Align LacK, component of Lactose porter (characterized)
to candidate GFF5028 PS417_25760 spermidine/putrescine ABC transporter ATP-binding protein
Query= TCDB::Q01937 (363 letters) >FitnessBrowser__WCS417:GFF5028 Length = 370 Score = 241 bits (614), Expect = 3e-68 Identities = 130/297 (43%), Positives = 184/297 (61%), Gaps = 8/297 (2%) Query: 4 VRLTDIRKSY-GSLEVIKGVNLEVSSGEFVVFVGPSGCGKSTLLRMIAGLEDISSGELTI 62 V ++KSY G ++K +NLE+ GEF+ +GPSG GK+T L M+AG E ++GE+ + Sbjct: 11 VSFRGVQKSYDGENLIVKDLNLEIRKGEFLTLLGPSGSGKTTSLMMLAGFETPTAGEIQL 70 Query: 63 GGTVMNDVDPSKRGIAMVFQTYALYPHMTVRENMGFALRFAGMAKDEIERRVNAAAKILE 122 G +N+V P KR I MVFQ YAL+PHMTV EN+ F L ++K +I RV +++ Sbjct: 71 AGRSINNVPPHKRDIGMVFQNYALFPHMTVAENLAFPLSVRALSKTDISERVKRVLSMVQ 130 Query: 123 LDALMDRKPKALSGGQRQRVAIGRAIVRQPDVFLFDEPLSNLDAELRVHMRVEIARLHKE 182 LDA R P LSGGQ+QRVA+ RA+V +P + L DEPL LD +LR HM++EI LH+ Sbjct: 131 LDAFAQRYPAQLSGGQQQRVALARALVFEPQLVLMDEPLGALDKQLREHMQMEIKHLHQR 190 Query: 183 LNATIVYVTHDQVEAMTLADKIVVMRGGIVEQVGAPLALYDDPDNMFVAGFIG-SPRMNF 241 L T+VYVTHDQ EA+T++D++ V G ++Q+ AP LY++P N FVA FIG + R+N Sbjct: 191 LGVTVVYVTHDQGEALTMSDRVAVFHQGEIQQIAAPRTLYEEPKNTFVANFIGENNRLNG 250 Query: 242 LPAVVIGQAEGGQVTVALKARPDTQLTVACATPPQGGDAVTVGVRPEHFLPAGSGDT 298 + G+ V AR + ++ Q G VT+ VRPE GS ++ Sbjct: 251 RL-----HSHSGERCVVELARGE-KVEALAVNVGQVGGPVTLSVRPERVSLNGSSES 301 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: 347 Number of extensions: 10 Number of successful extensions: 1 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: 370 Length adjustment: 30 Effective length of query: 333 Effective length of database: 340 Effective search space: 113220 Effective search space used: 113220 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