GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bcaP in Lysobacter daejeonensis GH1-9

Align Branched chain amino acid (Leucine/isoleucine/valine) uptake transporter of 469 aas and 12 TMSs, BcaP or CitA (characterized)
to candidate WP_036136362.1 N800_RS06835 amino acid permease

Query= TCDB::S6EX81
         (469 letters)



>NCBI__GCF_000768355.1:WP_036136362.1
          Length = 491

 Score =  281 bits (720), Expect = 3e-80
 Identities = 163/458 (35%), Positives = 253/458 (55%), Gaps = 20/458 (4%)

Query: 21  QVLTTRDFLALGVGTIISTSIFTLPGQVAAQFAGPGVVFSYLLAALVAGFVALAYAEMST 80
           +VLT R  + LGVG II   IF + G  AA +AGP V+ S+++AA+  GF  L YAE ++
Sbjct: 35  RVLTARHLVMLGVGAIIGAGIFVMTGTAAANYAGPAVILSFVMAAVACGFAGLCYAEFAS 94

Query: 81  VMPFAGSAYSWISVLFGEGFGWIAGWALLAEYFIAVAFVGSGFSANLQQLLAPLGFHLPK 140
           +MP +GSAYS+     GE   W  GW L+ EY  A + V  G+S  L   L   G  +P 
Sbjct: 95  MMPVSGSAYSYTYSTLGEVVAWFIGWNLVLEYLFAASSVAVGWSGYLNSFLTTHGAGVPA 154

Query: 141 VLA----------NPFGTDGGVVDIISLLVILLSAIIVFRGASDAGRISQILVVLKVAAV 190
            LA          + F + G +V++ ++L++   + + +RG + +  ++ ++V +KV  +
Sbjct: 155 ALAQAPFHYSAETSSFVSTGSIVNLPAVLIVAAISGLCYRGITQSAWVNALIVAIKVTVI 214

Query: 191 IAFIIVGITVIKPANYHPFIPPHNPKTGFGGFSGIWSGVSMIFLAYIGFDSIAANSAEAK 250
           +AF+      I P N+ PFIP +   T F G  G+  G +++F AYIGFD+++  + EAK
Sbjct: 215 VAFLGFAAQYINPDNWQPFIPENEGGTRF-GTEGVVRGAAVVFFAYIGFDAVSTAAGEAK 273

Query: 251 NPQKTMPRGIIGSLLIAVVLFAAVTLVLVGMHPYSAYAGNAAPVGWALQQSGYSVLSEVV 310
           NPQ+ MP GI+GSL +  VL+ AV   L G+ PY      A PV  AL+   Y  L  + 
Sbjct: 274 NPQRDMPIGILGSLAVCTVLYIAVAATLTGLLPY-PQLDTAKPVATALE--AYPTLGWLK 330

Query: 311 TAI---ALAGMFIALLGMVLAGSRLLYAFGRDGLLPKGLGKMNAR-NLPANGVWTLAIVA 366
            A+   A+AG+   +L M++   R+ YA  +DGL+PK  G+++ +   P  G   + +VA
Sbjct: 331 MAVEIGAIAGLSSVILVMLMGQPRIFYAMAKDGLMPKIFGRVHPKFQTPYVGTVIVGVVA 390

Query: 367 IVIGAFFPFAFLAQLISAGTLIAFMFVTLGIYSLRRRQGKDLPEATYKMPFYPVLPALGF 426
            ++    P  FL  L+S GTL+AF  V  G+  LR  +  DL +  +++P   V+ +LG 
Sbjct: 391 AIMAGLLPLDFLGDLVSMGTLLAFATVCAGVLILRYTR-PDL-QRPFRVPGAIVVCSLGV 448

Query: 427 IGSLFVFWGLDVQAKLYSGIWFLIGILIYFAYGNRRSR 464
           +  L++FW            W +IG +IYF YG R S+
Sbjct: 449 LSCLYLFWQPFKDHWQVMLGWTVIGFVIYFGYGYRNSK 486


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: 672
Number of extensions: 42
Number of successful extensions: 8
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: 491
Length adjustment: 34
Effective length of query: 435
Effective length of database: 457
Effective search space:   198795
Effective search space used:   198795
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