GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutV in Acidovorax caeni R-24608

Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate WP_054256055.1 BN2503_RS07360 methionine ABC transporter ATP-binding protein

Query= reanno::pseudo5_N2C3_1:AO356_09610
         (276 letters)



>NCBI__GCF_001298675.1:WP_054256055.1
          Length = 348

 Score =  163 bits (412), Expect = 6e-45
 Identities = 91/218 (41%), Positives = 134/218 (61%), Gaps = 1/218 (0%)

Query: 43  GCVVGVNDLSLSIGTGEIFVIMGLSGSGKSTLVRHFNRLIDPTSGAILVDGEDILQLDMD 102
           G V  +  + LSI  GE+F I+G SG+GKS+LVR  N L  PT GA++V G D+ QL+ +
Sbjct: 16  GPVEALRGIDLSIAPGEVFGIIGRSGAGKSSLVRVINLLNRPTRGAVVVAGRDLTQLNGE 75

Query: 103 ALREFRRHKISMVFQSFGLLPHKSVLDNVAYGLKVRGESKQVCAERALHWINTVGLKGYE 162
            LR  RR  I MVFQ F LL  ++V DNVA  L++ G +     ER    +  VGL    
Sbjct: 76  QLRAARRD-IGMVFQHFNLLSSRTVYDNVALPLELAGMAPAAMRERVGPLLELVGLSHLA 134

Query: 163 NKYPHQLSGGMRQRVGLARALAADTDIILMDEAFSALDPLIRAEMQDQLLELQKTLHKTI 222
           ++YP Q+SGG +QRVG+ARALA+   ++L DEA SALDP     + D L ++ + L  T+
Sbjct: 135 DRYPAQISGGQKQRVGIARALASRPKVLLSDEATSALDPETTRSILDLLRQVNRELGLTV 194

Query: 223 VFITHDLDEAVRIGNRIAILKDGKLIQVGTPREILHSP 260
           V ITH +    +I +R+A++  G+++++G   ++   P
Sbjct: 195 VLITHQMQVIKQIADRVAVIDAGQIVEMGPVLDVFTRP 232


Lambda     K      H
   0.321    0.138    0.387 

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: 237
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: 276
Length of database: 348
Length adjustment: 27
Effective length of query: 249
Effective length of database: 321
Effective search space:    79929
Effective search space used:    79929
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 (21.9 bits)
S2: 48 (23.1 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