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_084005217.1 BEN30_RS07660 ABC transporter ATP-binding protein

Query= TCDB::Q8YT15
         (247 letters)



>NCBI__GCF_001746755.1:WP_084005217.1
          Length = 262

 Score =  146 bits (368), Expect = 5e-40
 Identities = 84/226 (37%), Positives = 136/226 (60%), Gaps = 10/226 (4%)

Query: 21  YIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHT--GKITFKGKNIAG 78
           Y  +  I+QGVNF +  GE+V ++G NGAGK++  +TI  +  P    G+I    + +  
Sbjct: 40  YYGESYIVQGVNFDIHEGEIVALLGRNGAGKTSTLRTIARMDDPQLRHGEIWLDHQPLHT 99

Query: 79  LKSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRNDSLQPLK---DKIFAMFPRLSD 135
           ++S Q  RLG+  VP+  ++ P L+VEENL +          P+    ++I+  FPRL++
Sbjct: 100 MQSWQAARLGVGLVPEDRSIIPGLTVEENLTLSQIA-----PPIGWSIERIYEHFPRLAE 154

Query: 136 RRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFEQVKQINQEGTA 195
           RR Q   TLSGGE+QMLA+ +AL  +  LL+LDEP   L+P++V ++   ++ + + G  
Sbjct: 155 RRMQEGVTLSGGEQQMLAVARALARDIKLLLLDEPYEGLAPVIVHEIESILEGVKKLGIT 214

Query: 196 IILVEQNARKALEMADRGYVLESGRDAISGPGQELLTDPKVAELYL 241
            I+VEQNA  AL ++DR  +L+ G    +G  QE+L + ++ + YL
Sbjct: 215 TIIVEQNAIAALHLSDRAIILDMGEVVFNGSAQEVLDNKELRDEYL 260


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: 155
Number of extensions: 7
Number of successful extensions: 3
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: 262
Length adjustment: 24
Effective length of query: 223
Effective length of database: 238
Effective search space:    53074
Effective search space used:    53074
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: 47 (22.7 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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