GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cycA in Pseudomonas simiae WCS417

Align D-serine/D-alanine/glycine transporter (characterized)
to candidate GFF1065 PS417_05405 D-alanine/D-serine/glycine permease

Query= SwissProt::P0AAE0
         (470 letters)



>FitnessBrowser__WCS417:GFF1065
          Length = 472

 Score =  378 bits (971), Expect = e-109
 Identities = 187/436 (42%), Positives = 280/436 (64%), Gaps = 4/436 (0%)

Query: 19  LRRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVMRAMGELL 78
           L+R L  RHI+L+A+G  IG GLF+GS K I +AGP+I+  Y+I G  +  +MRA+GE+ 
Sbjct: 18  LKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIMRALGEMA 77

Query: 79  LSNLEYKSFSDFASDLLGPWAGYFTGWTYWFCWVVTGMADVVAITAYAQFWFPDLSDWVA 138
           + N    SFS +A D LGP AG+ TGW YWF W+VT +A++ A+  Y   WFPD   W+ 
Sbjct: 78  VHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGVWFPDTPRWIW 137

Query: 139 SLAVIVLLLTLNLATVKMFGEMEFWFAMIKIVAIVSLIVVGLVMVAMHFQSPTGVEASFA 198
           +LA ++ + ++NL  VK FGE EFWFA+IKIV I+++++ G+ ++A  F +  GV    +
Sbjct: 138 ALAALISMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVGIIAFGFGN-DGVALGIS 196

Query: 199 HLWNDGGWFPKGLSGFFAGFQIAVFAFVGIELVGTTAAETKDPEKSLPRAINSIPIRIIM 258
           +LW  GG+ P G+ G     Q+ +FA++G+E++G TA E K+P+K++P AI S+  RI++
Sbjct: 197 NLWAHGGFMPNGVQGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPSAIGSVFWRILL 256

Query: 259 FYVFALIVIMSVTPWSSVVPEKSPFVELFVLVGLPAAASVINFVVLTSAASSANSGVFST 318
           FYV AL VI+S+ PW+ +  + SPFV  F  +G+  AA +INFVV+T+A SS N G+FST
Sbjct: 257 FYVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFVVITAALSSCNGGIFST 316

Query: 319 SRMLFGLAQEGVAPKAFAKLSKRAVPAKGLTFSCICLLGGVVMLYVNPSVIGAFTMITTV 378
            RML+ LAQ G AP  FAK S   VP K L  S   LL GV++ Y+ P  +  F  +T++
Sbjct: 317 GRMLYSLAQNGQAPATFAKTSSNGVPRKALLLSIFALLLGVLLNYLVPEKV--FVWVTSI 374

Query: 379 SAILFMFVWTIILCSYLVYRKQRPHLHEKSI-YKMPLGKLMCWVCMAFFVFVVVLLTLED 437
           +    ++ W +IL + L +RK      +  + Y+M L  +  ++ +AF + VV L+    
Sbjct: 375 ATFGAIWTWLMILLAQLKFRKSLSPAEQAGLKYRMWLYPVSSYLALAFLLLVVGLMAYFP 434

Query: 438 DTRQALLVTPLWFIAL 453
           DTR AL V P++ + L
Sbjct: 435 DTRIALYVGPVFLVLL 450


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: 650
Number of extensions: 38
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: 472
Length adjustment: 33
Effective length of query: 437
Effective length of database: 439
Effective search space:   191843
Effective search space used:   191843
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 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