Align LacK, component of Lactose porter (characterized)
to candidate Ac3H11_2941 Various polyols ABC transporter, ATP-binding component
Query= TCDB::Q01937 (363 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2941 Length = 350 Score = 343 bits (880), Expect = 4e-99 Identities = 186/360 (51%), Positives = 233/360 (64%), Gaps = 17/360 (4%) Query: 1 MAEVRLTDIRKSYGSLEVIKGVNLEVSSGEFVVFVGPSGCGKSTLLRMIAGLEDISSGEL 60 MA ++L I K +G IKG++L + GEF+VFVGPSGCGKSTLLR+IAGLE I G L Sbjct: 1 MAYLQLRGIEKFFGEHRAIKGIDLTIQQGEFIVFVGPSGCGKSTLLRLIAGLEAIDGGSL 60 Query: 61 TIGGTVMNDVDPSKRGIAMVFQTYALYPHMTVRENMGFALRFAGMAKDEIERRVNAAAKI 120 + G + D SKR +AMVFQ+YALYPHM+V ENM FAL+ A + K I+ +V AA+I Sbjct: 61 MLDGRDITDQPSSKRDLAMVFQSYALYPHMSVYENMSFALKLAKVDKQVIDEKVQNAARI 120 Query: 121 LELDALMDRKPKALSGGQRQRVAIGRAIVRQPDVFLFDEPLSNLDAELRVHMRVEIARLH 180 L L + R PK LSGGQRQRVAIGRAIVR P VFLFDEPLSNLDA LR RVEIA+LH Sbjct: 121 LNLTQYLQRTPKELSGGQRQRVAIGRAIVRAPKVFLFDEPLSNLDAALRGQTRVEIAKLH 180 Query: 181 KELNATIVYVTHDQVEAMTLADKIVVMRGGIVEQVGAPLALYDDPDNMFVAGFIGSPRMN 240 ++L AT +YVTHDQVEAMTLAD++VV+R GI+EQVG PL LYD P N FVA FIG+P+MN Sbjct: 181 RDLGATTIYVTHDQVEAMTLADRVVVLRDGIIEQVGTPLELYDKPANQFVAQFIGTPQMN 240 Query: 241 FLPAVVIGQAEGGQVTVALKARPDTQLTVACATPPQGGDAVTVGVRPEHFLPAGSGDTQL 300 +P + Q Q A P G +G+RPE+ +G T + Sbjct: 241 VVPVDKLPQPVQQQAPAA----------------PAGAAVGAIGLRPENITVRTTGATPV 284 Query: 301 TAHVDVVEHLGNTSYVYAHTVPGEQIIIEQEERRHGGRYGDEIAVGISAKTSFLFDASGR 360 VD++E LG + +Y T G Q + Q +R R GD +++ I A + FD +GR Sbjct: 285 GGQVDLIEALGAETLIYVTTPGGAQFVSRQNDRT-DLRVGDAVSLDIDASQAHWFDTAGR 343 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: 358 Number of extensions: 12 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: 350 Length adjustment: 29 Effective length of query: 334 Effective length of database: 321 Effective search space: 107214 Effective search space used: 107214 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