GapMind for catabolism of small carbon sources

 

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

Align histidine permease (characterized)
to candidate Pf6N2E2_5459 D-serine/D-alanine/glycine transporter

Query= reanno::pseudo3_N2E3:AO353_12275
         (468 letters)



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

 Score =  512 bits (1318), Expect = e-149
 Identities = 245/445 (55%), Positives = 327/445 (73%), Gaps = 2/445 (0%)

Query: 8   LKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVMRALGEMA 67
           LKR L  RHIR MALG+ IG GLF GSA AI+MAGPA++L+Y+IGG A+ ++MRALGEMA
Sbjct: 18  LKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIMRALGEMA 77

Query: 68  VHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMVIVGMADVTAFGIYMGFWFPEVSRWIW 127
           VHNPVAGSF +YA  YLGP+AGF+ GW Y F  ++  +A++TA  +YMG WFP+V RWIW
Sbjct: 78  VHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGIWFPDVPRWIW 137

Query: 128 VLGVVSIVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIMLFGISTAPGQVTDIS 187
            L  +  +G +NL  VK FGE EFW +L+K+  I+AM++GG GI+ FG     G    IS
Sbjct: 138 ALAALVSMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVGIIAFGFGN-DGVALGIS 196

Query: 188 NLWTQGGFMPNGMGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQHVLPRAINAVPLRILL 247
           NLWT GGFMPNG+ G++ S  +VMFA+ G+E+IG+TAGEAK+PQ  +P AI +V  RILL
Sbjct: 197 NLWTHGGFMPNGVQGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPNAIGSVFWRILL 256

Query: 248 FYVLTMLVLMSIFPWQQIGSQGSPFVQIFDKLGISSAATILNIVVITAAISAINSDIFGA 307
           FYV  + V++SI+PW +IG+QGSPFV  F++LGI +AA I+N VVITAA+S+ N  IF  
Sbjct: 257 FYVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFVVITAALSSCNGGIFST 316

Query: 308 GRMMFGLAQQGHAPKGFAHLSRNGVPWMTVVVMSVALLLGVLLNYLIPENVFLLIASIAT 367
           GRM++ LAQ G AP GFA  S NGVP   +++   ALLLGVLLNYL+PE VF+ + SIAT
Sbjct: 317 GRMLYSLAQNGQAPAGFATTSANGVPRRALLLSIAALLLGVLLNYLVPEKVFVWVTSIAT 376

Query: 368 FATVWVWLMILFTQVAMRRSMTAEQVAQLKFPVPFWPYAPMAAIAFMLFVFGVLGYFPDT 427
           F  +W W+MIL  Q+  R+S++A + A LK+ +  +P +   A+AF++ V G++ YFPDT
Sbjct: 377 FGAIWTWVMILLAQLKFRKSLSASERAALKYRMWLYPVSSYLALAFLVLVVGLMAYFPDT 436

Query: 428 QAALIVGVVWIVLL-VLAYLMWVKP 451
           + AL VG  ++VLL VL Y+  ++P
Sbjct: 437 RVALYVGPAFLVLLTVLFYVFKLQP 461


Lambda     K      H
   0.329    0.142    0.441 

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: 788
Number of extensions: 39
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: 468
Length of database: 473
Length adjustment: 33
Effective length of query: 435
Effective length of database: 440
Effective search space:   191400
Effective search space used:   191400
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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