GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS17020 in Sphingomonas koreensis DSMZ 15582

Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate Ga0059261_2293 Ga0059261_2293 cell division ATP-binding protein FtsE

Query= uniprot:D8IPI1
         (406 letters)



>FitnessBrowser__Korea:Ga0059261_2293
          Length = 235

 Score =  123 bits (309), Expect = 5e-33
 Identities = 78/220 (35%), Positives = 117/220 (53%), Gaps = 10/220 (4%)

Query: 13  YAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGTLRIGGTVVNDLP 72
           Y  G   L  +   +  G F  + G SG GK+++LR++   +  + G +R+ G     LP
Sbjct: 14  YGTGAETLSDVSFTLSAGSFYFVTGASGAGKTSLLRLLYLAQRPTRGIVRLFGEDAGALP 73

Query: 73  ARE-----RNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAALLNLEAL 127
            +      R + +VFQ++ L PH+S YDN+A  LR    P A+I+  VRE+ A + L+  
Sbjct: 74  RKRLPGFRRRIGVVFQDFRLLPHLSAYDNVALPLRVAGIPEADIEGPVREMIAWVGLKDR 133

Query: 128 LERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRLHQRLRTT 187
              KP  +SGG+QQR AIARA+I  P + + DEP  N+D  +  +L      L+ RL TT
Sbjct: 134 DSAKPPTLSGGEQQRIAIARAVITRPEILIADEPTGNVDPDMAERLLHLFDSLN-RLGTT 192

Query: 188 TVYVTHD-QLEAMTLADRVILMQDGRIVQAGSPAELYRYP 226
            V  THD QL +     R++ ++ GR+     P    RYP
Sbjct: 193 VVVATHDFQLISRIPDARMMRIEKGRL---NDPTGALRYP 229


Lambda     K      H
   0.321    0.137    0.403 

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: 213
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: 406
Length of database: 235
Length adjustment: 27
Effective length of query: 379
Effective length of database: 208
Effective search space:    78832
Effective search space used:    78832
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