GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcV in Sphingomonas koreensis DSMZ 15582

Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate Ga0059261_3874 Ga0059261_3874 ABC-type antimicrobial peptide transport system, ATPase component

Query= BRENDA::Q97UY8
         (353 letters)



>FitnessBrowser__Korea:Ga0059261_3874
          Length = 243

 Score =  121 bits (303), Expect = 2e-32
 Identities = 78/229 (34%), Positives = 127/229 (55%), Gaps = 10/229 (4%)

Query: 4   IIVKNVSKVFKKGKVVA--LDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGE 61
           I  + VSK +  G+V    L  V++++  GE   ++GPSG GK+T + I++GL +P  GE
Sbjct: 9   IDAREVSKSYTVGQVRTQILFGVSVSVMPGELTLVVGPSGCGKSTLLAILSGLTLPDQGE 68

Query: 62  LYFDDRLVASNGKLIVPPEDR----KIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEI 117
           +   D L     ++     D       G VFQ + L+  LTA E +A+ L  MK+   E 
Sbjct: 69  V---DALGNPICRMKAGARDAFRLANTGFVFQGFNLFNALTAEEQVAYVLQCMKVKPAEA 125

Query: 118 RKRVEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRD 177
           R+R     + + +   +   P ELSGG++QRVA+ARAL K P +L  DEP S LD+    
Sbjct: 126 RQRARAALEAVGLGPRMRLRPFELSGGEKQRVAIARALAKQPRILFADEPTSALDSHNGH 185

Query: 178 SARALVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPE 226
           +  AL++++    G  +L V+HDP  + + ADR+  +  G++++  +P+
Sbjct: 186 AVIALLRDIAHNQGAAVLCVTHDPR-LLSFADRIIHMEDGRIIRDERPD 233


Lambda     K      H
   0.319    0.139    0.390 

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: 181
Number of extensions: 7
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: 353
Length of database: 243
Length adjustment: 26
Effective length of query: 327
Effective length of database: 217
Effective search space:    70959
Effective search space used:    70959
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 (21.7 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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