GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctM in Marinobacter adhaerens HP15

Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized, see rationale)
to candidate GFF3083 HP15_3026 TRAP dicarboxylate transporter, DctM subunit

Query= uniprot:Q9KQS1
         (453 letters)



>FitnessBrowser__Marino:GFF3083
          Length = 499

 Score =  191 bits (484), Expect = 6e-53
 Identities = 126/463 (27%), Positives = 228/463 (49%), Gaps = 41/463 (8%)

Query: 5   LLFILVIGMMIVGVPIAISLGLSSILFLLWHSDASLASVAQTLFNAFAGHYTLLAIPFFI 64
           L+F  +   +++G+P+A   G   ++F+    DA + ++          +  + AIP FI
Sbjct: 58  LMFGSLAVALMMGLPLAFVTGGLGVMFIYLVGDAMMLNIVPGRIFPLMANPDIAAIPLFI 117

Query: 65  LASTFMSTGGVAKRIIRFAIAMVGWFRGGLAIASVVACMMFAALSGSSPATVVAIGSIVI 124
             ++ +   G+ + +       +G   GGLA A++VA  + AA+ G   A VV +G I +
Sbjct: 118 FMASMLERAGLIEEMFSVVYKWMGGISGGLAAATIVASTILAAMVGVIGAAVVTMGIIAL 177

Query: 125 AGMVKNGYSKEFAAGVICNAGTLGILIPPSIVMVVYSAATNVSVGRMFLGGVVPGL-LAG 183
             M+K  Y  + A G I   GTLGILIPPSI+ ++Y+     SVG ++LG ++PGL L+G
Sbjct: 178 PAMLKRHYDHKIAIGSIMAGGTLGILIPPSILAILYAVVAQQSVGELYLGSLLPGLMLSG 237

Query: 184 LML---IIAIYITARI-KNLPKQPFVGWKEALKAAKEASWGLLLVVIILGGIYGGIFTPT 239
           L L   ++  ++  ++   +P +  +  KE LK        L LV ++LG ++GGI TP 
Sbjct: 238 LYLTYVLVRSWLNPKLGPPIPVEDRISLKEKLKLLGNLIAPLALVGLVLGLLFGGIATPV 297

Query: 240 EAAAVAAVYSFFIANFIYRDMGPFADKTNTKPVLVKVVETFVHKDTKATLYDAGKLTIML 299
           EAA + +  +  +A                      + + F     +       K + M+
Sbjct: 298 EAAGIGSFGAIIVA---------------------MMHKKFSIAGLREASVTTAKASAMV 336

Query: 300 MFIIANALILKHVLTEERIPQMITESMLSAGLGPITFLIVVNLILLVGGQFMEPSGLLVI 359
           ++I+  A +       +   Q +T+++L  G+     L ++ ++L+V G F++  G+L++
Sbjct: 337 LWIMFGASVFVGFYILQGGQQFVTDAILGTGMSAYGILFLLMVLLVVLGMFLDWVGILLL 396

Query: 360 VAPLVFPIAIAL------GIDPI-------HLGIMMVVNMEIGMITPPVGLNLFVTSGVA 406
             P+  PI  AL      G  P+         G++ +VNM++  ++PP G  LF   GV 
Sbjct: 397 AVPIFIPIVKALEFPGLFGFPPVAGDDVVLWFGVLYLVNMQMSFLSPPFGYALFYIRGVC 456

Query: 407 --KMSMMNVVKAALPWVGVMFLFLIIVTYVPWVSTWLPTLLMG 447
             ++SM  + K++L ++ +    L +   +P + TWLP L+ G
Sbjct: 457 PPEISMGTIFKSSLVFLAIQAFGLFMCVLIPGIVTWLPGLVYG 499


Lambda     K      H
   0.329    0.142    0.421 

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: 641
Number of extensions: 29
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 453
Length of database: 499
Length adjustment: 33
Effective length of query: 420
Effective length of database: 466
Effective search space:   195720
Effective search space used:   195720
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 (21.8 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