GapMind for catabolism of small carbon sources

 

Aligments for a candidate for dctA in Shewanella loihica PV-4

Align aerobic C4-dicarboxylate transport protein (characterized)
to candidate 5208721 Shew_1224 sodium:dicarboxylate symporter (RefSeq)

Query= CharProtDB::CH_014038
         (428 letters)



>lcl|FitnessBrowser__PV4:5208721 Shew_1224 sodium:dicarboxylate
           symporter (RefSeq)
          Length = 416

 Score =  238 bits (607), Expect = 3e-67
 Identities = 136/411 (33%), Positives = 224/411 (54%), Gaps = 12/411 (2%)

Query: 12  QVLTAIAIGILLGHFYPEIGEQMKPLGDGFVKLIKMIIAPVIFCTVVTGIAGMESMKAVG 71
           +VL    +G+ LG    E   Q+KPLGD F+  IKM++AP+IFC +V  I  + +  ++ 
Sbjct: 13  KVLAGFILGVGLGVVLGEQATQLKPLGDLFIAAIKMLVAPLIFCAIVVSITSLGNDVSLK 72

Query: 72  RTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAVAVYADQAKDQGIVA 131
           R     L  F +  TIA +IGL I +++  G  + +  AT + +   V        G   
Sbjct: 73  RLSIKTLAMFMLTGTIASLIGLAIGSLIDMGGSLEL--ATTEVRERNV-------PGFAQ 123

Query: 132 FIMDVIPASVIGAFASGNILQVLLFAVLFGFALHRLGSKGQLIFNVIESFSQVIFGIINM 191
            ++D+IP +   + A G +LQ+++FA L G A++++G K + +   IE+ ++V+F +  M
Sbjct: 124 VLLDMIPVNPFASLAEGKVLQIIVFAALVGIAINKIGEKAEPLKRTIEAGAEVMFQLTRM 183

Query: 192 IMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLIICFYITCILFVVLVLGSIAK-ATGFSIF 250
           +++L PIG FG MA+ +G+YG+ TL+ LG+ I   YI  ++ +V V G + +   G S  
Sbjct: 184 VLQLTPIGVFGLMAWVVGEYGLSTLLPLGKFIGAIYIAALIHMVFVYGGLVRFGAGLSAV 243

Query: 251 KFIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYSFNLDGT-SIYL 309
           +F R      L+   T+SS   LP      E +G  K     V+P G + N+DG   IY 
Sbjct: 244 QFFRKAMPAQLVAFTTASSFGTLPASTRATETMGVSKKYGAFVLPLGATMNMDGCGGIYP 303

Query: 310 TMAAVFIAQATNSQMDIVHQITLLIVLLLSSKGAAGVTGSGFIVLAATLSAVGHLPVAGL 369
            +AA+FIAQ     +++   + + +   ++S G AGV GS  ++L+ TL  VG LP+ G+
Sbjct: 304 AIAAIFIAQIYGIPLEMTDYMLIAVTATVASVGTAGVPGSAMVMLSVTLGVVG-LPLEGI 362

Query: 370 ALILGIDRFMSEARALTNLVGNGVATIVVAKWVKELDHKKLDDVLNNRAPD 420
           A I  IDR +   R  TN+ G+ +  +VV K   +LD ++      + AP+
Sbjct: 363 AFIASIDRVIDMIRTATNVTGDMMTAVVVGKSEGQLDQEQFYRNEESDAPE 413


Lambda     K      H
   0.327    0.142    0.401 

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: 437
Number of extensions: 22
Number of successful extensions: 6
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: 428
Length of database: 416
Length adjustment: 32
Effective length of query: 396
Effective length of database: 384
Effective search space:   152064
Effective search space used:   152064
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 (21.7 bits)
S2: 50 (23.9 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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