Align LacK, component of Lactose porter (characterized)
to candidate HSERO_RS22750 HSERO_RS22750 sugar ABC transporter ATP-binding protein
Query= TCDB::Q01937 (363 letters) >FitnessBrowser__HerbieS:HSERO_RS22750 Length = 377 Score = 363 bits (932), Expect = e-105 Identities = 200/366 (54%), Positives = 254/366 (69%), Gaps = 8/366 (2%) Query: 1 MAEVRLTDIRKSY-GSLEVIKGVNLEVSSGEFVVFVGPSGCGKSTLLRMIAGLEDISSGE 59 MA V + +RK+Y G +V+ G+NL++ GEF V VGPSGCGKSTLLRM+ GLE+IS GE Sbjct: 1 MAHVNIKQLRKTYDGRADVLAGLNLDIRDGEFCVLVGPSGCGKSTLLRMLCGLEEISGGE 60 Query: 60 LTIGGTVMNDVDPSKRGIAMVFQTYALYPHMTVRENMGFALRFAGMAKDEIERRVNAAAK 119 L IGG V+N + P++RGIAMVFQ+YALYPHM V +NM F L+ AG +K +I+ R+ AA Sbjct: 61 LAIGGQVVNHLPPAERGIAMVFQSYALYPHMNVYKNMAFGLKVAGNSKSDIDARIRHAAA 120 Query: 120 ILELDALMDRKPKALSGGQRQRVAIGRAIVRQPDVFLFDEPLSNLDAELRVHMRVEIARL 179 IL++D L+ R P+ LSGGQRQRVAIGRAIVRQP +FLFDEPLSNLDA LRV R+EIA+L Sbjct: 121 ILKIDHLLQRLPRELSGGQRQRVAIGRAIVRQPRLFLFDEPLSNLDAALRVQTRLEIAKL 180 Query: 180 HKELNATIVYVTHDQVEAMTLADKIVVMRGGIVEQVGAPLALYDDPDNMFVAGFIGSPRM 239 H++L ATIVYVTHDQVEAMTL DKIVVM G ++Q G PL LY P N+FVAGFIGSP+M Sbjct: 181 HRQLAATIVYVTHDQVEAMTLGDKIVVMHEGRIQQAGTPLELYQQPQNLFVAGFIGSPKM 240 Query: 240 NFLPAVVIGQAEGG-QVTVALKARPDTQLTVACATPPQGGDAVTVGVRPEHFLPAGSGDT 298 NF VV + G QV +A R + TP G AVT+G+R E + G GD Sbjct: 241 NFFQGVVTRCDDSGVQVEIAGGLRLLADVDPLGVTP---GAAVTLGLRAEQ-IREGLGDG 296 Query: 299 Q-LTAHVDVVEHLGNTSYVYAHTVPGEQIIIEQEERRHGGRYGDEIAVGISAKTSFLFDA 357 Q L V++VEHLG +++Y G I++ + R+ G IA+ + + LFDA Sbjct: 297 QPLHGVVNLVEHLGEANFLYVTLDGGHDIVVRGDGNRNVD-IGQPIALSVHSHAFHLFDA 355 Query: 358 SGRRIR 363 G+ +R Sbjct: 356 QGQALR 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: 420 Number of extensions: 9 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: 377 Length adjustment: 30 Effective length of query: 333 Effective length of database: 347 Effective search space: 115551 Effective search space used: 115551 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