GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Dshi_0546 in Sphingomonas koreensis DSMZ 15582

Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate Ga0059261_3874 Ga0059261_3874 ABC-type antimicrobial peptide transport system, ATPase component

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



>FitnessBrowser__Korea:Ga0059261_3874
          Length = 243

 Score =  116 bits (291), Expect = 5e-31
 Identities = 72/221 (32%), Positives = 114/221 (51%), Gaps = 11/221 (4%)

Query: 2   AGIKIDKINKFYGT----TQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSS 57
           A I   +++K Y      TQ LF +++ +  GE  + VGPSGCGKSTLL  L+GL     
Sbjct: 7   AAIDAREVSKSYTVGQVRTQILFGVSVSVMPGELTLVVGPSGCGKSTLLAILSGLTLPDQ 66

Query: 58  GRIEIGGRDVTTVEPADRDL------AMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRK 111
           G ++  G  +  ++   RD         VFQ + L+  +T  E + + ++    +P   +
Sbjct: 67  GEVDALGNPICRMKAGARDAFRLANTGFVFQGFNLFNALTAEEQVAYVLQCMKVKPAEAR 126

Query: 112 ERIAEAARVLQLEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQ 171
           +R   A   + L   +  +P +LSGG++QRVAI RA+ K P +   DEP S LD+     
Sbjct: 127 QRARAALEAVGLGPRMRLRPFELSGGEKQRVAIARALAKQPRILFADEPTSALDSHNGHA 186

Query: 172 MRVELEGLHKQLGATMIYVTHDQVEAMTMADKIVVLNRGRI 212
           +   L  +    GA ++ VTHD    ++ AD+I+ +  GRI
Sbjct: 187 VIALLRDIAHNQGAAVLCVTHDP-RLLSFADRIIHMEDGRI 226


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: 178
Number of extensions: 9
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: 243
Length adjustment: 26
Effective length of query: 312
Effective length of database: 217
Effective search space:    67704
Effective search space used:    67704
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: 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