GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natE in Phaeobacter inhibens BS107

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 GFF1630 PGA1_c16520 putative branched-chain amino acid transporter, ATP-binding protein

Query= TCDB::Q8YT15
         (247 letters)



>FitnessBrowser__Phaeo:GFF1630
          Length = 229

 Score =  145 bits (365), Expect = 9e-40
 Identities = 88/233 (37%), Positives = 139/233 (59%), Gaps = 8/233 (3%)

Query: 11  LLEVENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKIT 70
           LL ++NV A Y      L GV   +  GE+V ++G NG GKST  KTI G+L    G + 
Sbjct: 3   LLSLKNVTASYGPS-QALFGVELDIGEGEVVALMGRNGMGKSTTIKTICGMLPASEGTLH 61

Query: 71  FKGKNIAGLKSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRNDSLQPLKDKIFAMF 130
           F G ++  L S++I RLG+  VP+    F  L+VEENL   A         + D    +F
Sbjct: 62  FAGNDLRKLHSHKIARLGIGLVPEGRRCFAPLTVEENLRAAARPGPWDFAMVAD----LF 117

Query: 131 PRLSDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFEQVKQIN 190
           PRL++RR Q A +LSGGE+QMLA+G+ALM+ P LL+LDE +  L+P++  +++  + ++ 
Sbjct: 118 PRLAERRDQTASSLSGGEQQMLAIGRALMINPRLLILDEATEGLAPVVRQEIWAAIARLK 177

Query: 191 QE-GTAIILVEQNARKALEMADRGYVLESGRDAISGPGQELLTDPKVAELYLG 242
           ++ G +I++V++  R+   +ADR  ++  G    +G   + LT P++ + YLG
Sbjct: 178 RDSGLSILVVDKTLRELAAVADRAVIVNKGATVWTG-AMDALT-PELKDRYLG 228


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: 141
Number of extensions: 8
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: 229
Length adjustment: 23
Effective length of query: 224
Effective length of database: 206
Effective search space:    46144
Effective search space used:    46144
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