TL   L GE
Sbjct: 365 AGLALLIGVDRFMSEARALTSLASNAVATVVVSLSENACDRQTLHSRLNGE 415


Lambda     K      H
   0.325    0.140    0.406 

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: 577
Number of extensions: 29
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: 436
Length of database: 435
Length adjustment: 32
Effective length of query: 404
Effective length of database: 403
Effective search space:   162812
Effective search space used:   162812
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: 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