GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bcaP in Desulfoscipio geothermicus DSM 3669

Align Branched chain amino acid (Leucine/isoleucine/valine) uptake transporter of 469 aas and 12 TMSs, BcaP or CitA (characterized)
to candidate WP_092483642.1 BM299_RS10185 amino acid permease

Query= TCDB::S6EX81
         (469 letters)



>NCBI__GCF_900115975.1:WP_092483642.1
          Length = 484

 Score =  289 bits (739), Expect = 2e-82
 Identities = 170/461 (36%), Positives = 262/461 (56%), Gaps = 20/461 (4%)

Query: 15  ADKHYNQ-----VLTTRDFLALGVGTIISTSIFTLPGQVAAQFAGPGVVFSYLLAALVAG 69
           ADK  N+      L   D  ALGVG +I T IF L G  AA +AGPGVVFS++L+ + A 
Sbjct: 14  ADKKKNKRGLVPTLGVADLTALGVGAVIGTGIFVLTGVAAANYAGPGVVFSFILSGIAAT 73

Query: 70  FVALAYAEMSTVMPFAGSAYSWISVLFGEGFGWIAGWALLAEYFIAVAFVGSGFSANLQQ 129
             A+ YAE+   +P AGSAY++  V  GE   W+ GW L+ EY +A   V  G+S+ +  
Sbjct: 74  LAAMVYAELGAAIPSAGSAYTFSYVSLGEIIAWLVGWNLILEYLVAAGAVSIGWSSYMGD 133

Query: 130 LLAPLGFHLPKVL-ANPFGTDGGVVDIISLLVILLSAIIVFRGASDAGRISQILVVLKVA 188
           LL  +G  LP    ++PF  DGG+V++ + L++L+   ++  G   +   ++I+VV K+A
Sbjct: 134 LLQSVGITLPAAFTSSPF--DGGIVNLPAALIVLVITGLIITGTQHSTTANKIIVVAKLA 191

Query: 189 AVIAFIIVGITVIKPANYHPFIPPHNPKTGFGGFSGIWSGVSMIFLAYIGFDSIAANSAE 248
           A+  FI +G+  I PAN+ P +P         G SG++ G +++F AYIGFD++A  S E
Sbjct: 192 AIALFIALGVQHINPANWRPVLP--------YGISGVFHGAAIVFFAYIGFDAVATASEE 243

Query: 249 AKNPQKTMPRGIIGSLLIAVVLFAAVTLVLVGMHPYSAYAGNAAPVGWALQQSGYSVLSE 308
            KNPQ+ +PRGII +L+I+ +L+  V  +L GM  Y+     A+PV  AL ++G    S 
Sbjct: 244 VKNPQRDLPRGIIWTLVISTLLYIVVAGILTGMVKYT-NLNTASPVATALLRAGIPWASA 302

Query: 309 VVTAIALAGMFIALLGMVLAGSRLLYAFGRDGLLPKGLGKMNAR-NLPANGVWTLAIVAI 367
           +V+  ALAG+   LL  +   SR+ +A  RD LLP     ++ R   P      + ++  
Sbjct: 303 LVSVGALAGLTSVLLVAMYGQSRIFFAMARDDLLPPIFDWLHPRLRTPVWDSIIIGVLVA 362

Query: 368 VIGAFFPFAFLAQLISAGTLIAFMFVTLGIYSLRRRQGKDLPEATYKMPFYPVLPALGFI 427
           +IGAF P   +A+L + GTL AF+ V+ G   L RR   DL    +++P+ P +P L  I
Sbjct: 363 LIGAFLPIGLVAELANIGTLTAFIAVSTGAIIL-RRTNPDL-RRPFRLPWMPAIPVLTII 420

Query: 428 GSLFVFWGLDVQAKLYSGIWFLIGILIYFAYGNRRSRKSEE 468
            + ++   L     +    W  IG+++Y+ YG R+S+ + E
Sbjct: 421 SAGYLAINLPPLTWVRFIAWVAIGLVVYWLYGYRKSKLARE 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: 657
Number of extensions: 33
Number of successful extensions: 7
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 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