GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2561 in Magnetospirillum magneticum AMB-1

Align ABC transporter for L-Histidine, permease component 2 (characterized)
to candidate WP_011384260.1 AMB_RS09380 ABC transporter permease

Query= reanno::acidovorax_3H11:Ac3H11_2561
         (252 letters)



>NCBI__GCF_000009985.1:WP_011384260.1
          Length = 256

 Score =  140 bits (354), Expect = 2e-38
 Identities = 87/244 (35%), Positives = 130/244 (53%), Gaps = 7/244 (2%)

Query: 5   ARWMLGLAFFVVFVAVWAFFTLGGFVSPTFLASPITMAKEGWLLFTEYGFIKDIGMTIWR 64
           AR+   L+   + VA WA     G  +P  L SP  +A     +     F +D+G ++ R
Sbjct: 10  ARFSSALSGLGLLVAFWAL-AAAGLDNPVLLPSPAEVAGVLGEVIGSGAFHRDLGASLRR 68

Query: 65  VVGGFVLAAVIAVPLGIAMGAYKGIEAFFEPFISFCRYLPASAFIPLLILWAGIGEAQKI 124
           V+GG+VLA+ +AVPL + M A+  +     P +S  R +P  A+IPL ILW G+G+A   
Sbjct: 69  VLGGYVLASGLAVPLALVMAAWGPLRQSLLPVVSLLRPIPPIAWIPLAILWFGLGDAPSF 128

Query: 125 LVIFIGSVFQITLMV---AVTVGGARRDLVEAAYTLGAGHKGIVTRVLIPGAAPEIAETL 181
            +  I + F I L      + VGG   D   AA  LGA    ++  V +P A P IA  L
Sbjct: 129 FITAIAAFFPIFLNAFAGGLAVGGRYLD---AARCLGATRLALLLEVRLPAALPMIATGL 185

Query: 182 RLVLGWAWTYVIVAELIGSSSGIGHMITDSQSLLNTGQIIFGIIIIGLIGLVSDFAFKAL 241
           R+ LG +W  V+ AELI + SG+G+MI  ++  L T  ++ G++ IG +G +  +AF   
Sbjct: 186 RIGLGQSWMAVVTAELIAAQSGLGYMIQANRLTLQTAHVLVGMVTIGTLGALMTWAFTLA 245

Query: 242 NHRL 245
             RL
Sbjct: 246 ERRL 249


Lambda     K      H
   0.331    0.145    0.456 

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: 214
Number of extensions: 12
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: 252
Length of database: 256
Length adjustment: 24
Effective length of query: 228
Effective length of database: 232
Effective search space:    52896
Effective search space used:    52896
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 17 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