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 GFF344 PS417_01755 proline-specific permease

Query= SwissProt::P0AAE0
         (470 letters)



>FitnessBrowser__WCS417:GFF344
          Length = 469

 Score =  366 bits (940), Expect = e-106
 Identities = 184/457 (40%), Positives = 286/457 (62%), Gaps = 4/457 (0%)

Query: 16  EQSLRRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVMRAMG 75
           E+ L+R L+ RHI+ +A+G AIGTGLF GS   I +AGP+++  Y+I G  +F VMRA+G
Sbjct: 5   EKGLKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVMRALG 64

Query: 76  ELLLSNLEYKSFSDFASDLLGPWAGYFTGWTYWFCWVVTGMADVVAITAYAQFWFPDLSD 135
           E+ + N    SF  +AS  LGP AG+  GWTY F  ++  +ADV A   Y  FWFPD++ 
Sbjct: 65  EMAVHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMIIVCLADVTAFGIYMGFWFPDVAR 124

Query: 136 WVASLAVIVLLLTLNLATVKMFGEMEFWFAMIKIVAIVSLIVVGLVMVAMHFQSPTGVEA 195
           WV  L +++L+  LNL  VK+FGEMEFW +++K+ AIV++I+ G  ++     S    +A
Sbjct: 125 WVWVLGIVLLIGGLNLCNVKVFGEMEFWLSLLKVGAIVAMILGGFGIMLFGIHSAGETQA 184

Query: 196 S-FAHLWNDGGWFPKGLSGFFAGFQIAVFAFVGIELVGTTAAETKDPEKSLPRAINSIPI 254
           S  ++LW  GG+ P G+ G  A F + +FAF GIE++G TA E KDP++ +P+AIN++P+
Sbjct: 185 SGLSNLWAHGGFMPNGIGGLIASFAVVMFAFGGIEIIGITAGEAKDPQRVIPKAINAVPL 244

Query: 255 RIIMFYVFALIVIMSVTPWSSVVPEKSPFVELFVLVGLPAAASVINFVVLTSAASSANSG 314
           RI++FYV  L V+M++ PW  +  + SPFV++F  +G+ +AA+++N VV+++A S+ NS 
Sbjct: 245 RILLFYVLTLFVLMAIYPWPQIGSQGSPFVQIFSNLGIGSAATILNIVVISAAVSAINSD 304

Query: 315 VFSTSRMLFGLAQEGVAPKAFAKLSKRAVPAKGLTFSCICLLGGVVMLYVNPSVIGAFTM 374
           +F   RM++GLAQ+G APK FA+LSK+ VP   +      LLGGVV+ Y+ P     F +
Sbjct: 305 IFGAGRMMYGLAQQGQAPKGFAQLSKQGVPWMTVVVMGAALLGGVVLNYLIPE--NVFLV 362

Query: 375 ITTVSAILFMFVWTIILCSYLVYRKQRPHLHEKSI-YKMPLGKLMCWVCMAFFVFVVVLL 433
           I +++    ++VW +IL + +  R+         + + +P         + F +FV  +L
Sbjct: 363 IASIATFATVWVWLMILFTQVAMRRSMTKEQVAELKFPVPFWPYAPAAAIVFMLFVFGVL 422

Query: 434 TLEDDTRQALLVTPLWFIALGLGWLFIGKKRAAELRK 470
               DT+ ALLV  +W + L + +L   K  A +  K
Sbjct: 423 GYFPDTQAALLVGAVWIVLLVVAYLLWVKPSAGQAAK 459


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: 668
Number of extensions: 34
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: 469
Length adjustment: 33
Effective length of query: 437
Effective length of database: 436
Effective search space:   190532
Effective search space used:   190532
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