GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cycA in Catellicoccus marimammalium M35/04/3

Align D-serine/D-alanine/glycine transporter (characterized)
to candidate WP_009490181.1 C683_RS03825 amino acid permease

Query= SwissProt::A0A0H2VDI7
         (470 letters)



>NCBI__GCF_000313915.1:WP_009490181.1
          Length = 448

 Score =  470 bits (1209), Expect = e-137
 Identities = 221/439 (50%), Positives = 323/439 (73%), Gaps = 3/439 (0%)

Query: 15  AEQSLRRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVMRAM 74
           +++ L R L+NRH+QLI+IGGAIGTGLF+ SGK+I++AGPS++  YMI+G  +FF+MR++
Sbjct: 2   SQEKLERGLSNRHVQLISIGGAIGTGLFLASGKSIAIAGPSVLLAYMIVGMFVFFIMRSL 61

Query: 75  GELLLSNLEYKSFSDFASDLLGPWAGYFTGWTYWFCWVVTGMADVVAITAYAQFWFPGLS 134
           GELLL+NL+  SF + A   LG    + TGWTYWFCW+   M+D+ A+  Y ++WFP L 
Sbjct: 62  GELLLANLDCHSFVELAHQYLGRRWAFVTGWTYWFCWITVAMSDLTAVGMYMRYWFPHLP 121

Query: 135 DWVASLSVIILLLVLNLATVKMFGEMEFWFAMIKIVAIVSLIVVGLVMVAMHFQSPTGVE 194
            W+ +L +++ L+ LNL +VK+FGE+EFW A+IKI+AIV+LI VGL M+  H +   G+ 
Sbjct: 122 QWIPALLMLLFLMALNLLSVKLFGEIEFWLALIKILAIVALIGVGLYMIFTHHKLENGIV 181

Query: 195 ASFAHLWNDGGWFPKGLSGFFAGFQIAVFAFVGIELVGTTAAETKDPEKSLPRAINSIPI 254
           ASFA+L+ DGG+FP G SGF   FQ+AVF+F G+ELVG TA ET+DPEK+LP+AIN+IP+
Sbjct: 182 ASFANLYQDGGFFPHGFSGFILSFQLAVFSFTGVELVGLTAGETQDPEKTLPKAINNIPV 241

Query: 255 RIIMFYVFSLIVIMSVTPWSSVVPEKSPFVELFVLVGLPAAASVINFVVLTSAASSANSG 314
           RI++FYV SL VIM+V PW+ + P +SPFV +F  +G+ AAAS+INFVVL+SAAS+ NS 
Sbjct: 242 RILLFYVGSLAVIMAVQPWNIIDPTQSPFVTVFSSIGIAAAASIINFVVLSSAASACNSA 301

Query: 315 VFSTSRMLFGLAQEGVAPKAFAKLSKRAVPAKGLTFSCICLLGGVVMLYVNPSVIGAFTM 374
           +FSTSRML+GLA++  APK FAKL+K + PA  L  S + +   +V+ YV P   G F++
Sbjct: 302 LFSTSRMLYGLAKDDNAPKTFAKLNKNSTPAMALLMSSVVVGITIVLNYVMPE--GVFSL 359

Query: 375 ITTVSAILFMFVWTIILCSYLVYRKQRPHLHEKSIYKMPLGKLMCWVCMAFFVFVLVLLT 434
           I+ +S + F+F+WTII+  ++ + KQ     ++  +++   K++  + + F   ++V+  
Sbjct: 360 ISGISTVCFLFIWTIIVICHMKFLKQTKD-EDRPKFRLKGAKVINILSLIFLALIIVICA 418

Query: 435 LEDDTRQALLVTPLWFIAL 453
           + + TR AL +TP+WFIAL
Sbjct: 419 VLESTRIALFITPIWFIAL 437


Lambda     K      H
   0.329    0.141    0.441 

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: 635
Number of extensions: 24
Number of successful extensions: 4
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: 448
Length adjustment: 33
Effective length of query: 437
Effective length of database: 415
Effective search space:   181355
Effective search space used:   181355
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