GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacK in Klebsiella michiganensis M5al

Align LacK, component of Lactose porter (characterized)
to candidate BWI76_RS01840 BWI76_RS01840 ABC transporter ATP-binding protein

Query= TCDB::Q01937
         (363 letters)



>FitnessBrowser__Koxy:BWI76_RS01840
          Length = 369

 Score =  363 bits (933), Expect = e-105
 Identities = 198/363 (54%), Positives = 247/363 (68%), Gaps = 2/363 (0%)

Query: 1   MAEVRLTDIRKSYGSLEVIKGVNLEVSSGEFVVFVGPSGCGKSTLLRMIAGLEDISSGEL 60
           MA V+L ++ K++G + V K +NLE+  GEFVVFVGPSGCGKSTLLRMIAGLE ++SG+L
Sbjct: 1   MASVQLRNVTKAWGDVVVSKDINLEIQDGEFVVFVGPSGCGKSTLLRMIAGLETVTSGDL 60

Query: 61  TIGGTVMNDVDPSKRGIAMVFQTYALYPHMTVRENMGFALRFAGMAKDEIERRVNAAAKI 120
            IG T MNDV P++RGI MVFQ+YALYPH++V ENM F L+ AG  K+ I +RV   A++
Sbjct: 61  LIGDTRMNDVPPAERGIGMVFQSYALYPHLSVAENMSFGLKLAGAKKELINQRVTQVAEV 120

Query: 121 LELDALMDRKPKALSGGQRQRVAIGRAIVRQPDVFLFDEPLSNLDAELRVHMRVEIARLH 180
           L+L  L++RKPKALSGGQRQRVAIGR +V +P VFL DEPLSNLDA LRV MR+EI+RLH
Sbjct: 121 LQLAHLLERKPKALSGGQRQRVAIGRTLVAEPRVFLLDEPLSNLDAALRVQMRIEISRLH 180

Query: 181 KELNATIVYVTHDQVEAMTLADKIVVMRGGIVEQVGAPLALYDDPDNMFVAGFIGSPRMN 240
           K L  T++YVTHDQVEAMTLADKIVV+  G V QVG PL LY  P + FVAGFIGSP+MN
Sbjct: 181 KRLGRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFIGSPKMN 240

Query: 241 FLPAVVIGQAEGGQVTVALKARPDTQLTVACATPPQGGDAVTVGVRPEHFLPAGSGDTQL 300
           FLP  V   A   QV V L  R    L V  A   Q G  +++G+RPEH LP+   D  L
Sbjct: 241 FLPVKVTATAI-EQVQVELPNRQQVWLPVDSAR-VQVGANMSLGIRPEHLLPSDIADVTL 298

Query: 301 TAHVDVVEHLGNTSYVYAHTVPGEQIIIEQEERRHGGRYGDEIAVGISAKTSFLFDASGR 360
              V VVE LG+ + ++       Q ++ ++        G   A+G+  +   LF   G 
Sbjct: 299 EGEVQVVEQLGHETQIHIQIPSIRQNLVYRQNDVVLVEEGATFAIGLPPERCHLFREDGT 358

Query: 361 RIR 363
             R
Sbjct: 359 ACR 361


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: 363
Number of extensions: 10
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: 363
Length of database: 369
Length adjustment: 30
Effective length of query: 333
Effective length of database: 339
Effective search space:   112887
Effective search space used:   112887
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