GapMind for catabolism of small carbon sources

 

Alignments for a candidate for RR42_RS28305 in Pseudomonas putida KT2440

Align D-serine/D-alanine/glycine transporter (characterized, see rationale)
to candidate PP_5031 PP_5031 proline (histidine) APC transporter

Query= uniprot:A0A0C4YRF7
         (472 letters)



>FitnessBrowser__Putida:PP_5031
          Length = 467

 Score =  410 bits (1053), Expect = e-119
 Identities = 197/445 (44%), Positives = 294/445 (66%), Gaps = 2/445 (0%)

Query: 13  VHEEKDLHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGPGLMLSYAIGGVAIFFIMR 72
           + + + L RGL  RHI+ +A+G AIG GLF G+  AI +AGP ++L+Y IGG A+F +MR
Sbjct: 1   MQQAQGLKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVMR 60

Query: 73  ALGELLLYRPVSGSFATYAEEFVGPFAGFATGWSYWFMWVVTGMAEITAVAVYVHYWFPD 132
           ALGE+ ++ PV+GSF  YA  ++GP AGF  GW+Y F  V+  +A++TA  +Y+ +WFP+
Sbjct: 61  ALGEMAVHNPVAGSFGHYATTYLGPMAGFILGWTYAFEMVIVAIADVTAFGIYMGFWFPE 120

Query: 133 VPQWIPALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIGLAIIFFGVTPLGP 192
           V +WI  L  + ++  +N   V VFGE+EFW +L+KV  IVAMI+ GL I+ FG + +G 
Sbjct: 121 VARWIWVLGIVFLIGGLNLCNVKVFGEMEFWLSLLKVGAIVAMILAGLGIMAFGFSQVGT 180

Query: 193 --TASFSNLWTHGGFMPFGTLGVVLTLQIVMFAYQGVELIGVTAGEAQNPEKVLPHATNG 250
                 SNL+ HGGFMP G  G++ +  +VMFA+ G+E+IGVTAGEA++P++V+P A N 
Sbjct: 181 GHAVGMSNLFDHGGFMPNGVGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQRVIPKAINA 240

Query: 251 VVWRILIFYVGALIIMMALVPWNELKPGVSPFVYVFERIGVPGAAAIVNLVVITAAASSC 310
           V  RIL+FYV  L ++M L PW ++    SPFV +F  +G+  AAA++N+VVI+AA S+ 
Sbjct: 241 VPLRILLFYVLTLFVLMCLYPWPQIGSQGSPFVQIFSNLGIGSAAAVLNVVVISAAISAI 300

Query: 311 NSGIFSTGRMLYTLAQFGQAPRAFGRVSSKHVPSIAITFSAALMGIGVLLNYIVPEQVFV 370
           NS IF  GRM+Y LAQ G APR F ++S   VP + +    A + IGVLLNY++PE VF+
Sbjct: 301 NSDIFGAGRMMYGLAQQGHAPRGFSKLSKHGVPWMTVVVMGAALLIGVLLNYLIPENVFL 360

Query: 371 WVTSISLVGSLWTWSIIMIAHLGYRKAIAAGRVKAVAFRMPGAPYANWLVVAFMIAVAVL 430
            + SI+   ++W W +I++  +  R++++  +V  + F +P  PY   + +AFM+ +  +
Sbjct: 361 LIASIATFATVWVWLMILLTQVAMRRSMSREQVAQLKFPVPFWPYGPAMAIAFMVFIFGV 420

Query: 431 LSLDPGTRVALYVAPVWFALLGIGY 455
           L   P T+ AL V  +W   L   Y
Sbjct: 421 LGYFPDTQAALIVGVIWVVFLVASY 445


Lambda     K      H
   0.328    0.142    0.445 

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: 787
Number of extensions: 55
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: 472
Length of database: 467
Length adjustment: 33
Effective length of query: 439
Effective length of database: 434
Effective search space:   190526
Effective search space used:   190526
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