GapMind for catabolism of small carbon sources

 

Aligments for a candidate for RR42_RS28305 in Pseudomonas fluorescens FW300-N2E2

Align D-serine/D-alanine/glycine transporter (characterized, see rationale)
to candidate Pf6N2E2_5459 D-serine/D-alanine/glycine transporter

Query= uniprot:A0A0C4YRF7
         (472 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5459
           D-serine/D-alanine/glycine transporter
          Length = 473

 Score =  520 bits (1340), Expect = e-152
 Identities = 251/449 (55%), Positives = 335/449 (74%)

Query: 19  LHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGPGLMLSYAIGGVAIFFIMRALGELL 78
           L R L +RHI+++A+G  IGVGLFLG+ +AI +AGP +MLSY IGG+AI  IMRALGE+ 
Sbjct: 18  LKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIMRALGEMA 77

Query: 79  LYRPVSGSFATYAEEFVGPFAGFATGWSYWFMWVVTGMAEITAVAVYVHYWFPDVPQWIP 138
           ++ PV+GSF+ YA++++GP AGF TGW+YWF+W+VT +AEITAVAVY+  WFPDVP+WI 
Sbjct: 78  VHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGIWFPDVPRWIW 137

Query: 139 ALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIGLAIIFFGVTPLGPTASFSN 198
           ALA L  +  +N +AV  FGE EFWFALIK+VTI+AM++ G+ II FG    G     SN
Sbjct: 138 ALAALVSMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVGIIAFGFGNDGVALGISN 197

Query: 199 LWTHGGFMPFGTLGVVLTLQIVMFAYQGVELIGVTAGEAQNPEKVLPHATNGVVWRILIF 258
           LWTHGGFMP G  GV+++LQ+VMFAY GVE+IG+TAGEA+NP+K +P+A   V WRIL+F
Sbjct: 198 LWTHGGFMPNGVQGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPNAIGSVFWRILLF 257

Query: 259 YVGALIIMMALVPWNELKPGVSPFVYVFERIGVPGAAAIVNLVVITAAASSCNSGIFSTG 318
           YVGAL +++++ PWNE+    SPFV  FER+G+  AA I+N VVITAA SSCN GIFSTG
Sbjct: 258 YVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFVVITAALSSCNGGIFSTG 317

Query: 319 RMLYTLAQFGQAPRAFGRVSSKHVPSIAITFSAALMGIGVLLNYIVPEQVFVWVTSISLV 378
           RMLY+LAQ GQAP  F   S+  VP  A+  S A + +GVLLNY+VPE+VFVWVTSI+  
Sbjct: 318 RMLYSLAQNGQAPAGFATTSANGVPRRALLLSIAALLLGVLLNYLVPEKVFVWVTSIATF 377

Query: 379 GSLWTWSIIMIAHLGYRKAIAAGRVKAVAFRMPGAPYANWLVVAFMIAVAVLLSLDPGTR 438
           G++WTW +I++A L +RK+++A    A+ +RM   P +++L +AF++ V  L++  P TR
Sbjct: 378 GAIWTWVMILLAQLKFRKSLSASERAALKYRMWLYPVSSYLALAFLVLVVGLMAYFPDTR 437

Query: 439 VALYVAPVWFALLGIGYRFTKSRALLEGH 467
           VALYV P +  LL + +   K +   E H
Sbjct: 438 VALYVGPAFLVLLTVLFYVFKLQPTGETH 466


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: 878
Number of extensions: 53
Number of successful extensions: 1
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: 473
Length adjustment: 33
Effective length of query: 439
Effective length of database: 440
Effective search space:   193160
Effective search space used:   193160
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.

Links

Downloads

Related tools

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, the preprint 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