GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natE in Erythrobacter gangjinensis K7-2

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_047006707.1 AAW01_RS07015 ABC transporter ATP-binding protein

Query= TCDB::Q8YT15
         (247 letters)



>NCBI__GCF_001010925.1:WP_047006707.1
          Length = 317

 Score = 99.4 bits (246), Expect = 8e-26
 Identities = 68/206 (33%), Positives = 113/206 (54%), Gaps = 6/206 (2%)

Query: 28  LQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKITFKGKNIAGLKSNQIVRL 87
           L+GV+F V  G +  ++GPNGAGKSTL   + GL+    G +   G++I     N  + +
Sbjct: 27  LKGVSFDVPQGSVFGLLGPNGAGKSTLINIMAGLVNKTGGTVRIWGRDIDEDHRNAKLNI 86

Query: 88  GMCYVPQIANVFPSLSVEENLE--MGAFIRNDSLQPLKDKIFAMFPRLSDRRRQRAGTLS 145
           G+  VPQ     P  +  E LE   G +    +L+  ++ + A+  RL D+R   A TLS
Sbjct: 87  GI--VPQEIVFDPFFTPYEVLENQSGFYGIAKALRRSEELLRAV--RLEDKRDAYARTLS 142

Query: 146 GGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFEQVKQINQEGTAIILVEQNARK 205
           GG ++ L + KA++  P +LVLDEP+A +   L  Q++E V ++N EG  ++L      +
Sbjct: 143 GGMKRRLLIAKAMVHSPPILVLDEPTAGVDVELRKQLWELVGELNAEGVTVVLTTHYLEE 202

Query: 206 ALEMADRGYVLESGRDAISGPGQELL 231
           A E+ ++  ++  G    + P +EL+
Sbjct: 203 AEELCEQIAIINHGELIANKPTRELV 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: 170
Number of extensions: 9
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: 317
Length adjustment: 26
Effective length of query: 221
Effective length of database: 291
Effective search space:    64311
Effective search space used:    64311
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.

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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