Align L-lactate permease (characterized)
to candidate WP_057509294.1 ABB28_RS14460 L-lactate permease
Query= SwissProt::P33231 (551 letters) >NCBI__GCF_001431535.1:WP_057509294.1 Length = 540 Score = 473 bits (1218), Expect = e-138 Identities = 247/532 (46%), Positives = 350/532 (65%), Gaps = 15/532 (2%) Query: 3 LWQQNYDPAGNIWLSSLIASLPILFFFFALIKLKLKGYVAASWTVAIALAVALLFYKMPV 62 +WQQNYDP GN LS+L+A+LP+L F AL L+LKG AA V +++ V+ L + MP Sbjct: 1 MWQQNYDPLGNPNLSALLAALPVLVFLLALTVLRLKGLTAALLAVVVSVLVSALVFGMPA 60 Query: 63 ANALASVVYGFFYGLWPIAWIIIAAVFVYKISVKTGQFDIIRSSILSITPDQRLQMLIVG 122 + + G G++PI++I++ AV++YK+++++G+FD+IR SI +I+ DQR+Q+L++ Sbjct: 61 GTIAGAGLLGIANGVFPISFIVLMAVWLYKLAIRSGKFDVIRGSIATISEDQRIQVLLIA 120 Query: 123 FCFGAFLEGAAGFGAPVAITAALLVGLGFKPLYAAGLCLIVNTAPVAFGAMGIPILVAGQ 182 FCFG FLEGAAGFG P+AI AALLV LGF+PL AA LCL+ N A A+GA+GIP++V Q Sbjct: 121 FCFGGFLEGAAGFGVPIAICAALLVELGFRPLKAAMLCLLANGAAGAYGAIGIPVVVGAQ 180 Query: 183 VTGIDSFEIGQMVGRQLPFMTIIVLFWIMAIMDGWRGIKETWPAVVVAGGSFAIAQYLSS 242 G+ + M+ + + ++ ++ ++DGWRG++ETWP ++V GG F+ Q Sbjct: 181 QGGVSLEAMSLMLMALVQVIALLSPAILVLMLDGWRGVRETWPVLLVVGGVFSGVQTAVL 240 Query: 243 NFIGPELPDIISSLVSLLCLTLFLKRWQPVRVFRFGDLGASQVDMTLAHTGYTAGQVLRA 302 +GPEL DII L ++ L F++ W+P R++R D YT QVL A Sbjct: 241 YLLGPELVDIIGPLAAMAALAGFMQVWRPRRIYREADTPPGPAQR------YTLKQVLLA 294 Query: 303 WTPFLFLTATVTLWSIPPFKALFASGGALYEWVINIPVPYLDKLVARMPPVVSEATAYAA 362 W+PF LT + LWS+P FKALFA+GGAL V+++P+ LD V +PP+V A Sbjct: 295 WSPFYILTGAILLWSLPAFKALFAAGGALASTVLHLPIGLLDGRVQELPPLVVNVHTLPA 354 Query: 363 VFKFDWFSATGTAILFAALLSIVW-----LKMKPSDAISTFGSTLKELALPIYSIGMVLA 417 V+ W +A+GTAIL AA+L++V L+M + T G E+ P+ ++ +V+A Sbjct: 355 VWNVGWLNASGTAILVAAVLTVVLSPRLNLRMSGEELAQTAG----EMWKPLATVSLVMA 410 Query: 418 FAFISNYSGLSSTLALALAHTGHAFTFFSPFLGWLGVFLTGSDTSSNALFAALQATAAQQ 477 A+I+NYSG SST+ LALA TG F +P +GW+GVF+TGS +SN LFA LQA A Q Sbjct: 411 VAYITNYSGASSTIGLALAQTGGVFPLLAPVIGWMGVFITGSVVNSNTLFAHLQAVTAAQ 470 Query: 478 IGVSDLLLVAANTTGGVTGKMISPQSIAIACAAVGLVGKESDLFRFTVKHSL 529 IGV + LLVAANT GGV K++SPQSIAIA AAV LVG+ES + R T+ SL Sbjct: 471 IGVPEALLVAANTAGGVMAKLVSPQSIAIAAAAVKLVGQESAIMRTTLGISL 522 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: 805 Number of extensions: 34 Number of successful extensions: 3 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: 540 Length adjustment: 35 Effective length of query: 516 Effective length of database: 505 Effective search space: 260580 Effective search space used: 260580 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 24 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