GapMind for catabolism of small carbon sources

 

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

Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate 5208231 Shew_0743 sodium:dicarboxylate symporter (RefSeq)

Query= TCDB::Q848I3
         (444 letters)



>FitnessBrowser__PV4:5208231
          Length = 433

 Score =  254 bits (648), Expect = 5e-72
 Identities = 139/410 (33%), Positives = 236/410 (57%), Gaps = 16/410 (3%)

Query: 11  LYFQVIVAIAIGILLGHFYPQTGVALKPLGDGFIKLIKMVIAPIIFCTVVSGIAGMQNMK 70
           L+ Q+++ + +GI  G    +  V LKP+G  F+  IKM+I P++FC+++ G+  MQ+  
Sbjct: 22  LWLQILIGMLLGICAGLGLGEQAVLLKPIGTLFVNTIKMLIVPLVFCSLIVGVTSMQDTA 81

Query: 71  SVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGNGMHIDVSTLDASKVAAYVTAGKDQS 130
            +G+ G  +  ++   ++IA+ +GL V +++QPG G+ +       +   ++    +  S
Sbjct: 82  KMGRIGFKSFAFYLGTTSIAITLGLAVGHIMQPGAGLAM-------TSAESHNAVKEVPS 134

Query: 131 IVGFILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPVLDFIDRFAHVMFNI 190
           I+  ++N++P   + A A+G ILQV++F+V  G AL  +G +GKP +   +  A  M+ +
Sbjct: 135 IMETLINIVPTNPIAALASGQILQVIVFAVALGIALVLIGDHGKPAIKVFESLAEAMYKL 194

Query: 191 INMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITCVLFVL----VVLGAICRA 246
            +M+MKLAP G  G MA+  G YG+  L+ L ++++  YI C L ++    +VL  + + 
Sbjct: 195 TDMVMKLAPYGVFGLMAWVAGEYGMDMLMPLIKVILAVYIGCALHIIGFYSLVLTFVAK- 253

Query: 247 HGFSVLKLIRYIREELLIVLGTSSSESALP-RMLIKMERLGAKKSVVGLVIPTGYSFNLD 305
              + ++  + I   L +   TSSS   LP  M    E LG  K +   V+P G + N+D
Sbjct: 254 --LNPMQFFKGISNALAVAYTTSSSAGTLPASMKCASESLGINKKISSFVLPLGTTINMD 311

Query: 306 GTSIYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIVLAATLSAVGH 365
           GT++Y  + A+F+AQA    +     IT++L   L+S G AGV G+G ++L   L+ VG 
Sbjct: 312 GTALYQGVTALFVAQAFGIDLTWVDYITIILTATLASIGTAGVPGAGLVMLTLVLTTVG- 370

Query: 366 LPVAGLALILGIDRFMSEARALTNLVGNAVATVVVAKWVKELDEDQLQAE 415
           LP+ G+A+I GIDR +  AR + N+ G+ VAT V+AK   ELD +   A+
Sbjct: 371 LPLEGVAIIAGIDRILDMARTVVNVSGDLVATTVIAKSEDELDLEHYNAD 420


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: 466
Number of extensions: 35
Number of successful extensions: 5
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: 433
Length adjustment: 32
Effective length of query: 412
Effective length of database: 401
Effective search space:   165212
Effective search space used:   165212
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