GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ansP in Pseudomonas fluorescens FW300-N2E3

Align Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized)
to candidate AO353_24335 AO353_24335 L-asparagine permease

Query= TCDB::P40812
         (497 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_24335
          Length = 494

 Score =  665 bits (1715), Expect = 0.0
 Identities = 311/451 (68%), Positives = 380/451 (84%)

Query: 15  KRRWLNAHEEGYHKAMGNRQVQMIAIGGAIGTGLFLGAGARLQMAGPALALVYLICGIFS 74
           +  WL++HE GY K +  R VQM+A+GGAIGTGLFLGAGARLQ+AGPALA++YL+CGIF+
Sbjct: 21  RSNWLDSHESGYSKHLKKRHVQMMALGGAIGTGLFLGAGARLQIAGPALAVIYLVCGIFA 80

Query: 75  FFILRALGELVLHRPSSGSFVSYAREFLGEKAAYVAGWMYFINWAMTGIVDITAVALYMH 134
           FFILRALGELV+HRPSSGSFVSY REF+GE+A++VAGWMYF+ WA+TG+VDITA+A+YM 
Sbjct: 81  FFILRALGELVMHRPSSGSFVSYTREFMGERASFVAGWMYFVVWALTGVVDITAIAIYMK 140

Query: 135 YWGAFGDVPQWVFALGALTIVGTMNMIGVKWFAEMEFWFALIKVLAIVIFLVVGTIFLGT 194
           YW  F DVPQWVFAL AL +V  MNM+GVKWF EMEFWFA+IKV AI IFLV+G+ F  T
Sbjct: 141 YWSVFSDVPQWVFALSALGVVTLMNMVGVKWFGEMEFWFAVIKVAAISIFLVIGSFFFAT 200

Query: 195 GQPLEGNATGFHLITDNGGFFPHGLLPALVLIQGVVFAFASIELVGTAAGECKDPQKMVP 254
           G  + G+  G HLITDNGG FPHGLLPA++++QGV+FA+ASIELVGTAAGE  D +K++P
Sbjct: 201 GHEVAGHIPGLHLITDNGGIFPHGLLPAIIIVQGVIFAYASIELVGTAAGETADARKVIP 260

Query: 255 KAINSVIWRIGLFYVGSVVLLVLLLPWNAYQAGQSPFVTFFSKLGVPYIGSIMNIVVLTA 314
           KAIN VIWRI LFYVGSV LLV +LPW AY A  SPFVTFF  LGVP IGS+MNIVV+TA
Sbjct: 261 KAINGVIWRISLFYVGSVFLLVTVLPWTAYSANVSPFVTFFEALGVPGIGSVMNIVVMTA 320

Query: 315 ALSSLNSGLYCTGRILRSMSMGGSAPKFMAKMSRQHVPYAGILATLVVYVVGVFLNYLVP 374
           ALSSLNSGLY TGR+LRS++MGGSAPK   +MS Q VPY GIL T+ + V GV LN+L+P
Sbjct: 321 ALSSLNSGLYATGRVLRSLAMGGSAPKMFKRMSSQGVPYMGILVTMGINVFGVVLNFLIP 380

Query: 375 SRVFEIVLNFASLGIIASWAFIMVCQMRLRQAIKEGKAADVSFKLPGAPFTSWLTLLFLL 434
           +++FE++LN  SLGII++WAFI++ Q+  R+A+K G+   VSF++PGAPFTSWLTL+FLL
Sbjct: 381 AQLFELLLNLVSLGIISTWAFIVLSQINYRRAVKRGEVEMVSFRMPGAPFTSWLTLVFLL 440

Query: 435 SVLVLMAFDYPNGTYTIASLPLIAILLVAGW 465
            VLVL+AFDYPNGTYT+ S+PL+A  L+ GW
Sbjct: 441 VVLVLLAFDYPNGTYTVLSIPLVAGALMLGW 471


Lambda     K      H
   0.328    0.140    0.434 

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: 838
Number of extensions: 47
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: 497
Length of database: 494
Length adjustment: 34
Effective length of query: 463
Effective length of database: 460
Effective search space:   212980
Effective search space used:   212980
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