GapMind for catabolism of small carbon sources

 

Alignments for a candidate for RR42_RS28305 in Pseudomonas fluorescens FW300-N1B4

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

Query= uniprot:A0A0C4YRF7
         (472 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1580
          Length = 469

 Score =  427 bits (1099), Expect = e-124
 Identities = 201/441 (45%), Positives = 299/441 (67%), Gaps = 2/441 (0%)

Query: 17  KDLHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGPGLMLSYAIGGVAIFFIMRALGE 76
           K L RGL  RHI+ +A+G AIG GLF G+  AI +AGP ++L+Y IGG A+F +MRALGE
Sbjct: 6   KGLKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVMRALGE 65

Query: 77  LLLYRPVSGSFATYAEEFVGPFAGFATGWSYWFMWVVTGMAEITAVAVYVHYWFPDVPQW 136
           + ++ PV+GSF  YA  ++GP AGF  GW+Y F  V+ GMA++TA  +Y+ +WFP+V +W
Sbjct: 66  MAVHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMVIVGMADVTAFGIYMGFWFPEVDRW 125

Query: 137 IPALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIGLAIIFFGVT--PLGPTA 194
           I  L  ++V+  +N   V VFGE+EFW +L+KV  IVAMI+ G  I+ FG++  P     
Sbjct: 126 IWVLGIVSVVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIMLFGISTAPGAQAT 185

Query: 195 SFSNLWTHGGFMPFGTLGVVLTLQIVMFAYQGVELIGVTAGEAQNPEKVLPHATNGVVWR 254
             SNLW+HGGFMP G  G++ +  +VMFA+ G+E+IGVTAGEA++P++VLP A N V  R
Sbjct: 186 DISNLWSHGGFMPNGVGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQRVLPRAINAVPLR 245

Query: 255 ILIFYVGALIIMMALVPWNELKPGVSPFVYVFERIGVPGAAAIVNLVVITAAASSCNSGI 314
           IL+FYV  ++++M++ PW ++    SPFV +F+ +G+  AA I+N+VVI+AA S+ NS I
Sbjct: 246 ILLFYVLTMLVLMSIFPWQQIGSQGSPFVQIFDNLGISSAATILNIVVISAAVSAINSDI 305

Query: 315 FSTGRMLYTLAQFGQAPRAFGRVSSKHVPSIAITFSAALMGIGVLLNYIVPEQVFVWVTS 374
           F  GRM+Y LAQ G AP+ F R+S   VP + +   ++ + +GVLLNY++PE VF+ + S
Sbjct: 306 FGAGRMMYGLAQQGHAPKGFARLSRNGVPWLTVVVMSSALLLGVLLNYLIPENVFLLIAS 365

Query: 375 ISLVGSLWTWSIIMIAHLGYRKAIAAGRVKAVAFRMPGAPYANWLVVAFMIAVAVLLSLD 434
           ++   ++W W +I+   +  R++++A +V  + F +P  PYA    +AFM+ +  +L   
Sbjct: 366 VATFATVWVWLMILFTQVAMRRSMSAEQVAQLKFPVPFWPYAPMAAIAFMLFIFGVLGYF 425

Query: 435 PGTRVALYVAPVWFALLGIGY 455
           P T+ AL V  VW  LL + Y
Sbjct: 426 PDTQAALIVGVVWIVLLVLAY 446


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: 762
Number of extensions: 45
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: 472
Length of database: 469
Length adjustment: 33
Effective length of query: 439
Effective length of database: 436
Effective search space:   191404
Effective search space used:   191404
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