GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bcaP in Caulobacter crescentus NA1000

Align Branched chain amino acid (Leucine/isoleucine/valine) uptake transporter of 469 aas and 12 TMSs, BcaP or CitA (characterized)
to candidate CCNA_00435 CCNA_00435 amino acid transporter

Query= TCDB::S6EX81
         (469 letters)



>FitnessBrowser__Caulo:CCNA_00435
          Length = 483

 Score =  251 bits (642), Expect = 3e-71
 Identities = 144/463 (31%), Positives = 253/463 (54%), Gaps = 14/463 (3%)

Query: 15  ADKHY-NQVLTTRDFLALGVGTIISTSIFTLPGQVAAQFAGPGVVFSYLLAALVAGFVAL 73
           AD H   + L+    +ALGVG I+ T I+TL G V A  AGPGV+ S+L+A  V    AL
Sbjct: 25  ADSHQLKKTLSWPHLVALGVGAIVGTGIYTLTG-VGAGLAGPGVILSFLIAGAVCACAAL 83

Query: 74  AYAEMSTVMPFAGSAYSWISVLFGEGFGWIAGWALLAEYFIAVAFVGSGFSANLQQLLAP 133
            YAE+ST++P +GSAY++     GE   W  GW+L+ EY +  A V  G+SA+   L   
Sbjct: 84  CYAELSTMIPASGSAYTYSYAAMGEPVAWFVGWSLILEYTLVCAAVAVGWSAHAHGLFKM 143

Query: 134 LGFHLPKVLANPFGTDGGVVDIISLLVILLSAIIVFRGASDAGRISQILVVLKVAAVIAF 193
           +GF    +LA P    GG++++ ++ + +  A ++  G  ++  ++ +LV +K+ A+I F
Sbjct: 144 IGFP-DALLAGPH--QGGLINMPAVFISMAVAGLLALGTRESATVNMVLVFVKIIALIVF 200

Query: 194 IIVGITVIKPANYHPFIP----PHNPKTGFGGFS--GIWSGVSMIFLAYIGFDSIAANSA 247
           +++ +     A++ PF+P     H P+      +  G+ +  S+IF A+ GFD+++  + 
Sbjct: 201 VVLCLPAFNLAHFTPFMPNGFQAHVPEGAAADAAKVGVMAAASLIFFAFYGFDAVSTAAE 260

Query: 248 EAKNPQKTMPRGIIGSLLIAVVLFAAVTLVLVGMHPYSAYAGNAAPVGWALQQSGYSVLS 307
           E KNP++ +  GI+GS+ +   ++  V  V +G      ++ + AP+ + L+   +  ++
Sbjct: 261 ETKNPKRDLTIGIVGSMAVCTAIYMIVAAVSIGASRTEVFSKSEAPLVFILESLNHGKIA 320

Query: 308 EVVTAIALAGMFIALLGMVLAGSRLLYAFGRDGLLPKGLGKMNAR-NLPANGVWTLAIVA 366
           ++V   A+  +   +L  +   SR+ +   RDGLLP+ L K+NA+   P        ++A
Sbjct: 321 QLVALAAVIALPTVILAFMYGQSRIFFVMARDGLLPRALSKVNAKTGTPVMMTLLTGVLA 380

Query: 367 IVIGAFFPFAFLAQLISAGTLIAFMFVTLGIYSLRRRQGKDLPEATYKMPFYPVLPALGF 426
            VI        +A+L +AGTL AF+ V   +  LR R+        +  P +P++   G 
Sbjct: 381 AVISGLLSLKDIAELANAGTLWAFIAVGASVILLRLREPN--RPRVFSTPLWPIVAPAGI 438

Query: 427 IGSLFVFWGLDVQAKLYSGIWFLIGILIYFAYGNRRSRKSEEK 469
           +G L++F  L  + +LY     LIG ++Y AYG R+S  ++++
Sbjct: 439 LGCLYLFLSLPGKTQLYFLYAHLIGAVVYLAYGMRKSVLAQQE 481


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: 632
Number of extensions: 41
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: 483
Length adjustment: 33
Effective length of query: 436
Effective length of database: 450
Effective search space:   196200
Effective search space used:   196200
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 17 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