GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__PV4:5208721
          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:

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