GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctM in Desulfuromonas acetexigens DSM 1397

Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate WP_092058810.1 BQ4888_RS16820 TRAP transporter large permease subunit

Query= SwissProt::O07838
         (440 letters)



>NCBI__GCF_900111775.1:WP_092058810.1
          Length = 425

 Score =  251 bits (642), Expect = 2e-71
 Identities = 146/432 (33%), Positives = 245/432 (56%), Gaps = 13/432 (3%)

Query: 4   LIIFGLLIALMLTGMPISISLGLTVLTFLFTMTQVPIDTVALKLFTGIEKFEIMAIPFFI 63
           LI  GL + L L G P+   +    L   +   ++ +  +A+++F   E   ++AIP F 
Sbjct: 3   LIALGLFL-LALLGAPLFAIIAAGALLG-YQRAEIDLAALAVEVFRLAEMPVLLAIPLFT 60

Query: 64  LAGNFLTHGGVAKRMINFATAMVGHWHGGLGLAGVIACALFAAVSGSSPATVVAIGSVIL 123
           LAG  L   G  +R++N   A+ G   G L    ++ACA F A +G+S  T+VA+G+++ 
Sbjct: 61  LAGYLLGESGAPRRLVNLTQALFGWLPGSLAAVALVACAFFTAFTGASGVTIVALGALLY 120

Query: 124 PAMVNQGFPKQFGAGVITTSGALGILIPPSIVMVMYAVATSGMVVTGPDGQPVSSASVGE 183
           PA+   G+ + F  G+ITTSG+LG+L  PS+ +++Y +      V    G+ V    + +
Sbjct: 121 PALQQAGYDEHFNLGLITTSGSLGLLFAPSLPLILYGIVAQQTEV----GRGVG---IDQ 173

Query: 184 LFMAGVVPGL-MLAGFLAFTTWNRARKFGYPRLEKASLRQRWTAFREAAWGLMLIVVVIG 242
           LF+AG++PGL ML   L +  W+  R    PR  K +      A  +AAW L L  +V+G
Sbjct: 174 LFVAGLLPGLLMLVLLLGYAFWHSRR---LPRERKTAAVGPGRALVDAAWELPLPFIVLG 230

Query: 243 GIYAGIFTPTEAAAMSAVYAFFISVFVYKDLTLRDVPRVLLSSANMSAMLLYIITNAVLF 302
           GIY+G F  +EAAA++A+Y   + V + +++TL  +P ++  +  M   +L I+  ++  
Sbjct: 231 GIYSGYFAVSEAAAVTALYVLVVEVVILREITLLQLPGIVRQAMVMVGGILIILGVSLAS 290

Query: 303 SFLMAHEGIPQALGEWMVNAGLSWWMFLIIVNILLLAAGNFMEPSSIVLIMAPILFPVAV 362
           + ++   G+P+ L +W+     S   FL+ +N+ LL  G  ++  S ++++ P++ PVAV
Sbjct: 291 TNVLIDAGVPERLFDWVQAHVSSRLTFLLWLNLFLLLLGCLLDIFSALVLVVPLILPVAV 350

Query: 363 RLGIDPVHFGIMIVVNMEVGMCHPPVGLNLYVASGITKMGITELTVAVWPWLLTMLAFLV 422
              +DP+H GI+ + NM++G   PPVGLNL++AS      I  L  A  P+LL +L  ++
Sbjct: 351 GFNVDPLHLGIIFLANMQIGYLTPPVGLNLFIASYRFDQPILTLYRATLPFLLLLLFCVL 410

Query: 423 LVTYVPAISLAL 434
           L+TY P +SL L
Sbjct: 411 LITYWPWLSLGL 422


Lambda     K      H
   0.329    0.142    0.431 

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: 596
Number of extensions: 42
Number of successful extensions: 3
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: 440
Length of database: 425
Length adjustment: 32
Effective length of query: 408
Effective length of database: 393
Effective search space:   160344
Effective search space used:   160344
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 Apr 09 2024. 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