Align L-lactate permease (characterized)
to candidate BPHYT_RS13235 BPHYT_RS13235 lactate permease
Query= SwissProt::P33231 (551 letters) >FitnessBrowser__BFirm:BPHYT_RS13235 Length = 532 Score = 387 bits (993), Expect = e-112 Identities = 215/551 (39%), Positives = 327/551 (59%), Gaps = 22/551 (3%) Query: 3 LWQQNYDPAGNIWLSS-LIASLPILFFFFALIKLKLKGYVAASWTVAIALAVALLFYKMP 61 ++ Q P GN L S L+A+LPI+ L + + A+ + + L VA+ ++ P Sbjct: 1 MFHQLLTPVGNSLLPSFLVAALPIIVVLLLLGWARRPAWQASLAGLVVGLIVAIFVWQFP 60 Query: 62 VANALASVVYGFFYGLWPIAWIIIAAVFVYKISVKTGQFDIIRSSILSITP-DQRLQMLI 120 V A+ SVV G + WP+ WI+ AA+ +Y IS ++G+F R ++ P D+R+ +++ Sbjct: 61 VGLAVDSVVAGAVFACWPVMWIVFAAILLYNISQRSGRFAAFRMWMIDNLPNDRRVVLVV 120 Query: 121 VGFCFGAFLEGAAGFGAPVAITAALLVGLGFKPLYAAGLCLIVNTAPVAFGAMGIPILVA 180 +GF FGA LEG +GFG PVAIT++LL+ LGF L A LI NTAPVAFGA+G+PI V Sbjct: 121 IGFSFGALLEGISGFGTPVAITSSLLILLGFPTLEALTFTLIFNTAPVAFGALGVPITVL 180 Query: 181 GQVTGIDSFEIGQMVGRQLPFMTIIVLFWIMAIMDGWRGIKETWPAVVVAGGSFAIAQYL 240 G VT + + + +MVGRQLPF ++ F+++ + G+R + WP ++V+G SFA+ Q++ Sbjct: 181 GAVTHLPADSLAKMVGRQLPFFAFLLPFYVIGVYAGFRNMLRVWPVLLVSGASFALTQFV 240 Query: 241 SSNFIGPELPDIISSLVSLLCLTLFLKRWQPVRVFRFGDLGASQVDMTLAHTGYTAGQVL 300 +SN++ L D++SS+VSL+ FL+ W+P +F A +D G G Sbjct: 241 ASNYVNYSLTDVLSSMVSLILTIAFLRVWKPAADPKF----AVNIDRVGEVRGKIGG--A 294 Query: 301 RAWTPFLFLTATVTLWSIPPFKALFASGGALYEWVINIPVPYLDKLVARMPPVVSEATAY 360 + W P++ ++ V +W++ +F G + +P P LDK V + T Y Sbjct: 295 QGWYPWIIVSVVVIIWTV---AKIFLIGD------VKVPWPGLDKAVF----ITLYNTPY 341 Query: 361 AAVFKFDWFSATGTAILFAALLSIVWLKMKPSDAISTFGSTLKELALPIYSIGMVLAFAF 420 +AV+ F ATGTAIL AAL++ +K+ P + + T + + I ++ ++ A+ Sbjct: 342 SAVWDFQPL-ATGTAILVAALITAAVVKLSPREFGAAVADTWVQTRIAILTVATIVGLAY 400 Query: 421 ISNYSGLSSTLALALAHTGHAFTFFSPFLGWLGVFLTGSDTSSNALFAALQATAAQQIGV 480 + NYSGL+ TL L + G F S FLGW+ VFL+GSDTS NALF LQ AA Q+ + Sbjct: 401 LMNYSGLTYTLGLGASSVGPFFPLVSAFLGWVAVFLSGSDTSGNALFGNLQVVAANQLNL 460 Query: 481 SDLLLVAANTTGGVTGKMISPQSIAIACAAVGLVGKESDLFRFTVKHSLIFTCIVGVITT 540 + +L+ AAN++GGV GKMISPQ+I+ A L GKE +F T KHS++ T ++GV+ Sbjct: 461 NPILMAAANSSGGVMGKMISPQNISTGVATTELKGKEGVVFAKTFKHSILLTVLLGVLVW 520 Query: 541 LQAYVLTWMIP 551 LQ L WMIP Sbjct: 521 LQQNFLQWMIP 531 Lambda K H 0.328 0.140 0.436 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: 894 Number of extensions: 46 Number of successful extensions: 4 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: 551 Length of database: 532 Length adjustment: 35 Effective length of query: 516 Effective length of database: 497 Effective search space: 256452 Effective search space used: 256452 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 52 (24.6 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