GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Dshi_0546 in Magnetospirillum magneticum AMB-1

Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate WP_011384263.1 AMB_RS09395 ABC transporter ATP-binding protein

Query= reanno::Dino:3607124
         (338 letters)



>NCBI__GCF_000009985.1:WP_011384263.1
          Length = 273

 Score =  150 bits (379), Expect = 4e-41
 Identities = 85/205 (41%), Positives = 123/205 (60%), Gaps = 3/205 (1%)

Query: 4   IKIDKINKFYGTTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRIEIG 63
           I I +++  +G   A+ D +L+IE GEFV  +GPSGCGKST L  +AG    + GR+ + 
Sbjct: 17  IGIQRLSVSFGAHAAVEDFSLEIEPGEFVCLLGPSGCGKSTALNAVAGFLRPARGRVAVD 76

Query: 64  GRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAARVLQL 123
           G +VT   P   +  MVFQ ++L+P  TV EN+ FG ++ G      ++   E   ++ L
Sbjct: 77  GVEVTGPGP---ERGMVFQQHSLFPWKTVLENVAFGPRMQGKTRAEARDLAREYLDLVGL 133

Query: 124 EDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGLHKQL 183
                R P  LSGG  QRV I RA+V +PSV L DEP   LDA+ R  M+  L  L  Q+
Sbjct: 134 GGSAQRYPAALSGGMAQRVGIARALVNHPSVLLMDEPFGALDAQTRSIMQESLLRLWGQI 193

Query: 184 GATMIYVTHDQVEAMTMADKIVVLN 208
           G T+++VTHD  EA+ +AD++VV++
Sbjct: 194 GNTVLFVTHDIDEALFLADRVVVMS 218


Lambda     K      H
   0.320    0.139    0.396 

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: 234
Number of extensions: 13
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: 338
Length of database: 273
Length adjustment: 27
Effective length of query: 311
Effective length of database: 246
Effective search space:    76506
Effective search space used:    76506
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: 48 (23.1 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