GapMind for catabolism of small carbon sources

 

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

Align NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate Pf6N2E2_1429 Branched-chain amino acid transport ATP-binding protein LivF (TC 3.A.1.4.1)

Query= TCDB::Q8YT15
         (247 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1429
          Length = 253

 Score =  160 bits (404), Expect = 3e-44
 Identities = 89/243 (36%), Positives = 143/243 (58%), Gaps = 9/243 (3%)

Query: 10  PLLEVENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTG-- 67
           P+L+++++   Y + +  ++ V+  V  G++V ++G NGAGKST  K    L+    G  
Sbjct: 6   PILQIDDIEVLYEQTILAVRSVSLEVGKGQVVVLLGANGAGKSTTLKAASNLVRAERGEV 65

Query: 68  ---KITFKGKNIAGLKSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRNDSLQPLK- 123
              +I ++G+++     + +   G+  V +  + F  L+VEENL  GA  R    + L  
Sbjct: 66  VRGRIVYQGRDVTRSAPHTLAASGLVQVLEGRHCFAQLTVEENLLAGALARQVPRRQLLA 125

Query: 124 --DKIFAMFPRLSDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQ 181
             + ++  FPRL  RR+  AG  SGGE+QM+A+G+ALM +P L++LDEPS  L+P +V +
Sbjct: 126 DLESVYGHFPRLKLRRKSLAGYTSGGEQQMIAIGRALMAKPQLVLLDEPSMGLAPQIVEE 185

Query: 182 VFEQVKQINQ-EGTAIILVEQNARKALEMADRGYVLESGRDAISGPGQELLTDPKVAELY 240
           +FE V+Q+NQ +G + ++ EQN   AL  A  GYVLESGR    G  ++L     + + Y
Sbjct: 186 IFEIVRQLNQRDGVSFLIAEQNINIALRYAHHGYVLESGRVVSEGSAEQLAARGDLQDFY 245

Query: 241 LGA 243
           LGA
Sbjct: 246 LGA 248


Lambda     K      H
   0.317    0.136    0.377 

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: 180
Number of extensions: 8
Number of successful extensions: 4
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: 247
Length of database: 253
Length adjustment: 24
Effective length of query: 223
Effective length of database: 229
Effective search space:    51067
Effective search space used:    51067
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: 46 (22.3 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