GapMind for catabolism of small carbon sources

 

Alignments for a candidate for CAT in Methylocystis bryophila S285

Align Plastidic cationic amino acid transporter, CAT, of 582 aas and 14 TMSs (characterized)
to candidate WP_085770386.1 B1812_RS03615 amino acid permease

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



>NCBI__GCF_002117405.1:WP_085770386.1
          Length = 488

 Score =  222 bits (565), Expect = 3e-62
 Identities = 137/438 (31%), Positives = 226/438 (51%), Gaps = 23/438 (5%)

Query: 38  ETSRVRARSGGDMKRSLRWYDLVGFGVGGMVGAGVFVTSGRASSHCAGPAVVLSYAIAGF 97
           E+ +  A   G ++R+L  + LVG G+GG++G G+FV +G  ++  AGP V LS+ IAG 
Sbjct: 13  ESLQAEALERGALRRALGLWQLVGIGLGGLIGVGIFVLTGVVAATQAGPGVALSFLIAGV 72

Query: 98  CALLSAFCYTEFAVDMPVAGGAFSYIRITFGEFLAFLTGANLIIDYVLSNAAVARSFTGY 157
            +  +A CY EFA  +PVAG A++Y     GE  A++ G +L+++Y L  A V+  ++GY
Sbjct: 73  ASGAAALCYAEFASMLPVAGSAYTYAYAVLGELPAWIIGWDLLLEYALVVAVVSIGWSGY 132

Query: 158 LCTALGI----ESKLRITVNGLPDGFNEIDVVAVLVVLALTVIICYSTRESSVLNMVLTV 213
           L   L +      +      G  DG + +D+ A+L    + +++       +  N  + +
Sbjct: 133 LRALLALFGVAPPEWAAGAPGTGDG-HILDLFAMLGAFGVALLLTLRVEWGARFNTAMVL 191

Query: 214 LHIVFIVFVIVIGFTRGDTKNFTKAGDSNHASGFFPFGASGVFNGAAMVYLSYIGYDAVS 273
           L I  ++ VI+      +  N+           F PFG  GV  GAA+V+ +  GYD ++
Sbjct: 192 LKIAAVIVVILAAAPHINPANWRP---------FMPFGFGGVVEGAAVVFFAVFGYDTLT 242

Query: 274 TMAEEVKNPVKDIPVGVSGSVILVTVLYCLMAASMSMLLPYDMIDPDAPFSGAFMGSDGW 333
           T  EE   P +D+P  V  S+++   LY LM+ +++ +  YD +D  AP + AF  + G 
Sbjct: 243 TAGEEALEPQRDLPRAVLLSLVVSLTLYILMSLALTGIARYDTLDNAAPVASAF-AALGM 301

Query: 334 RWVSNVIGVGAGFGILTSLLVAMLGQARYMCVIGRSSVVPAWFAKVHPKTSTPVNASAFL 393
            W + V+   A  GIL+ +L  +LG AR    + R  ++PAWFA+ HP+ +TP   +   
Sbjct: 302 GWATLVVSAAAVVGILSVMLAFLLGCARIWFAMSRDGLLPAWFARPHPQFATPYRPTLIA 361

Query: 394 GICTAAIALFTDLQILLNLVSIGTLFVFYMVANAVIYKRYVSVGVTNPW--------PTL 445
           G   A ++ F  ++ +  LV+IGTL  F ++  AVI  R+    V   +        P +
Sbjct: 362 GGLCALVSAFFPIREVAELVNIGTLSAFVVICLAVIALRHTRPDVPRGFRAPLSPYLPLI 421

Query: 446 SYLFCFSLTSILFTLLWQ 463
              F   L S L  + W+
Sbjct: 422 GVGFSLWLLSKLPAIAWE 439


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: 643
Number of extensions: 42
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 582
Length of database: 488
Length adjustment: 35
Effective length of query: 547
Effective length of database: 453
Effective search space:   247791
Effective search space used:   247791
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