GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natE in Hyphomicrobium sulfonivorans WDL6

Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_068463382.1 APY04_RS13115 urea ABC transporter ATP-binding subunit UrtE

Query= TCDB::P73650
         (240 letters)



>NCBI__GCF_001541235.1:WP_068463382.1
          Length = 232

 Score =  128 bits (321), Expect = 1e-34
 Identities = 71/211 (33%), Positives = 116/211 (54%), Gaps = 1/211 (0%)

Query: 4   LLVVKDVFAGYVADVPILQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTPSQGEII 63
           +L+  D  + Y     IL+ ++F +  G+ + V+G NG GK+T+ +TI GL   + G I 
Sbjct: 1   MLLSFDKVSSYYGATQILRNVSFDLEQGQCLCVLGRNGVGKTTIMRTIMGLTDRTTGSIT 60

Query: 64  FKGENITGLGSDQIVRRGMCYVPQVCNVFGSLTVAENLDMGAFLHQGPTQTLKDRIYTMF 123
              E I      Q    G+ YVPQ   +    TV EN+ +G F  +     + +    +F
Sbjct: 61  MGDEAIANKPPYQRAGYGIGYVPQGRGILADFTVRENILLGTFARKDSAPEIPELCLRIF 120

Query: 124 PKLAQRRNQRAGTLSGGERQMLAMGRALMLDPDLLLLDEPSAALSPILVKDVFAQIKAIN 183
           P L +  ++RAG LSGG++Q LA+ RAL + P +LLLDEP+  + P +V ++   ++ +N
Sbjct: 121 PYLRENLDRRAGLLSGGQKQQLAIARALAVGPQVLLLDEPTEGIQPNIVHEIGEILRMLN 180

Query: 184 -ATGKAIILVEQNAKQALMMADRGYVLENGR 213
              G ++IL EQ+ K A  + D   +++NGR
Sbjct: 181 KELGISLILTEQHIKVARKLGDAFLMVDNGR 211


Lambda     K      H
   0.320    0.139    0.393 

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: 123
Number of extensions: 5
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: 240
Length of database: 232
Length adjustment: 23
Effective length of query: 217
Effective length of database: 209
Effective search space:    45353
Effective search space used:    45353
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Apr 09 2024. 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