GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ansP in Pseudomonas fluorescens FW300-N2E2

Align L-asparagine permease; L-asparagine transport protein (characterized)
to candidate Pf6N2E2_5459 D-serine/D-alanine/glycine transporter

Query= SwissProt::P77610
         (499 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5459
          Length = 473

 Score =  365 bits (937), Expect = e-105
 Identities = 181/436 (41%), Positives = 278/436 (63%), Gaps = 3/436 (0%)

Query: 28  KAMGNRQVQMIAIGGAIGTGLFLGAGARLQMAGPALALVYLICGLFSFFILRALGELVLH 87
           + +G R ++++A+G  IG GLFLG+   ++MAGPA+ L Y+I GL    I+RALGE+ +H
Sbjct: 20  RELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIMRALGEMAVH 79

Query: 88  RPSSGSFVSYAREFLGEKAAYVAGWMYFINWAMTGIVDITAVALYMHYWGAFGGVPQWVF 147
            P +GSF  YA+++LG  A ++ GW Y+  W +T + +ITAVA+YM  W  F  VP+W++
Sbjct: 80  NPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGIW--FPDVPRWIW 137

Query: 148 ALAALTIVGTMNMIGVKWFAEMEFWFALIKVLAIVTFLVVGTVFLGSGQPLDGNTTGFHL 207
           ALAAL  +G++N+I VK F E EFWFALIK++ I+  ++ G   +  G   DG   G   
Sbjct: 138 ALAALVSMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVGIIAFGFGNDGVALGISN 197

Query: 208 ITDNGGFFPHGLLPALVLIQGVVFAFASIEMVGTAAGECKDPQTMVPKAINSVIWRIGLF 267
           +  +GGF P+G+   L+ +Q V+FA+  +EM+G  AGE K+PQ  +P AI SV WRI LF
Sbjct: 198 LWTHGGFMPNGVQGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPNAIGSVFWRILLF 257

Query: 268 YVGSVVLLVMLLPWSAYQAGQSPFVTFFSKLGVPYIGSIMNIVVLTAALSSLNSGLYCTG 327
           YVG++ +++ + PW+      SPFV  F +LG+     I+N VV+TAALSS N G++ TG
Sbjct: 258 YVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFVVITAALSSCNGGIFSTG 317

Query: 328 RILRSMAMGGSAPSFMAKMSRQHVPYAGILATLVVYVVGVFLNYLVPSRVFEIVLNFASL 387
           R+L S+A  G AP+  A  S   VP   +L ++   ++GV LNYLVP +VF  V + A+ 
Sbjct: 318 RMLYSLAQNGQAPAGFATTSANGVPRRALLLSIAALLLGVLLNYLVPEKVFVWVTSIATF 377

Query: 388 GIIASWAFIIVCQMRLRKAIKEGKAADVSFKLPGAPFTSWLTLLFLLSVLVLMAFDYPNG 447
           G I +W  I++ Q++ RK++   + A + +++   P +S+L L FL+ V+ LMA+ +P+ 
Sbjct: 378 GAIWTWVMILLAQLKFRKSLSASERAALKYRMWLYPVSSYLALAFLVLVVGLMAY-FPDT 436

Query: 448 TYTIAALPIIGILLVI 463
              +   P   +LL +
Sbjct: 437 RVALYVGPAFLVLLTV 452


Lambda     K      H
   0.327    0.141    0.435 

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: 763
Number of extensions: 51
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: 499
Length of database: 473
Length adjustment: 34
Effective length of query: 465
Effective length of database: 439
Effective search space:   204135
Effective search space used:   204135
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 (21.7 bits)
S2: 52 (24.6 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 (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