GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natE in Pseudomonas simiae WCS417

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 GFF3454 PS417_17680 ABC transporter

Query= TCDB::Q8YT15
         (247 letters)



>FitnessBrowser__WCS417:GFF3454
          Length = 231

 Score =  184 bits (468), Expect = 1e-51
 Identities = 96/231 (41%), Positives = 147/231 (63%), Gaps = 4/231 (1%)

Query: 11  LLEVENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKIT 70
           +L VEN+H+ Y K   +L+GV+  V  GELVT++G NGAGK+T  ++I G++ P  G+I 
Sbjct: 1   MLIVENIHSYYDKS-HVLEGVSLTVNPGELVTLLGRNGAGKTTTLRSILGIICPRKGQIH 59

Query: 71  FKGKNIAGLKSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRNDSLQPLKDKIFAMF 130
           F G+ + G K  +I R G+  VP+   +F  L+VEENL +    R  S   L+D ++ MF
Sbjct: 60  FNGQALVGQKIFEIARQGLALVPENRGIFRLLTVEENLRIAT--RKTSRWQLED-VYGMF 116

Query: 131 PRLSDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFEQVKQIN 190
           PRL +RR+     LSGGE+QMLA+ +AL+ +P LL+LDEP+  L+P++V ++ + ++++ 
Sbjct: 117 PRLKERRKNAGHALSGGEQQMLAIARALLNDPKLLILDEPTEGLAPVIVDELVKILRKVK 176

Query: 191 QEGTAIILVEQNARKALEMADRGYVLESGRDAISGPGQELLTDPKVAELYL 241
            +G  ++LVEQN     ++ADR YVLE GR    G  +    DP +   YL
Sbjct: 177 DDGLPVLLVEQNLMVCDKLADRHYVLEQGRVVYEGSAEAFRADPTIKNRYL 227


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: 150
Number of extensions: 5
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: 247
Length of database: 231
Length adjustment: 23
Effective length of query: 224
Effective length of database: 208
Effective search space:    46592
Effective search space used:    46592
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