GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacK in Echinicola vietnamensis KMM 6221, DSM 17526

Align ABC transporter for Lactose, ATPase component (characterized)
to candidate Echvi_1022 Echvi_1022 ABC-type spermidine/putrescine transport systems, ATPase components

Query= reanno::Smeli:SM_b20002
         (358 letters)



>FitnessBrowser__Cola:Echvi_1022
          Length = 345

 Score =  144 bits (362), Expect = 5e-39
 Identities = 83/244 (34%), Positives = 133/244 (54%), Gaps = 15/244 (6%)

Query: 1   MSELQLSDVRKSYGGLE--VIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSG 58
           MS LQL  + K +   +   +K + ++I+ G     VG +G GK+TLL++IAGLE    G
Sbjct: 1   MSLLQLHGISKKFPQTKQFAVKDIHMEIEEGSVQAIVGENGSGKTTLLKLIAGLEHPDKG 60

Query: 59  DLTIDDVRM----NDVDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRV 114
           ++      +    + +  ++R + ++FQ YAL+P MT+ EN+  AL        +I    
Sbjct: 61  EIVFSGQTIVNGKSALPANQREVGVIFQEYALFPQMTLLENVREALHQESRNARQI---- 116

Query: 115 NEAAHILELGALLDR---KPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVH 171
             A   L L  L D     P QLS GQRQR A+ RA+   PK+ L D+P  +LD   +  
Sbjct: 117 --AMDSLALAGLEDSFSAYPHQLSSGQRQRAALARALASRPKLLLLDDPFRSLDTRFKNE 174

Query: 172 MRIEIARLHKQLATTIVYVTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVA 231
           +  +I  + K    T +  +H   +A++LAD I ++  G+++QVG+P+++Y  PAN +VA
Sbjct: 175 ISEDIRDIVKATGITAIVASHHAKDALSLADSIAILHKGILQQVGTPVEIYKKPANAYVA 234

Query: 232 GFIG 235
            F G
Sbjct: 235 NFFG 238


Lambda     K      H
   0.321    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: 286
Number of extensions: 8
Number of successful extensions: 3
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: 358
Length of database: 345
Length adjustment: 29
Effective length of query: 329
Effective length of database: 316
Effective search space:   103964
Effective search space used:   103964
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: 49 (23.5 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