GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natF in Pseudomonas putida KT2440

Align Extracellular solute-binding protein, family 3 (characterized, see rationale)
to candidate PP_1297 PP_1297 putative amino-acid ABC transporter-binding protein YhdW

Query= uniprot:Q31RP1
         (359 letters)



>FitnessBrowser__Putida:PP_1297
          Length = 342

 Score =  311 bits (798), Expect = 1e-89
 Identities = 152/334 (45%), Positives = 222/334 (66%), Gaps = 4/334 (1%)

Query: 28  LAACRSLGGNET-ESNSRLNQVQARGKLLCGVEGRLPGFSFLDSQGNYSGLDVDICKAIA 86
           L A  +LG   T ++ + L+ V+ +G + CGV   LPGFS  D+QG   G+D D+C+A+A
Sbjct: 11  LTAAAALGAVSTAQAGATLDAVKKKGFVQCGVSDGLPGFSVPDAQGKIVGIDADVCRAVA 70

Query: 87  AALFNDPKAIEYRSLDSVERFPALASGEVDLLSRNTTWTLSRDAKGGNNLEFAPTTFYDG 146
           AA+F D   +++  L++ ERF AL SGEVD+LSRNTTWT SRDA  G  L FA  T+YDG
Sbjct: 71  AAVFGDATKVKFSQLNAKERFTALQSGEVDVLSRNTTWTSSRDA--GMGLVFAGVTYYDG 128

Query: 147 QGLMVRRNSGIQSLQDFQGKSICVETGTTSELNLADTMRELGVQYQEIKFPNSDANYAAY 206
            G +V +  G+ S ++  G +IC++ GTT+ELN++D  R  G++Y  I F  SD +  + 
Sbjct: 129 VGFLVNKKLGVSSAKELDGATICIQAGTTTELNVSDFFRANGLKYTPITFDTSDESAKSL 188

Query: 207 AQGRCEGVTSDRSQLAARRTTLSDADQHQLLDAVISKEPLSPATLNNDSPWFDVVKWVVN 266
             GRC+ +TSD+SQL A+R+ L+   ++ +L   ISKEPL P     D  WF +VKW + 
Sbjct: 189 ESGRCDVLTSDKSQLFAQRSKLAAPTEYVVLPETISKEPLGPVVRKGDEEWFSIVKWTLF 248

Query: 267 ATIQAEEFGITQANID-QFKTSKNPEIRRFLGLEGELGQQLGLSNDFAYRAIKAVGNYGE 325
           A + AEE GIT  N++ + K +KNP++ R LG +GE G+ L L  D+  + +K VGNYGE
Sbjct: 249 AMLNAEEAGITSKNVEAEAKATKNPDVARLLGADGEYGKDLKLPKDWVVQIVKQVGNYGE 308

Query: 326 IYERNVGQQSPLKLNRGLNQLYKNGGLLYSPPFR 359
           ++E+N+GQ + LK++RG+N L+ NGG+ Y+PP R
Sbjct: 309 VFEKNLGQSTDLKIDRGMNALWNNGGIQYAPPVR 342


Lambda     K      H
   0.317    0.134    0.391 

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: 293
Number of extensions: 8
Number of successful extensions: 3
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: 359
Length of database: 342
Length adjustment: 29
Effective length of query: 330
Effective length of database: 313
Effective search space:   103290
Effective search space used:   103290
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 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