Align LacK, component of Lactose porter (characterized)
to candidate GFF2754 PGA1_c27970 ATP-binding transport protein SmoK
Query= TCDB::Q01937 (363 letters) >FitnessBrowser__Phaeo:GFF2754 Length = 331 Score = 326 bits (836), Expect = 5e-94 Identities = 178/365 (48%), Positives = 237/365 (64%), Gaps = 37/365 (10%) Query: 1 MAEVRLTDIRKSYGSLEVIKGVNLEVSSGEFVVFVGPSGCGKSTLLRMIAGLEDISSGEL 60 M ++LT++ KS+G +EV+K +NL V GEFVVFVGPSGCGKSTLLR+I+GLED ++GE+ Sbjct: 1 MTALQLTNVCKSFGPVEVLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGEI 60 Query: 61 TIGGTVMNDVDPSKRGIAMVFQTYALYPHMTVRENMGFALRFAGMAKDEIERRVNAAAKI 120 +IGG + P+KRGIAMVFQ+YALYPH++VRENM AL+ K+EI RV A+++ Sbjct: 61 SIGGQTVTTTPPAKRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARVAEASRM 120 Query: 121 LELDALMDRKPKALSGGQRQRVAIGRAIVRQPDVFLFDEPLSNLDAELRVHMRVEIARLH 180 L L+ +DR+P LSGGQRQRVAIGRA+VR+P +FLFDEPLSNLDA LR++ R+EIARLH Sbjct: 121 LSLEDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIARLH 180 Query: 181 KELNATIVYVTHDQVEAMTLADKIVVMRGGIVEQVGAPLALYDDPDNMFVAGFIGSPRMN 240 ++L+A+++YVTHDQ+EAMTLADKIVV+R G +EQVG P+ LY++P N FVA FIG+P MN Sbjct: 181 RQLSASMIYVTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAEFIGAPAMN 240 Query: 241 FLPAVVIGQAEGGQVTVALKARPDTQLTVACATPPQGGDAVTVGVRPEH--FLPAGSGDT 298 F+PA +G G +G+RPE+ P G Sbjct: 241 FVPAQRLG----------------------------GNPGQFIGIRPEYARISPVG---- 268 Query: 299 QLTAHVDVVEHLGNTSYVYAHTVPGEQIIIEQE-ERRHGGRYGDEIAVGISAKTSFLFDA 357 L V VE LG + + GE + +H G+ + FD Sbjct: 269 PLAGEVIHVEKLGGDTNILVDM--GEDLTFTARLFGQHDTNVGETLQFDFDPANCLSFDE 326 Query: 358 SGRRI 362 +G+RI Sbjct: 327 AGQRI 331 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: 372 Number of extensions: 15 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: 331 Length adjustment: 29 Effective length of query: 334 Effective length of database: 302 Effective search space: 100868 Effective search space used: 100868 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