GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cycA in Kocuria turfanensis HO-9042

Align D-serine/D-alanine/glycine transporter (characterized)
to candidate WP_084271517.1 AYX06_RS08205 amino acid permease

Query= SwissProt::P0AAE0
         (470 letters)



>NCBI__GCF_001580365.1:WP_084271517.1
          Length = 471

 Score =  259 bits (663), Expect = 1e-73
 Identities = 147/441 (33%), Positives = 243/441 (55%), Gaps = 5/441 (1%)

Query: 22  NLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVMRAMGELLLSN 81
           +L  RH+ ++A+G AIGTGLF+G+G  I  AGP+++  +++   +L  VMRA+GE+  ++
Sbjct: 30  HLKARHLVMMALGSAIGTGLFIGTGAAIRTAGPAVLLSFLVACVLLVLVMRALGEMAAAD 89

Query: 82  LEYKSFSDFASDLLGPWAGYFTGWTYWFCWVVTGMADVVAITAYAQFWFPDLSDWVASLA 141
               +FS +A   +G   G   GW +W   VV   A+  A        +P    WV +L 
Sbjct: 90  PSPGAFSTYAEKAMGRTVGRTLGWLWWAQIVVVVAAEATAAAQLLTELWPVAEQWVLALL 149

Query: 142 VIVLLLTLNLATVKMFGEMEFWFAMIKIVAIVSLIVVGLVMVAMHFQSPTGVEASFAHLW 201
            +V+   +NL  V+  GE EFWFA++K++A+++ + VGL ++      P+       +L 
Sbjct: 150 FMVVFTAVNLVKVRTLGETEFWFALMKVLAVLAFLGVGLAVLLGLTDVPS---PGLGNLT 206

Query: 202 NDGGWFPKGLSGFFAGFQIAVFAFVGIELVGTTAAETKDPEKSLPRAINSIPIRIIMFYV 261
             GG+ P GL+G  A   + +FAF G ELV   AAET+DP+ ++ RA+ +I +RI++FYV
Sbjct: 207 AHGGFLPNGLTGVAAALLVVIFAFGGTELVTIAAAETEDPQHNVARAVRTILVRILVFYV 266

Query: 262 FALIVIMSVTPWSSVVPEKSPFVELFVLVGLPAAASVINFVVLTSAASSANSGVFSTSRM 321
            A+ V++ V PW       SPFV +    G+P A  V+  +++ +  S+ N+ V+ +SRM
Sbjct: 267 GAVTVMVLVLPWDDEQLSVSPFVAVLETAGVPGADVVMAVIIILALLSALNANVYGSSRM 326

Query: 322 LFGLAQEGVAPKAFAKLSKRAVPAKGLTFSCICLLGGVVMLYVNPSVIGAFTMITTVSAI 381
           L+ LA+ G AP+AFA +S R VP   +  S     G VV+ Y+ P  +    M+ TV A 
Sbjct: 327 LYSLARRGSAPRAFADVSARGVPRTAVLVSVAFGFGAVVLNYLWPETV-LLWMLNTVGAT 385

Query: 382 LFMFVWTIILCSYLVYRKQRPHLHEKSIYKMPLGKLMCWVCMAFFVFVVVLLTLEDDTRQ 441
             + VW + L S +V R++      +   +M     + W+ +A    +++L  L+D  R 
Sbjct: 386 C-LVVWGLALVSQIVLRRRADRDGTELPLRMWAFPWLSWLALAILAGILLLGLLDDAVRG 444

Query: 442 ALLVTPLWFIALGLGWLFIGK 462
            LL+T    + + L    +G+
Sbjct: 445 QLLLTAGLVLLIALASKLLGR 465


Lambda     K      H
   0.329    0.141    0.440 

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: 545
Number of extensions: 23
Number of successful extensions: 3
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: 470
Length of database: 471
Length adjustment: 33
Effective length of query: 437
Effective length of database: 438
Effective search space:   191406
Effective search space used:   191406
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 (21.8 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