Align LacK, component of Lactose porter (characterized)
to candidate SM_b21605 SM_b21605 sugar uptake ABC transporter ATP-binding protein
Query= TCDB::Q01937 (363 letters) >FitnessBrowser__Smeli:SM_b21605 Length = 362 Score = 385 bits (988), Expect = e-111 Identities = 203/366 (55%), Positives = 262/366 (71%), Gaps = 7/366 (1%) Query: 1 MAEVRLTDIRKSYGSLEVIKGVNLEVSSGEFVVFVGPSGCGKSTLLRMIAGLEDISSGEL 60 M+ ++LT + KS+G+++VI GV++E+ GEF VFVGPSGCGKSTLLRMIAGLE+ + GE+ Sbjct: 1 MSGIKLTGVSKSFGAVKVIHGVDIEIGQGEFAVFVGPSGCGKSTLLRMIAGLEETTGGEI 60 Query: 61 TIGGTVMNDVDPSKRGIAMVFQTYALYPHMTVRENMGFALRFAGMAKDEIERRVNAAAKI 120 I + +PSKRG+AMVFQ+YALYPH++V +NM F+L A K EIE++V AAA+I Sbjct: 61 RIDAEDVTHKEPSKRGVAMVFQSYALYPHLSVFDNMAFSLSIARRPKAEIEQKVKAAAEI 120 Query: 121 LELDALMDRKPKALSGGQRQRVAIGRAIVRQPDVFLFDEPLSNLDAELRVHMRVEIARLH 180 L L +D KP LSGGQRQRVAIGRAIVR+P VFLFDEPLSNLDAELRV MR+EIARLH Sbjct: 121 LRLSDYLDSKPSQLSGGQRQRVAIGRAIVREPRVFLFDEPLSNLDAELRVKMRMEIARLH 180 Query: 181 KELNATIVYVTHDQVEAMTLADKIVVMRGGIVEQVGAPLALYDDPDNMFVAGFIGSPRMN 240 +++ AT+VYVTHDQVEAMTLAD+IVV++ G+V+Q GAPL LY +PDNMFVAGFIGSP MN Sbjct: 181 RQIGATMVYVTHDQVEAMTLADRIVVLKAGVVQQTGAPLELYRNPDNMFVAGFIGSPGMN 240 Query: 241 FLPAVVIGQAEGGQVTVALKARPDTQLTVACATPPQGGDAVTVGVRPEHF-LPAGSGDTQ 299 FL A V+ G ++T+ L P + T P G+ + VGVRPEH L G Sbjct: 241 FLKARVV-PGSGDRLTIELHDAPGVPFEIPARTGPAVGEEIFVGVRPEHITLGEREGGVG 299 Query: 300 LTAHVDVVEHLGNTSYVYAHTVPGEQIIIE--QEERRHGGRYGDEIAVGISAKTSFLFDA 357 L + +E LG T Y++A TV GE++ IE EER + + + ++ + F F+ Sbjct: 300 LDVTAEFIEELGGTGYLHALTVTGEEMTIECRGEERPQPKQ---AVRLTLAPEEMFAFEG 356 Query: 358 SGRRIR 363 SG R+R Sbjct: 357 SGERLR 362 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: 424 Number of extensions: 16 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: 362 Length adjustment: 29 Effective length of query: 334 Effective length of database: 333 Effective search space: 111222 Effective search space used: 111222 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.
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:
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