GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctM in Halopiger salifodinae KCY07-B2

Align Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale)
to candidate WP_049989147.1 LT39_RS03805 TRAP transporter large permease

Query= uniprot:Q88NP0
         (426 letters)



>NCBI__GCF_000784335.1:WP_049989147.1
          Length = 431

 Score =  276 bits (705), Expect = 1e-78
 Identities = 149/424 (35%), Positives = 253/424 (59%), Gaps = 6/424 (1%)

Query: 4   FILLGSFIVLILIGMPVAYALGLSALIGAWWIDIPLQAMMIQ--VASGVNKFSLLAIPFF 61
           FIL+   + L LIG+PVA+ALGL++LI      +     ++   + SG + F LLAIP F
Sbjct: 9   FILV--LLALYLIGVPVAFALGLTSLILMLTPMVSYSPELVAQTLVSGADSFVLLAIPLF 66

Query: 62  VLAGAIMAEGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADTASVGSVL 121
           +L G  M   G++  +  FA  ++G +RGG++ VNI+AS  F  ++G++ AD A +G++ 
Sbjct: 67  LLTGLYMNSFGLTSIIFDFAEEMIGPIRGGIAHVNILASILFSGMTGTAAADAAGLGAIE 126

Query: 122 IPEMERKGYPREFSTAVTVSGSVQALLTPPSHNSVLYSLAAGGTVSIASLFMAGIMPGLL 181
              M+  GY + +S AVT S ++   + PPS   ++Y + A   VSI  LF+AGI+PGL+
Sbjct: 127 YEAMQDAGYEKGYSAAVTGSSAIIGPIIPPSVPLIMYGILA--QVSIGVLFIAGIVPGLI 184

Query: 182 LSAVMMGLCLIFAKKRNYPKGEVIPLREALKIAGEALWGLMAMVIILGGILSGVFTATES 241
           + A ++ LC  +A    Y +G    L +  +    A   L   V+I+GG+L G FTATE+
Sbjct: 185 MGATLLMLCTYYAHSHGYERGTWWSLPDIWESFKTAAPALGTPVLIIGGLLGGFFTATEA 244

Query: 242 AAVAVVWSFFVTMFIYRDYKWRDLPKLMHRTVRTISIVMILIGFAASFGYVMTLMQIPSK 301
            AVA+ ++ FV    Y   +  D  +  +  V T + +  ++  A  +G+++   Q+P  
Sbjct: 245 GAVALFYTLFVGYVFYGGVENGDFVETTYEGVVTTAALTFIVASATLYGFLVRRAQLPDA 304

Query: 302 ITTAFLTLSDNRYVILMCINFMLMLLGTVMDMAPLILILTPILLPVITGIGVDPVHFGMI 361
           +  A + ++ +  ++L+ I  +L+++G +M+    I ILTP+ LPVI   G+DP+HFG++
Sbjct: 305 LAEAVIGVTGDPTLLLLMIVGVLLIVGLMMETIAAITILTPVFLPVIDVAGIDPIHFGIV 364

Query: 362 MLVNLGIGLITPPVGAVLFVGSAIGKVSIESTVKALMPFYLALFLVLMAVTYIPAISLWL 421
           M++ L IGL+TPP G +LF+   +  V +E  +++++PFY+ L ++L+ V  +P ++LWL
Sbjct: 365 MILTLMIGLLTPPFGIILFILEKVTDVGLERIMRSMVPFYIPLLIILLLVVVLPGLTLWL 424

Query: 422 PSVV 425
           P  V
Sbjct: 425 PKFV 428


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: 607
Number of extensions: 30
Number of successful extensions: 4
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: 431
Length adjustment: 32
Effective length of query: 394
Effective length of database: 399
Effective search space:   157206
Effective search space used:   157206
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 24 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