GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bcaP in Methylocystis bryophila S285

Align Branched chain amino acid (Leucine/isoleucine/valine) uptake transporter of 469 aas and 12 TMSs, BcaP or CitA (characterized)
to candidate WP_085770386.1 B1812_RS03615 amino acid permease

Query= TCDB::S6EX81
         (469 letters)



>NCBI__GCF_002117405.1:WP_085770386.1
          Length = 488

 Score =  259 bits (663), Expect = 1e-73
 Identities = 154/438 (35%), Positives = 241/438 (55%), Gaps = 13/438 (2%)

Query: 29  LALGVGTIISTSIFTLPGQVAAQFAGPGVVFSYLLAALVAGFVALAYAEMSTVMPFAGSA 88
           + +G+G +I   IF L G VAA  AGPGV  S+L+A + +G  AL YAE ++++P AGSA
Sbjct: 35  VGIGLGGLIGVGIFVLTGVVAATQAGPGVALSFLIAGVASGAAALCYAEFASMLPVAGSA 94

Query: 89  YSWISVLFGEGFGWIAGWALLAEYFIAVAFVGSGFSANLQQLLAPLGFHLPKVLANPFGT 148
           Y++   + GE   WI GW LL EY + VA V  G+S  L+ LLA  G   P+  A   GT
Sbjct: 95  YTYAYAVLGELPAWIIGWDLLLEYALVVAVVSIGWSGYLRALLALFGVAPPEWAAGAPGT 154

Query: 149 -DGGVVDIISLLVILLSAIIVFRGASDAGRISQILVVLKVAAVIAFIIVGITVIKPANYH 207
            DG ++D+ ++L     A+++        R +  +V+LK+AAVI  I+     I PAN+ 
Sbjct: 155 GDGHILDLFAMLGAFGVALLLTLRVEWGARFNTAMVLLKIAAVIVVILAAAPHINPANWR 214

Query: 208 PFIPPHNPKTGFGGFSGIWSGVSMIFLAYIGFDSIAANSAEAKNPQKTMPRGIIGSLLIA 267
           PF+P         GF G+  G +++F A  G+D++     EA  PQ+ +PR ++ SL+++
Sbjct: 215 PFMP--------FGFGGVVEGAAVVFFAVFGYDTLTTAGEEALEPQRDLPRAVLLSLVVS 266

Query: 268 VVLFAAVTLVLVGMHPYSAYAGNAAPVGWALQQSGYSVLSEVVTAIALAGMFIALLGMVL 327
           + L+  ++L L G+  Y     NAAPV  A    G    + VV+A A+ G+   +L  +L
Sbjct: 267 LTLYILMSLALTGIARYDT-LDNAAPVASAFAALGMGWATLVVSAAAVVGILSVMLAFLL 325

Query: 328 AGSRLLYAFGRDGLLPKGLGKMNAR-NLPANGVWTLAIVAIVIGAFFPFAFLAQLISAGT 386
             +R+ +A  RDGLLP    + + +   P         +  ++ AFFP   +A+L++ GT
Sbjct: 326 GCARIWFAMSRDGLLPAWFARPHPQFATPYRPTLIAGGLCALVSAFFPIREVAELVNIGT 385

Query: 387 LIAFMFVTLGIYSLRRRQGKDLPEATYKMPFYPVLPALGFIGSLFVFWGLDVQAKLYSGI 446
           L AF+ + L + +LR  +  D+P   ++ P  P LP +G   SL++   L   A     +
Sbjct: 386 LSAFVVICLAVIALRHTR-PDVPRG-FRAPLSPYLPLIGVGFSLWLLSKLPAIAWERFVV 443

Query: 447 WFLIGILIYFAYGNRRSR 464
           W +IG+ +YF YG R SR
Sbjct: 444 WLIIGLAVYFLYGRRHSR 461


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: 652
Number of extensions: 42
Number of successful extensions: 6
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: 488
Length adjustment: 34
Effective length of query: 435
Effective length of database: 454
Effective search space:   197490
Effective search space used:   197490
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 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