Align L-lactate permease (characterized, see rationale)
to candidate WP_019895194.1 A377_RS11960 L-lactate permease
Query= uniprot:Q8EGS2 (547 letters) >NCBI__GCF_000384235.1:WP_019895194.1 Length = 560 Score = 489 bits (1258), Expect = e-142 Identities = 268/568 (47%), Positives = 364/568 (64%), Gaps = 43/568 (7%) Query: 1 MTILQLFASLTPVLSVMIFLVLLRMPASKAMPISMVVTAIAAVFIWQMDTTLLAASVVEG 60 MT+LQ + PVL+V++FLV+LR+PAS+AMP+S+V+ A+ A +WQM +AASV+EG Sbjct: 1 MTLLQFLTAAMPVLAVLVFLVILRLPASRAMPLSLVIVALLAWQVWQMPVDYIAASVLEG 60 Query: 61 LLSAITPLTIIFGAVFLLNTLKYSGAMDTIRAGFTNISADARVQVIIICWLFGAFIEGSA 120 + L I+FGA+ LLNTLK SGA+DTIR GF+ IS D RVQ +I+ WLF AF+EG++ Sbjct: 61 WVIGAAILIIVFGAIVLLNTLKVSGAVDTIRQGFSGISPDRRVQTVIVGWLFVAFLEGAS 120 Query: 121 GFGTPAAIGAPLLVLLGVPPVAAAVVALIADSACVSFGAIGLPVLFGMEQGLIQGGVSMA 180 GFGTPAAI APLL+ LG P +AA +ALIADSA VS+GA+G PV+ G+ +G+ Sbjct: 121 GFGTPAAIVAPLLLALGFPALAAVTLALIADSAAVSYGAVGTPVIVGIGEGV-------- 172 Query: 181 AEQFAAHGGTYAGYARYIVMHMITIDLITGTLIPLVMVTMLTGFFGRNKSFKEGLAIWKF 240 G TY V + ID++ + +PL+MV MLT FFG NKS++EGL WKF Sbjct: 173 ------EGITYEQMMEVAVTASL-IDVMVASFLPLLMVVMLTRFFGENKSWREGLGAWKF 225 Query: 241 AIFSGLAFTVPAWIINYLAGPEFPSVIGALIGMAMVIPVARKGYLLPKTPWNDFAENDNQ 300 A+ G +FT+PA + +L GPEFP+++G LIG+ + + AR L PKT W FA + + Sbjct: 226 ALLGGFSFTLPALGVAWLLGPEFPAILGGLIGLVITVTAARHNILTPKTVWG-FASDTPE 284 Query: 301 DG----------VKLETTAKFSQIA----------------AWTPYIIMAALLVLSR-TV 333 VK+E K ++ AW PY+++AA+LVL+R V Sbjct: 285 TAQTVHKPSPGLVKIEGCEKSPALSCLAVEPVRHACLPLWQAWLPYVLVAAILVLTRLEV 344 Query: 334 APLKAWLSGFNINWTGLLGTELKASFATLYAPGAFFVAVCILGFFLFKMKSPAIKQSIGV 393 PLK WL + + L GT + A LY PG+ F+ V +L + L ++ + + G Sbjct: 345 LPLKDWLQSVQLTFEQLAGTGISAKLVPLYLPGSVFLLVALLTWALHRVPVRQVTLAWGR 404 Query: 394 SCKSMLPTIISLGASVPMVKIFLNSGANGAGLASMPVALADMLASSMGAVWAWMAPIVGI 453 S K +LPTII+L ASVPMV+IFLNSG NGA L SMP+ALA + A + W AP VG Sbjct: 405 SIKVLLPTIIALAASVPMVRIFLNSGENGADLLSMPLALAQLAADTFAGQWPLAAPFVGA 464 Query: 454 FGAFLSGSATFSNMMFSSLQYSVADNIGMNHTLVLALQGIGANAGNMMCVMNVVAAATVV 513 G+F++GSATFSNMMFS LQ S A+ + M +LALQ +GANAGNM+CV+NVVAAA+VV Sbjct: 465 LGSFVAGSATFSNMMFSQLQASTAEALSMPSHWILALQMLGANAGNMICVVNVVAAASVV 524 Query: 514 GMAGRESEIIRKTMPVAIGYALLAGTIA 541 +AG+E +IIR T+ + YA G +A Sbjct: 525 NLAGKEGQIIRYTLVPMLFYATAVGVVA 552 Lambda K H 0.326 0.138 0.415 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: 970 Number of extensions: 49 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: 547 Length of database: 560 Length adjustment: 36 Effective length of query: 511 Effective length of database: 524 Effective search space: 267764 Effective search space used: 267764 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 (21.7 bits) S2: 53 (25.0 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