GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cycA in Pseudomonas fluorescens FW300-N1B4

Align D-serine/D-alanine/glycine transporter (characterized)
to candidate Pf1N1B4_1580 Histidine transport protein (permease)

Query= SwissProt::P0AAE0
         (470 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1580
          Length = 469

 Score =  366 bits (940), Expect = e-106
 Identities = 184/458 (40%), Positives = 288/458 (62%), Gaps = 5/458 (1%)

Query: 12  QAPAEQSLRRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVM 71
           Q PA+  L+R L+ RHI+ +A+G AIGTGLF GS   I +AGP+++  Y+I G  +F VM
Sbjct: 2   QQPAK-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
           ++  W+  L ++ ++  LNL  VK+FGEMEFW +++K+ AIV++I+ G  ++     +  
Sbjct: 121 EVDRWIWVLGIVSVVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIMLFGISTAP 180

Query: 192 GVEAS-FAHLWNDGGWFPKGLSGFFAGFQIAVFAFVGIELVGTTAAETKDPEKSLPRAIN 250
           G +A+  ++LW+ GG+ P G+ G  A F + +FAF GIE++G TA E KDP++ LPRAIN
Sbjct: 181 GAQATDISNLWSHGGFMPNGVGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQRVLPRAIN 240

Query: 251 SIPIRIIMFYVFALIVIMSVTPWSSVVPEKSPFVELFVLVGLPAAASVINFVVLTSAASS 310
           ++P+RI++FYV  ++V+MS+ PW  +  + SPFV++F  +G+ +AA+++N VV+++A S+
Sbjct: 241 AVPLRILLFYVLTMLVLMSIFPWQQIGSQGSPFVQIFDNLGISSAATILNIVVISAAVSA 300

Query: 311 ANSGVFSTSRMLFGLAQEGVAPKAFAKLSKRAVPAKGLTFSCICLLGGVVMLYVNPSVIG 370
            NS +F   RM++GLAQ+G APK FA+LS+  VP   +      LL GV++ Y+ P    
Sbjct: 301 INSDIFGAGRMMYGLAQQGHAPKGFARLSRNGVPWLTVVVMSSALLLGVLLNYLIPE--N 358

Query: 371 AFTMITTVSAILFMFVWTIILCSYLVYRKQRPHLHEKSI-YKMPLGKLMCWVCMAFFVFV 429
            F +I +V+    ++VW +IL + +  R+         + + +P         +AF +F+
Sbjct: 359 VFLLIASVATFATVWVWLMILFTQVAMRRSMSAEQVAQLKFPVPFWPYAPMAAIAFMLFI 418

Query: 430 VVLLTLEDDTRQALLVTPLWFIALGLGWLFIGKKRAAE 467
             +L    DT+ AL+V  +W + L L +L   K  A +
Sbjct: 419 FGVLGYFPDTQAALIVGVVWIVLLVLAYLTWVKPAAGQ 456


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: 635
Number of extensions: 33
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