GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natE in Haloterrigena daqingensis JX313

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_076583239.1 BB347_RS13945 ABC transporter ATP-binding protein

Query= TCDB::Q8YT15
         (247 letters)



>NCBI__GCF_001971705.1:WP_076583239.1
          Length = 253

 Score =  101 bits (252), Expect = 1e-26
 Identities = 66/205 (32%), Positives = 105/205 (51%), Gaps = 13/205 (6%)

Query: 2   SGSAQNFTPLLEVENVHAGYI--KDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIF 59
           SGSA      + +ENVH  Y   + V  L GV+  +  G    ++GP+G+GKSTL   + 
Sbjct: 12  SGSA------VSLENVHKTYHLGEPVHALDGVSLEIPRGSYTAIMGPSGSGKSTLMNLVG 65

Query: 60  GLLTPHTGKITFKGKNIAGLKSNQIVRLG---MCYVPQIANVFPSLSVEENLEMGAFIRN 116
            L TP +G +   G+++ GL   +   L    + +V Q  N+ P LS  EN+ M    RN
Sbjct: 66  CLDTPTSGTVVVDGRDVGGLSDAERTTLRGTTVGFVFQTFNLMPRLSALENVAMPQLFRN 125

Query: 117 DSLQPLKDKIFAMFPR--LSDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAAL 174
                 +++   +  R  L+DR       LSGG+RQ +A+ +AL+ EP L++ DEP+  L
Sbjct: 126 VGRAERRERASTLLERVGLADRADHHPNELSGGQRQRVALARALVNEPELVLADEPTGNL 185

Query: 175 SPILVTQVFEQVKQINQEGTAIILV 199
                  V E   + ++ GT +++V
Sbjct: 186 DTETGANVLELFAEFHEAGTTMVVV 210


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: 172
Number of extensions: 6
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: 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 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