Align LacK, component of Lactose porter (characterized)
to candidate RR42_RS18590 RR42_RS18590 hypothetical protein
Query= TCDB::Q01937 (363 letters) >FitnessBrowser__Cup4G11:RR42_RS18590 Length = 359 Score = 355 bits (910), Expect = e-102 Identities = 200/361 (55%), Positives = 249/361 (68%), Gaps = 12/361 (3%) Query: 1 MAEVRLTDIRKSYGSLEVIKGVNLEVSSGEFVVFVGPSGCGKSTLLRMIAGLEDISSGEL 60 MA V++ I+K +GS +VI+GV+++++ G+F V VGPSGCGKSTLLRMIAGLE+I++GE+ Sbjct: 1 MASVQIRGIQKYFGSTQVIRGVDIDIADGQFTVLVGPSGCGKSTLLRMIAGLEEITTGEI 60 Query: 61 TIGGTVMNDVDPSKRGIAMVFQTYALYPHMTVRENMGFALRFAGMAKDEIERRVNAAAKI 120 IG V+N + P +R IAMVFQ YALYPHMTV +NM F+L+ A K+EI+R+V A+ I Sbjct: 61 AIGNRVVNRLPPKERDIAMVFQNYALYPHMTVYDNMAFSLKLAKGDKEEIKRKVAKASAI 120 Query: 121 LELDALMDRKPKALSGGQRQRVAIGRAIVRQPDVFLFDEPLSNLDAELRVHMRVEIARLH 180 L LD+L++R P+ LSGGQRQRVA+GRAIVR P VFLFDEPLSNLDA+LRV MR EI LH Sbjct: 121 LGLDSLLERYPRQLSGGQRQRVAMGRAIVRDPQVFLFDEPLSNLDAKLRVQMRAEIKELH 180 Query: 181 KELNATIVYVTHDQVEAMTLADKIVVMRGGIVEQVGAPLALYDDPDNMFVAGFIGSPRMN 240 + L T VYVTHDQ+EAMT+AD+IVVMR G VEQ G PLALYD PDN+FVAGFIGSP MN Sbjct: 181 QRLRTTSVYVTHDQIEAMTMADQIVVMRDGRVEQRGKPLALYDHPDNLFVAGFIGSPAMN 240 Query: 241 FLPAVVIGQAEGGQVTVALKARPD-TQLTVAC---ATPPQGGDAVTVGVRPEHFLPAGSG 296 F+P V+ + GG V PD T+L AT G V GVRPEH L G Sbjct: 241 FVPGVL--RRSGGDAAVEF---PDGTRLPAPARFDATAGTDGQRVIYGVRPEH-LTLGMP 294 Query: 297 DTQLTAHVDVVEHLGNTSYVYAHTVPGEQIIIEQEERRHGGRYGDEIAVGISAKTSFLFD 356 L V VVE G + +Y+ E I I +E RH GD + + + + LFD Sbjct: 295 GQGLQTRVSVVEPTGANTEIYSRFCEAEFISIFRE--RHDFAAGDILNLVPDHQHTHLFD 352 Query: 357 A 357 A Sbjct: 353 A 353 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: 390 Number of extensions: 17 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: 359 Length adjustment: 29 Effective length of query: 334 Effective length of database: 330 Effective search space: 110220 Effective search space used: 110220 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