GapMind for catabolism of small carbon sources

 

Alignments for a candidate for permease in Pseudomonas simiae WCS417

Align histidine permease (characterized)
to candidate GFF1065 PS417_05405 D-alanine/D-serine/glycine permease

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



>FitnessBrowser__WCS417:GFF1065
          Length = 472

 Score =  506 bits (1303), Expect = e-148
 Identities = 247/453 (54%), Positives = 328/453 (72%), Gaps = 5/453 (1%)

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+  RWIW
Sbjct: 78  VHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGVWFPDTPRWIW 137

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

Query: 188 NLWTQGGFMPNGMGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQHVLPRAINAVPLRILL 247
           NLW  GGFMPNG+ G++ S  +VMFA+ G+E+IG+TAGEAK+PQ  +P AI +V  RILL
Sbjct: 197 NLWAHGGFMPNGVQGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPSAIGSVFWRILL 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  FA  S NGVP   +++   ALLLGVLLNYL+PE VF+ + SIAT
Sbjct: 317 GRMLYSLAQNGQAPATFAKTSSNGVPRKALLLSIFALLLGVLLNYLVPEKVFVWVTSIAT 376

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

Query: 428 QAALIVGVVWIVLL-VLAYLMWVKP---AAGQA 456
           + AL VG V++VLL VL Y+  ++P   A G+A
Sbjct: 437 RIALYVGPVFLVLLTVLFYVFKLQPTQVAQGEA 469


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: 793
Number of extensions: 41
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: 472
Length adjustment: 33
Effective length of query: 435
Effective length of database: 439
Effective search space:   190965
Effective search space used:   190965
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