Align L-lactate permease (characterized)
to candidate BPHYT_RS13235 BPHYT_RS13235 lactate permease
Query= SwissProt::P71067 (563 letters) >FitnessBrowser__BFirm:BPHYT_RS13235 Length = 532 Score = 400 bits (1029), Expect = e-116 Identities = 220/560 (39%), Positives = 334/560 (59%), Gaps = 33/560 (5%) Query: 5 QAYTPIGGNLLLSALAALVPIIFFFWALAIKRMKGYTAGLATLGIALIIAVLVYRMPAEK 64 Q TP+G +LL S L A +PII L R + A LA L + LI+A+ V++ P Sbjct: 4 QLLTPVGNSLLPSFLVAALPIIVVLLLLGWARRPAWQASLAGLVVGLIVAIFVWQFPVGL 63 Query: 65 ALMSATQGAVYGLLPIGWIIVTSVFLYKITVKTGQFDIIRSSVL-SITDDRRLQALLIAF 123 A+ S GAV+ P+ WI+ ++ LY I+ ++G+F R ++ ++ +DRR+ ++I F Sbjct: 64 AVDSVVAGAVFACWPVMWIVFAAILLYNISQRSGRFAAFRMWMIDNLPNDRRVVLVVIGF 123 Query: 124 SFGAFLEGAAGFGAPVAISAALLVGLGFNPLYAAGICLIANTAPVAFGAIGIPITAVEGP 183 SFGA LEG +GFG PVAI+++LL+ LGF L A LI NTAPVAFGA+G+PIT + Sbjct: 124 SFGALLEGISGFGTPVAITSSLLILLGFPTLEALTFTLIFNTAPVAFGALGVPITVLGAV 183 Query: 184 TGIPAMEISQMVGRQLPFLSVFIPLYLIIIMSGFRKALEIWPAILVSGVSFAVVQYLSSN 243 T +PA +++MVGRQLPF + +P Y+I + +GFR L +WP +LVSG SFA+ Q+++SN Sbjct: 184 THLPADSLAKMVGRQLPFFAFLLPFYVIGVYAGFRNMLRVWPVLLVSGASFALTQFVASN 243 Query: 244 FLGPELPDVLSALVSMAALAVFLKWWKPKTTFRFAGEQESAASIETARTNPAAPAYRGGQ 303 ++ L DVLS++VS+ FL+ WKP +FA + R G Q Sbjct: 244 YVNYSLTDVLSSMVSLILTIAFLRVWKPAADPKFA--------VNIDRVGEVRGKIGGAQ 295 Query: 304 IFKAWSPFLLLTAMISVWGIPSVKSALTGHYEGSAVFLKWLNAVGEKLTFSPGVPFLNNQ 363 W P+++++ ++ +W + + +FL +G+ PG+ Sbjct: 296 ---GWYPWIIVSVVVIIWTV-------------AKIFL-----IGDVKVPWPGLD--KAV 332 Query: 364 IVNADGTPIEAVYKLEVLGSAGTAILIAAVLSKFITAISWKDWGTVFKETVQELKLPILT 423 + TP AV+ + L + GTAIL+AA+++ + +S +++G +T + ++ ILT Sbjct: 333 FITLYNTPYSAVWDFQPL-ATGTAILVAALITAAVVKLSPREFGAAVADTWVQTRIAILT 391 Query: 424 IASVVGFAYVTNSSGMSTTLGMTLALTGSMFTFFSPVLGWLGVFITGSDTSANLLFGNLQ 483 +A++VG AY+ N SG++ TLG+ + G F S LGW+ VF++GSDTS N LFGNLQ Sbjct: 392 VATIVGLAYLMNYSGLTYTLGLGASSVGPFFPLVSAFLGWVAVFLSGSDTSGNALFGNLQ 451 Query: 484 KVTALSVGMDPVLSVAANSSGGVTGKMISPQSIAVACAAVGLAGKESDLFRFTIKHSLFL 543 V A + ++P+L AANSSGGV GKMISPQ+I+ A L GKE +F T KHS+ L Sbjct: 452 VVAANQLNLNPILMAAANSSGGVMGKMISPQNISTGVATTELKGKEGVVFAKTFKHSILL 511 Query: 544 LLLVCIITFLQHHVFSWMIP 563 +L+ ++ +LQ + WMIP Sbjct: 512 TVLLGVLVWLQQNFLQWMIP 531 Lambda K H 0.325 0.138 0.414 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: 877 Number of extensions: 38 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: 563 Length of database: 532 Length adjustment: 36 Effective length of query: 527 Effective length of database: 496 Effective search space: 261392 Effective search space used: 261392 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 53 (25.0 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