GapMind for catabolism of small carbon sources

 

Alignments for a candidate for CAT in Dyadobacter tibetensis Y620-1

Align Plastidic cationic amino acid transporter, CAT, of 582 aas and 14 TMSs (characterized)
to candidate WP_025765060.1 X939_RS0120010 amino acid permease

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



>NCBI__GCF_000566685.1:WP_025765060.1
          Length = 484

 Score =  226 bits (577), Expect = 1e-63
 Identities = 151/512 (29%), Positives = 255/512 (49%), Gaps = 77/512 (15%)

Query: 50  MKRSLRWYDLVGFGVGGMVGAGVFVTSGRASSHCAGPAVVLSYAIAGFCALLSAFCYTEF 109
           +KRSL    LV  G+G ++GAG+F  +G A++  +GPAV +S+ +A      +  CY EF
Sbjct: 25  LKRSLSSLSLVALGIGAIIGAGLFSLTGIAAAEHSGPAVTISFIVAAVGCGFAGLCYAEF 84

Query: 110 AVDMPVAGGAFSYIRITFGEFLAFLTGANLIIDYVLSNAAVARSFTGYLCTALG------ 163
           A  +P+AG A++Y   T GEF+A++ G +L+++Y L  A V+ S++ YL   L       
Sbjct: 85  ASMIPIAGSAYTYSYATMGEFVAWIIGWDLVLEYALGAATVSVSWSRYLLEFLSKFDIHL 144

Query: 164 ----IESKLRITVNGLPDGF----NEIDVVAVLVVLALTVIICYSTRESSVLNMVLTVLH 215
               + S   +    L DG       I++ A+L+V  L++++   T  S+ LN  L +L 
Sbjct: 145 PTQLVSSPFEVLT--LSDGTIIDNGIINLPAILIVWMLSLLLIRGTEGSAYLNNFLVILK 202

Query: 216 IVFIVFVIVIGFTRGDTKNFTKAGDSNHASGFFPFGASGVFNGAAMVYLSYIGYDAVSTM 275
           +  ++  I +G++  + +N+      N    +  FG SG+  GAA+V+ ++IG+DAVST 
Sbjct: 203 VAVVLIFIGLGWSHINPENYVPYIPEN-TGNYENFGWSGIATGAAVVFFAFIGFDAVSTA 261

Query: 276 AEEVKNPVKDIPVGVSGSVILVTVLYCLMAASMSMLLPYDMIDPDAPFSGAFMGSDGWRW 335
           A+E KNP K +P+G+ GS+I+ T+LY L A  M+ L+ Y     DA  +     + G+  
Sbjct: 262 AQEAKNPQKGMPIGILGSLIVCTILYVLFAHVMTGLVNYKEFANDAKPAATAFAATGYDS 321

Query: 336 VSNVIGVGAGFGILTSLLVAMLGQARYMCVIGRSSVVPAWFAKVHPKTSTPVNASAFLGI 395
           +   + V    G  + +LV +LGQ+R    + +  ++P +F+++HPK STP   + F  +
Sbjct: 322 LQTGLIVAILAGYTSVMLVMLLGQSRVFYSMSKDGLLPKFFSEIHPKFSTPWKTNIFFML 381

Query: 396 CTAAIALFTDLQILLNLVSIGTLFVFYMVANAVIYKRYVSVGVTNPWPTLSYLFCFSLTS 455
             +  A F  +  L ++VSIGTLF F +V           VGV   W             
Sbjct: 382 FVSIFAGFVPVSDLGHMVSIGTLFAFSLVC----------VGV---W------------- 415

Query: 456 ILFTLLWQFAPPGKPKAFMLGACTAIAIGVLQLFHYMVPQARKPEFWGVPLMPWIPSISI 515
                + +   P  P++F                               PL+P++P + I
Sbjct: 416 -----MLRVKRPDLPRSFR-----------------------------TPLVPFVPLMGI 441

Query: 516 FLNIFLLGSLDKPSYVRFGFFSALAVLVYVLY 547
            + ++L+ SL   S+ R   + AL + +Y  Y
Sbjct: 442 IVCVYLMYSLPIESWYRLAIWLALGLAIYFFY 473


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: 662
Number of extensions: 40
Number of successful extensions: 3
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: 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 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