Align L-lactate permease (characterized)
to candidate 8499614 DvMF_0381 L-lactate transport (RefSeq)
Query= SwissProt::P71067 (563 letters) >FitnessBrowser__Miya:8499614 Length = 506 Score = 295 bits (756), Expect = 2e-84 Identities = 188/542 (34%), Positives = 291/542 (53%), Gaps = 54/542 (9%) Query: 16 LSALAALVPIIFFFWALAIKRMKGYTAGLATLGIALIIAVLVY-RMPAEKALMSATQGAV 74 L AAL PI++ ++L + ++ Y TL L +AV + +MPA AL +A +GA Sbjct: 7 LQLAAALAPIVWLIFSLVVLKLPAYRTCALTLVCTLALAVFGWWKMPAFMALSAALEGAA 66 Query: 75 YGLLPIGWIIVTSVFLYKITVKTGQFDIIRSSVLSITDDRRLQALLIAFSFGAFLEGAAG 134 L PI +I+ +VF Y + TG D+I + SIT D+RL L++A+ FG FLEG AG Sbjct: 67 MALWPIMIVIIAAVFTYNLARHTGSMDVITRMLSSITTDKRLLVLIVAWGFGGFLEGVAG 126 Query: 135 FGAPVAISAALLVGLGFNPLYAAGICLIANTAPVAFGAIGIPITAVEGPTGIPAMEISQM 194 +G VAI A++L +GF P++AA ICL+ANT P AFGAIGIPI + G TG+P IS Sbjct: 127 YGTAVAIPASILAAMGFQPMFAAVICLVANTVPTAFGAIGIPIVTMAGVTGLPVETISYY 186 Query: 195 VGRQLPFLSVFIPLYLIIIMSGFRKALEIWPAILVSGVSFAVVQYLSSNFLGPELPDVLS 254 QL + I L+I+ +GF+ ++ A LVSG++FA Q ++ ++G ELP ++ Sbjct: 187 TALQLFVFIILITYLLVILTAGFKGIKGVFWATLVSGLAFAFPQLYTAKYMGAELPCLIG 246 Query: 255 ALVSMAALAVFLKWWKPKTTFRFAGEQESAASIETARTNPAAPAYRGGQIFKAWSPFLLL 314 ++ SM A V+ + + +++AA ++ PAA + KAW P++L+ Sbjct: 247 SVCSMIATIVWARLF----------HRDTAAQVDPI---PAA------EKVKAWLPYILV 287 Query: 315 TAMISVWG--IPSVKSALTGHYEGSAVFLKWLNAVGEKLTFSPGVPFLNNQIVNADGTPI 372 A I + P+++ A L +V + PF Sbjct: 288 FAFIILCSNLFPAIRDA--------------LGSVKTTVRIYGDNPF------------- 320 Query: 373 EAVYKLEVLGSAGTAILIAAVLSKFITAISWKDWGTVFKETVQELKLPILTIASVVGFAY 432 + + + G I+IA + I + ++ V T ++L +T+ S+V A Sbjct: 321 ----TFKWIATPGALIIIATYIGGMIQGVKVREITGVLGSTAKKLVYSGVTVVSIVALAK 376 Query: 433 VTNSSGMSTTLGMTLA-LTGSMFTFFSPVLGWLGVFITGSDTSANLLFGNLQKVTALSVG 491 V ++SGM T+ + +A T S F F SP+LG LG F+TGSDTS+N+LFG LQ A + Sbjct: 377 VMSTSGMINTIAIAVADSTSSYFPFISPLLGALGTFVTGSDTSSNVLFGQLQMEVANRIS 436 Query: 492 MDPVLSVAANSSGGVTGKMISPQSIAVACAAVGLAGKESDLFRFTIKHSLFLLLLVCIIT 551 +D V+A+++G GKMISPQSIAVA AA GL G E + T+ + +L++ + Sbjct: 437 IDSTWIVSASAAGATAGKMISPQSIAVATAATGLTGYEGRIMNRTLAVCVGYVLVLGTLV 496 Query: 552 FL 553 ++ Sbjct: 497 YV 498 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: 768 Number of extensions: 33 Number of successful extensions: 5 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: 506 Length adjustment: 35 Effective length of query: 528 Effective length of database: 471 Effective search space: 248688 Effective search space used: 248688 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: 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