GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1580 Histidine transport
           protein (permease)
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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