GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctA in Shewanella amazonensis SB2B

Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate 6938665 Sama_2768 proton/glutamate symporter (RefSeq)

Query= TCDB::Q848I3
         (444 letters)



>FitnessBrowser__SB2B:6938665
          Length = 430

 Score =  255 bits (652), Expect = 2e-72
 Identities = 140/421 (33%), Positives = 238/421 (56%), Gaps = 11/421 (2%)

Query: 11  LYFQVIVAIAIGILLGHFYPQTGVALKPLGDGFIKLIKMVIAPIIFCTVVSGIAGMQNMK 70
           L+ Q++  + +GI +G        ALKP+G  F+  IKM+I P++FC+++ G+  MQ+  
Sbjct: 18  LWLQILTGMLLGIGVGLVLGPDASALKPIGTLFVNTIKMLIVPLVFCSLIVGVTSMQDTA 77

Query: 71  SVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGNGMHIDVSTLDASKVAAYVTAGKDQS 130
            +G+ G  +  ++   + IA+ +GL+V  +++PG G+ ++   L A    A        S
Sbjct: 78  RMGRIGFKSFAFYLATTAIAISVGLMVGWLLEPGAGLSLEGHDLSAEVKTA-------PS 130

Query: 131 IVGFILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPVLDFIDRFAHVMFNI 190
           ++  ++N++P   V A A+G ILQV++F+V  G AL  +G +GKP +   +  A  M+ +
Sbjct: 131 VMDTLINIVPTNPVAALASGQILQVIVFAVALGVALVLIGDHGKPAIKVFESLAEAMYKL 190

Query: 191 INMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITCVLFVLVVLGAICR-AHGF 249
            +M+MKLAP G  G MA+  G YG+  L+ L +++I  Y+ C L +L     + +   G 
Sbjct: 191 TDMVMKLAPYGVFGLMAWVAGEYGIDMLLPLIKVIIAVYLGCALHILGFYSLVLKLVAGL 250

Query: 250 SVLKLIRYIREELLIVLGTSSSESALP-RMLIKMERLGAKKSVVGLVIPTGYSFNLDGTS 308
           S ++  + I   + +   TSSS   LP  M    E LG  K +   V+P G + N+DGT+
Sbjct: 251 SPIQFFKGISNAMAVAFTTSSSAGTLPASMKCASEYLGVNKKISSFVLPLGTTINMDGTA 310

Query: 309 IYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIVLAATLSAVGHLPV 368
           +Y  + A+F+AQA    +     +T++L   L+S G AGV G+G ++L   L+ VG LP+
Sbjct: 311 LYQGVTALFVAQAFGVDLTWVDYLTIVLTATLASIGTAGVPGAGLVMLTLVLTTVG-LPL 369

Query: 369 AGLALILGIDRFMSEARALTNLVGNAVATVVVAKWVKELDEDQLQAELASGGRAISDTRE 428
            G+A+I GIDR +  AR + N+ G+ VAT V+A+   E+D     A++ +    ++  RE
Sbjct: 370 EGVAIIAGIDRILDMARTVVNVSGDLVATTVIARSEGEIDIAHYNADMETSSE-MAQARE 428

Query: 429 E 429
           +
Sbjct: 429 D 429


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: 470
Number of extensions: 34
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: 444
Length of database: 430
Length adjustment: 32
Effective length of query: 412
Effective length of database: 398
Effective search space:   163976
Effective search space used:   163976
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