GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctM in Desulfoscipio geothermicus DSM 3669

Align Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale)
to candidate WP_092484450.1 BM299_RS11930 TRAP transporter large permease

Query= uniprot:Q88NP0
         (426 letters)



>NCBI__GCF_900115975.1:WP_092484450.1
          Length = 425

 Score =  334 bits (857), Expect = 3e-96
 Identities = 171/423 (40%), Positives = 275/423 (65%), Gaps = 3/423 (0%)

Query: 3   AFILLGSFIVLILIGMPVAYALGLSALIGAWWI-DIPLQAMMIQVASGVNKFSLLAIPFF 61
           + IL  SF VL+LIG+PVA++LGLS++    +   IPL   + ++ +G + F L+AIPFF
Sbjct: 2   SLILFASFFVLVLIGVPVAFSLGLSSIAALLYQGQIPLIVSVQRLFTGTDSFPLMAIPFF 61

Query: 62  VLAGAIMAEGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADTASVGSVL 121
           ++AGA+M  GG+SRRLV FA  +VG   GGL+ V  MAS  F A+SGS  A TA++G ++
Sbjct: 62  MMAGALMNTGGISRRLVDFASAVVGHKTGGLAYVTAMASMLFAAVSGSGAATTAAIGGMM 121

Query: 122 IPEMERKGYPREFSTAVTVSGSVQALLTPPSHNSVLYSLAAGGTVSIASLFMAGIMPGLL 181
           IP + +KGY +EF++A+  S     ++ PPS   VL+   +G  VSIA LF+AGI+PG+L
Sbjct: 122 IPALIKKGYGKEFASALQASSGSLGVVIPPSIPFVLFGFMSG--VSIAELFLAGIVPGVL 179

Query: 182 LSAVMMGLCLIFAKKRNYPKGEVIPLREALKIAGEALWGLMAMVIILGGILSGVFTATES 241
           ++ ++M +     K       E +P +E ++    AL  L+   IILGGI SG FT TE+
Sbjct: 180 IAVLLMVVSYFMVKNGPSTLEERVPFKEMVRRFFAALPALLMPAIILGGIFSGQFTPTEA 239

Query: 242 AAVAVVWSFFVTMFIYRDYKWRDLPKLMHRTVRTISIVMILIGFAASFGYVMTLMQIPSK 301
           A +AVV+ F V +F+YR+    ++ + M   V + ++V++L+ FA++F ++M    IP K
Sbjct: 240 AVIAVVYGFIVGIFVYRELNLANIMEAMKDAVISNAVVLMLLAFASTFSWIMASELIPQK 299

Query: 302 ITTAFLTLSDNRYVILMCINFMLMLLGTVMDMAPLILILTPILLPVITGIGVDPVHFGMI 361
           I     +++ N+++ L+ +   L+++GT ++  P +++L PIL+PV     V+ VHFG++
Sbjct: 300 IAALMSSIAPNQFIFLLLVTVFLLIIGTFLETTPALILLVPILVPVAQTFDVNLVHFGVL 359

Query: 362 MLVNLGIGLITPPVGAVLFVGSAIGKVSIESTVKALMPFYLALFLVLMAVTYIPAISLWL 421
           M+VNL IG++TPP+G  LFV S I KV + +  +A++PF L +   L+ +T++P ISL++
Sbjct: 360 MVVNLAIGMVTPPLGITLFVASNISKVPLANLFRAIVPFILCMIAALLVLTFVPQISLFV 419

Query: 422 PSV 424
           P +
Sbjct: 420 PEL 422


Lambda     K      H
   0.329    0.142    0.418 

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: 581
Number of extensions: 30
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: 426
Length of database: 425
Length adjustment: 32
Effective length of query: 394
Effective length of database: 393
Effective search space:   154842
Effective search space used:   154842
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