GapMind for catabolism of small carbon sources

 

Aligments for a candidate for cycA in Pseudomonas fluorescens FW300-N2E3

Align D-serine/D-alanine/glycine transporter (characterized)
to candidate AO353_12275 AO353_12275 proline-specific permease

Query= SwissProt::P0AAE0
         (470 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_12275 AO353_12275
           proline-specific permease
          Length = 468

 Score =  372 bits (956), Expect = e-107
 Identities = 187/457 (40%), Positives = 283/457 (61%), Gaps = 4/457 (0%)

Query: 12  QAPAEQSLRRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVM 71
           Q PA   L+R L+ RHI+ +A+G AIGTGLF GS   I +AGP+++  Y+I G  +F VM
Sbjct: 2   QKPAN-GLKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVM 60

Query: 72  RAMGELLLSNLEYKSFSDFASDLLGPWAGYFTGWTYWFCWVVTGMADVVAITAYAQFWFP 131
           RA+GE+ + N    SF  +AS  LGP AG+  GWTY F  V+ GMADV A   Y  FWFP
Sbjct: 61  RALGEMAVHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMVIVGMADVTAFGIYMGFWFP 120

Query: 132 DLSDWVASLAVIVLLLTLNLATVKMFGEMEFWFAMIKIVAIVSLIVVGLVMVAMHFQSPT 191
           ++S W+  L V+ ++  LNL  VK+FGEMEFW +++K+ AIV++I+ G  ++     +  
Sbjct: 121 EVSRWIWVLGVVSIVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIMLFGISTAP 180

Query: 192 GVEASFAHLWNDGGWFPKGLSGFFAGFQIAVFAFVGIELVGTTAAETKDPEKSLPRAINS 251
           G     ++LW  GG+ P G+ G  A F + +FAF GIE++G TA E KDP+  LPRAIN+
Sbjct: 181 GQVTDISNLWTQGGFMPNGMGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQHVLPRAINA 240

Query: 252 IPIRIIMFYVFALIVIMSVTPWSSVVPEKSPFVELFVLVGLPAAASVINFVVLTSAASSA 311
           +P+RI++FYV  ++V+MS+ PW  +  + SPFV++F  +G+ +AA+++N VV+T+A S+ 
Sbjct: 241 VPLRILLFYVLTMLVLMSIFPWQQIGSQGSPFVQIFDKLGISSAATILNIVVITAAISAI 300

Query: 312 NSGVFSTSRMLFGLAQEGVAPKAFAKLSKRAVPAKGLTFSCICLLGGVVMLYVNPSVIGA 371
           NS +F   RM+FGLAQ+G APK FA LS+  VP   +    + LL GV++ Y+ P     
Sbjct: 301 NSDIFGAGRMMFGLAQQGHAPKGFAHLSRNGVPWMTVVVMSVALLLGVLLNYLIPE--NV 358

Query: 372 FTMITTVSAILFMFVWTIILCSYLVYRKQRPHLHEKSI-YKMPLGKLMCWVCMAFFVFVV 430
           F +I +++    ++VW +IL + +  R+         + + +P         +AF +FV 
Sbjct: 359 FLLIASIATFATVWVWLMILFTQVAMRRSMTAEQVAQLKFPVPFWPYAPMAAIAFMLFVF 418

Query: 431 VLLTLEDDTRQALLVTPLWFIALGLGWLFIGKKRAAE 467
            +L    DT+ AL+V  +W + L L +L   K  A +
Sbjct: 419 GVLGYFPDTQAALIVGVVWIVLLVLAYLMWVKPAAGQ 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: 645
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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