GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_21720 in Amantichitinum ursilacus IGB-41

Align ABC transporter for D-glucosamine, permease component 2 (characterized)
to candidate WP_053937456.1 WG78_RS08860 amino acid ABC transporter permease

Query= reanno::pseudo3_N2E3:AO353_21720
         (220 letters)



>NCBI__GCF_001294205.1:WP_053937456.1
          Length = 221

 Score =  129 bits (323), Expect = 6e-35
 Identities = 66/189 (34%), Positives = 118/189 (62%)

Query: 29  SVLAIMLGTLIGIVAGLVLTYGTLWMRAPFRFYVDLIRGTPVFVLVLACFYMAPALGWQI 88
           +V A++ G L+G +  ++   G   ++ P   YV  +RGTP+ V +   +Y  PA+G Q 
Sbjct: 25  AVGAMVGGLLVGALLAVLRLSGIKALQWPAALYVSAMRGTPLLVQIFIIYYGLPAIGIQF 84

Query: 89  DAFQAGVLGLTLFCGSHVAEIVRGALQALPRGQMEASKAIGLTFYQALAYVLLPQALRQI 148
           +   AG+L L+L  G++V+E +RGA+  + RGQ EA+ + G+  +Q L Y++ PQALR  
Sbjct: 85  EPITAGILALSLNTGAYVSETMRGAINGVDRGQWEAAFSQGMGRWQTLHYIVWPQALRLA 144

Query: 149 LPTWVNSSTEIVKASTLLSVIGVAELLLSTQQIIARTFMTLEFYLFAGFLFFIINYAIEL 208
           +P+  NS   ++K ++L+SVI V EL+L+T+++I+ TF     Y+ A  +++ ++   E 
Sbjct: 145 VPSLSNSLISLIKDTSLVSVIAVTELMLATKEVISTTFQPFPLYVAAAAIYWCLSLIFEQ 204

Query: 209 LGRHIEKRV 217
           + R +E+R+
Sbjct: 205 VQRLLERRL 213


Lambda     K      H
   0.330    0.142    0.440 

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: 105
Number of extensions: 3
Number of successful extensions: 1
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: 220
Length of database: 221
Length adjustment: 22
Effective length of query: 198
Effective length of database: 199
Effective search space:    39402
Effective search space used:    39402
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 45 (21.9 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