GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaH in Pseudomonas fluorescens FW300-N1B4

Align Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized)
to candidate Pf1N1B4_1031 Oxidoreductase, short chain dehydrogenase/reductase family

Query= SwissProt::Q9NKW1
         (441 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1031
          Length = 303

 Score =  343 bits (879), Expect = 5e-99
 Identities = 162/292 (55%), Positives = 220/292 (75%), Gaps = 3/292 (1%)

Query: 2   ALNFKDKVVIVTGAGGGIGKVYALEFAKRGAKVVVNDLGGSHTGQGSSSKAADKVVEEIK 61
           ++ F+DKVVIVTGAGGG+G+ +AL FAK+GAKV+VNDLGGS  G+G+++ AAD+VV EI+
Sbjct: 4   SVRFEDKVVIVTGAGGGLGRAHALLFAKQGAKVLVNDLGGSAQGEGANASAADRVVAEIR 63

Query: 62  AAGGTAVANYDSVEDGEKIVQTAMDSFGGVDILINNAGILRDVSFGKMTDGDWDLVYRVH 121
            AGGTA AN+DSV DG+KIVQ A+D+FG VD+++NNAGILRD +F KM D DWDLVYRVH
Sbjct: 64  EAGGTAEANHDSVTDGDKIVQHALDTFGRVDVVVNNAGILRDKTFHKMDDSDWDLVYRVH 123

Query: 122 AKGAYKLSRAAWNHMREKNFGRIIMTSSAAGLYGNFGQANYGSMKMALVGLSNTLAQEGK 181
            +GAYK++RAAW HMRE+N+GR+I T+S +G+YGNFGQ+NYG  K+ L GL+ TLA EG+
Sbjct: 124 VEGAYKVTRAAWPHMREQNYGRVIFTASTSGIYGNFGQSNYGMAKLGLYGLTRTLAIEGR 183

Query: 182 SKNIHCNTIAPIAASRLTESVMPPEILEQMKPDYIVPLVLYLCHQDTTETGGVFEVGAGW 241
             NI  N IAP   +R+TE ++PP + EQ+KP+ + PLV+YL  +   ET G+FEVG GW
Sbjct: 184 KNNILVNAIAPTGGTRMTEGLIPPHVFEQLKPELVSPLVVYLASEHCQETSGLFEVGGGW 243

Query: 242 VSKVRLQRSAGVYMK---DLTPEKIKDNWAQIESFDNPSYPTSASESVSGIL 290
           + KVR +RS G         +PE +  +W QI  F+  ++P    E++  ++
Sbjct: 244 MGKVRWERSLGAGFDPRVGFSPEDVAAHWQQICDFEGAAHPKDNIEALKEMM 295


Lambda     K      H
   0.313    0.131    0.371 

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: 410
Number of extensions: 21
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: 441
Length of database: 303
Length adjustment: 30
Effective length of query: 411
Effective length of database: 273
Effective search space:   112203
Effective search space used:   112203
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 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