GapMind for catabolism of small carbon sources

 

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

Align Branched chain amino acid (Leucine/isoleucine/valine) uptake transporter of 469 aas and 12 TMSs, BcaP or CitA (characterized)
to candidate WP_025765060.1 X939_RS0120010 amino acid permease

Query= TCDB::S6EX81
         (469 letters)



>NCBI__GCF_000566685.1:WP_025765060.1
          Length = 484

 Score =  298 bits (763), Expect = 3e-85
 Identities = 164/482 (34%), Positives = 282/482 (58%), Gaps = 18/482 (3%)

Query: 3   FMRKADFELYRDADKHYNQV---LTTRDFLALGVGTIISTSIFTLPGQVAAQFAGPGVVF 59
           + +K   +L +++    NQ+   L++   +ALG+G II   +F+L G  AA+ +GP V  
Sbjct: 6   WFKKPIEKLLQESTGEENQLKRSLSSLSLVALGIGAIIGAGLFSLTGIAAAEHSGPAVTI 65

Query: 60  SYLLAALVAGFVALAYAEMSTVMPFAGSAYSWISVLFGEGFGWIAGWALLAEYFIAVAFV 119
           S+++AA+  GF  L YAE ++++P AGSAY++     GE   WI GW L+ EY +  A V
Sbjct: 66  SFIVAAVGCGFAGLCYAEFASMIPIAGSAYTYSYATMGEFVAWIIGWDLVLEYALGAATV 125

Query: 120 GSGFSANLQQLLAPLGFHLP-KVLANPF-------GT--DGGVVDIISLLVILLSAIIVF 169
              +S  L + L+    HLP +++++PF       GT  D G++++ ++L++ + ++++ 
Sbjct: 126 SVSWSRYLLEFLSKFDIHLPTQLVSSPFEVLTLSDGTIIDNGIINLPAILIVWMLSLLLI 185

Query: 170 RGASDAGRISQILVVLKVAAVIAFIIVGITVIKPANYHPFIPPHNPKTGFGGFSGIWSGV 229
           RG   +  ++  LV+LKVA V+ FI +G + I P NY P+IP +       G+SGI +G 
Sbjct: 186 RGTEGSAYLNNFLVILKVAVVLIFIGLGWSHINPENYVPYIPENTGNYENFGWSGIATGA 245

Query: 230 SMIFLAYIGFDSIAANSAEAKNPQKTMPRGIIGSLLIAVVLFAAVTLVLVGMHPYSAYAG 289
           +++F A+IGFD+++  + EAKNPQK MP GI+GSL++  +L+     V+ G+  Y  +A 
Sbjct: 246 AVVFFAFIGFDAVSTAAQEAKNPQKGMPIGILGSLIVCTILYVLFAHVMTGLVNYKEFAN 305

Query: 290 NAAPVGWALQQSGYSVLSEVVTAIALAGMFIALLGMVLAGSRLLYAFGRDGLLPKGLGKM 349
           +A P   A   +GY  L   +    LAG    +L M+L  SR+ Y+  +DGLLPK   ++
Sbjct: 306 DAKPAATAFAATGYDSLQTGLIVAILAGYTSVMLVMLLGQSRVFYSMSKDGLLPKFFSEI 365

Query: 350 NAR-NLP-ANGVWTLAIVAIVIGAFFPFAFLAQLISAGTLIAFMFVTLGIYSLRRRQGKD 407
           + + + P    ++ +  V+I  G F P + L  ++S GTL AF  V +G++ LR ++  D
Sbjct: 366 HPKFSTPWKTNIFFMLFVSIFAG-FVPVSDLGHMVSIGTLFAFSLVCVGVWMLRVKR-PD 423

Query: 408 LPEATYKMPFYPVLPALGFIGSLFVFWGLDVQAKLYSGIWFLIGILIYFAYGNRRSRKSE 467
           LP  +++ P  P +P +G I  +++ + L +++     IW  +G+ IYF YG + S+  +
Sbjct: 424 LPR-SFRTPLVPFVPLMGIIVCVYLMYSLPIESWYRLAIWLALGLAIYFFYGKKNSKLGK 482

Query: 468 EK 469
           E+
Sbjct: 483 EQ 484


Lambda     K      H
   0.328    0.143    0.433 

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: 650
Number of extensions: 36
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: 469
Length of database: 484
Length adjustment: 33
Effective length of query: 436
Effective length of database: 451
Effective search space:   196636
Effective search space used:   196636
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: 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