GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natE in Magnetovibrio blakemorei MV-1

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 WP_069956504.1 BEN30_RS01130 urea ABC transporter ATP-binding subunit UrtE

Query= TCDB::Q8YT15
         (247 letters)



>NCBI__GCF_001746755.1:WP_069956504.1
          Length = 231

 Score =  136 bits (342), Expect = 4e-37
 Identities = 74/220 (33%), Positives = 127/220 (57%), Gaps = 8/220 (3%)

Query: 22  IKDVDI-------LQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKITFKGK 74
           ++D+D+       L+GV+    +G++  V+G NG GK++L + I G      GK+ ++  
Sbjct: 4   VQDIDLHYGASQALRGVDLSAATGQVTCVMGRNGVGKTSLMRAIVGQQGTSAGKVMWEDD 63

Query: 75  NIAGLKSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRNDSLQPLKDKIFAMFPRLS 134
           +I  L  ++  R G+ +VPQ   +FP +SVEENL  G      SL+ ++D+IF +FP L 
Sbjct: 64  DITKLSPHERARRGIAFVPQGREIFPLMSVEENLRTGFAAVPRSLRHVQDEIFDLFPVLK 123

Query: 135 DRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFEQVKQINQEG- 193
           D   +R G LSGG++Q LA+ +AL+  P LLVLDEP+  + P ++  +   ++ +   G 
Sbjct: 124 DMLHRRGGDLSGGQQQQLAIARALVTRPRLLVLDEPTEGIQPSIIKDIERVIRLLASRGD 183

Query: 194 TAIILVEQNARKALEMADRGYVLESGRDAISGPGQELLTD 233
             ++LVEQ    A ++AD   V++ G   ++G   E++ +
Sbjct: 184 MGVLLVEQYFEFARDLADTFCVMDRGEVVLAGTKAEMVEE 223


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: 149
Number of extensions: 10
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 24 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