GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cycA in Pseudomonas fluorescens GW456-L13

Align D-serine/D-alanine/glycine transporter (characterized)
to candidate PfGW456L13_318 Histidine transport protein (permease)

Query= SwissProt::P0AAE0
         (470 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_318
          Length = 468

 Score =  374 bits (961), Expect = e-108
 Identities = 187/453 (41%), Positives = 284/453 (62%), Gaps = 3/453 (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  V+ GMADV A   Y  FWFP++S 
Sbjct: 65  EMAVHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMVIVGMADVTAFGIYMGFWFPEVSR 124

Query: 136 WVASLAVIVLLLTLNLATVKMFGEMEFWFAMIKIVAIVSLIVVGLVMVAMHFQSPTGVEA 195
           W+  L V+ ++  LNL  VK+FGEMEFW +++K+ AIV++I+ G  ++     S  G   
Sbjct: 125 WIWVLGVVSIVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIMWFGISSAPGQAT 184

Query: 196 SFAHLWNDGGWFPKGLSGFFAGFQIAVFAFVGIELVGTTAAETKDPEKSLPRAINSIPIR 255
             ++LW+ GG+ P G+ G  A F + +FAF GIE++G TA E KDP+  LPRAIN++P+R
Sbjct: 185 DISNLWSHGGFMPNGMGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQHVLPRAINAVPLR 244

Query: 256 IIMFYVFALIVIMSVTPWSSVVPEKSPFVELFVLVGLPAAASVINFVVLTSAASSANSGV 315
           I++FYV  ++V+MS+ PW  +  + SPFV++F  +G+ +AA+++N VV+T+A S+ NS +
Sbjct: 245 ILLFYVLTMLVLMSIFPWQQIGSQGSPFVQIFDKLGISSAATILNIVVITAAISAINSDI 304

Query: 316 FSTSRMLFGLAQEGVAPKAFAKLSKRAVPAKGLTFSCICLLGGVVMLYVNPSVIGAFTMI 375
           F   RM+FGLAQ+G APK FA+LS+  VP   +      LL GV++ Y+ P     F +I
Sbjct: 305 FGAGRMMFGLAQQGHAPKGFARLSRNGVPWMTVVVMSAALLLGVLLNYLIPE--NVFLLI 362

Query: 376 TTVSAILFMFVWTIILCSYLVYRKQRPHLHEKSI-YKMPLGKLMCWVCMAFFVFVVVLLT 434
            +V+    ++VW +IL + +  R+         + + +PL        +AF +F+  +L 
Sbjct: 363 ASVATFATVWVWLMILVTQVAMRRSMSAEQVAQLKFPVPLWPYAPAAAIAFMLFIFGVLG 422

Query: 435 LEDDTRQALLVTPLWFIALGLGWLFIGKKRAAE 467
              DT+ AL+V  +W + L L +L   K  A +
Sbjct: 423 YFPDTQAALIVGVVWIVLLVLAYLTWVKPAAGQ 455


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: 648
Number of extensions: 31
Number of successful extensions: 2
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: 468
Length adjustment: 33
Effective length of query: 437
Effective length of database: 435
Effective search space:   190095
Effective search space used:   190095
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