GapMind for catabolism of small carbon sources

 

Alignments for a candidate for CAT in Desulfoscipio geothermicus DSM 3669

Align Plastidic cationic amino acid transporter, CAT, of 582 aas and 14 TMSs (characterized)
to candidate WP_092483642.1 BM299_RS10185 amino acid permease

Query= TCDB::ALD51314.1
         (582 letters)



>NCBI__GCF_900115975.1:WP_092483642.1
          Length = 484

 Score =  234 bits (598), Expect = 5e-66
 Identities = 130/388 (33%), Positives = 221/388 (56%), Gaps = 15/388 (3%)

Query: 58  DLVGFGVGGMVGAGVFVTSGRASSHCAGPAVVLSYAIAGFCALLSAFCYTEFAVDMPVAG 117
           DL   GVG ++G G+FV +G A+++ AGP VV S+ ++G  A L+A  Y E    +P AG
Sbjct: 31  DLTALGVGAVIGTGIFVLTGVAAANYAGPGVVFSFILSGIAATLAAMVYAELGAAIPSAG 90

Query: 118 GAFSYIRITFGEFLAFLTGANLIIDYVLSNAAVA---RSFTGYLCTALGIESKLRITVNG 174
            A+++  ++ GE +A+L G NLI++Y+++  AV+    S+ G L  ++GI      T + 
Sbjct: 91  SAYTFSYVSLGEIIAWLVGWNLILEYLVAAGAVSIGWSSYMGDLLQSVGITLPAAFTSSP 150

Query: 175 LPDGFNEIDVVAVLVVLALTVIICYSTRESSVLNMVLTVLHIVFIVFVIVIGFTRGDTKN 234
              G   +++ A L+VL +T +I   T+ S+  N ++ V  +  I   I +G    +  N
Sbjct: 151 FDGGI--VNLPAALIVLVITGLIITGTQHSTTANKIIVVAKLAAIALFIALGVQHINPAN 208

Query: 235 FTKAGDSNHASGFFPFGASGVFNGAAMVYLSYIGYDAVSTMAEEVKNPVKDIPVGVSGSV 294
           +             P+G SGVF+GAA+V+ +YIG+DAV+T +EEVKNP +D+P G+  ++
Sbjct: 209 WRPV---------LPYGISGVFHGAAIVFFAYIGFDAVATASEEVKNPQRDLPRGIIWTL 259

Query: 295 ILVTVLYCLMAASMSMLLPYDMIDPDAPFSGAFMGSDGWRWVSNVIGVGAGFGILTSLLV 354
           ++ T+LY ++A  ++ ++ Y  ++  +P + A + + G  W S ++ VGA  G+ + LLV
Sbjct: 260 VISTLLYIVVAGILTGMVKYTNLNTASPVATALLRA-GIPWASALVSVGALAGLTSVLLV 318

Query: 355 AMLGQARYMCVIGRSSVVPAWFAKVHPKTSTPVNASAFLGICTAAIALFTDLQILLNLVS 414
           AM GQ+R    + R  ++P  F  +HP+  TPV  S  +G+  A I  F  + ++  L +
Sbjct: 319 AMYGQSRIFFAMARDDLLPPIFDWLHPRLRTPVWDSIIIGVLVALIGAFLPIGLVAELAN 378

Query: 415 IGTLFVFYMVANAVIYKRYVSVGVTNPW 442
           IGTL  F  V+   I  R  +  +  P+
Sbjct: 379 IGTLTAFIAVSTGAIILRRTNPDLRRPF 406


Lambda     K      H
   0.326    0.139    0.423 

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: 640
Number of extensions: 31
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: 582
Length of database: 484
Length adjustment: 35
Effective length of query: 547
Effective length of database: 449
Effective search space:   245603
Effective search space used:   245603
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 (21.7 bits)
S2: 52 (24.6 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