GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacK in Shewanella sp. ANA-3

Align LacK, component of Lactose porter (characterized)
to candidate 7023042 Shewana3_0280 ABC transporter related (RefSeq)

Query= TCDB::Q01937
         (363 letters)



>FitnessBrowser__ANA3:7023042
          Length = 367

 Score =  144 bits (363), Expect = 4e-39
 Identities = 87/214 (40%), Positives = 123/214 (57%), Gaps = 8/214 (3%)

Query: 28  SGEFVVFVGPSGCGKSTLLRMIAGLEDISSGELTIGGTVMND------VDPSKRGIAMVF 81
           +GE +  VGPSG GK+TLLRMIAGL    +G +  G T+  D      + P +R I  + 
Sbjct: 28  AGEVLAVVGPSGGGKTTLLRMIAGLNHPDAGSIVFGETLWFDHQSRTALTPQQRHIGYMP 87

Query: 82  QTYALYPHMTVRENMGFALRFAGMAKDEIERRVNAAAKILELDALMDRKPKALSGGQRQR 141
           Q + L+P++T  EN+   L    + K E   R     + + L  L DR P  LSGGQRQR
Sbjct: 88  QHFGLFPNLTALENVVAGLDH--IPKSERIARAKDWLERVNLHGLPDRLPMHLSGGQRQR 145

Query: 142 VAIGRAIVRQPDVFLFDEPLSNLDAELRVHMRVEIARLHKELNATIVYVTHDQVEAMTLA 201
           VA+ RA+ R+P V L DEP S +D E R  + +E+ARL ++L   ++ VTHD  EA+ LA
Sbjct: 146 VALARALAREPSVLLLDEPFSAVDRETRERLYLELARLKEQLLCPVIMVTHDLNEALLLA 205

Query: 202 DKIVVMRGGIVEQVGAPLALYDDPDNMFVAGFIG 235
           D ++++  G + Q GAP  +   P N  VA  +G
Sbjct: 206 DSMILISQGQMLQQGAPFEVLSRPRNEAVARQMG 239


Lambda     K      H
   0.320    0.137    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: 236
Number of extensions: 14
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: 363
Length of database: 367
Length adjustment: 30
Effective length of query: 333
Effective length of database: 337
Effective search space:   112221
Effective search space used:   112221
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.

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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