Align L-lactate permease (characterized, see rationale)
to candidate WP_041277907.1 DP_RS10655 L-lactate permease
Query= uniprot:L0GFN1 (564 letters) >NCBI__GCF_000025945.1:WP_041277907.1 Length = 570 Score = 474 bits (1220), Expect = e-138 Identities = 247/565 (43%), Positives = 357/565 (63%), Gaps = 12/565 (2%) Query: 1 MSNGLLALFAFTPILLAAIMLIGLRWPASRAMPLVFLFTAAIGLFVWDMSVNRIIASTLQ 60 MS G+LAL A P++LA ++++GLRWPA++AMP+ +L G+ VW + + I A TLQ Sbjct: 1 MSVGILALVALVPLMLALVLMVGLRWPATKAMPVAWLSCVIGGIAVWQLPASYIAALTLQ 60 Query: 61 GLVITLGLLWIIFGAILLLNTLKHSGGITAIRAGFTTISPDRRIQAIIIAWLFGCFIEGA 120 GLV +G+L I+FGAI++L TL++SGG+ I+ GF I+ DRRIQ +II ++F FIEGA Sbjct: 61 GLVTAIGILIIVFGAIIILYTLQYSGGMETIQYGFQNITRDRRIQVLIIGYMFAAFIEGA 120 Query: 121 SGFGTPAAIAAPLLVAVGFPAMAAVLLGMLVQSTPVSFGAVGTPIVVGINSGLDTATIGA 180 +GFGTPAA+AAPLL+++GFP + AV++ ++ S PV+FGAVGTP+V+G + Sbjct: 121 AGFGTPAALAAPLLLSLGFPPLCAVVMCLVFNSFPVTFGAVGTPVVLGFSYLTGLVDEAV 180 Query: 181 QLVAQG---SSWNAYLQQITSSVAITHAIVGTVMPLVMVLMLTRFFGKEKSWKAGFEVLP 237 Q+ A G +S + Q +T + H + ++P+ M+ +TR+FGK + W GF Sbjct: 181 QVAAPGVNFTSMEGFNQLVTQWATLMHLPMIFILPIFMLGFMTRYFGKNRKWSEGFAAWK 240 Query: 238 FAIFAGLAFTLPYAATGIFLGPEFPSLLGGLVGLAIVTTAARFKFLTPKTTWDFADAKEW 297 F IF+ +AF++PY T +GPEFPSL+GGLVGL IV A+ F PK +WDF + EW Sbjct: 241 FCIFSAVAFSVPYLLTAWLVGPEFPSLIGGLVGLGIVVFGAKKNFCMPKKSWDFGPSSEW 300 Query: 298 PAEWLGTIEMKLDEMAARPMSAFRAWLPYVLVGAILVISRVFPQ--VTAALKSVSIAFAN 355 EW G + MS RAW PY+L+G ILV++R+ P + L VSI F + Sbjct: 301 DKEWTGLVSADNSGEFKAHMSQLRAWAPYILIGLILVVTRI-PSLGLKGILAGVSIPFTD 359 Query: 356 ILGETGINAGIEPLYLPGGI-LVMVVLITFFLHGMRVSELKAAVKESSGVLLSAGFVLLF 414 ILG ++A I+ LYLPG I +V ++T FLH M ++ A KE+ + S L F Sbjct: 360 ILGFESVDASIKYLYLPGTIPFALVAILTIFLHRMPAAKAVIAWKEAISKMKSPAIALFF 419 Query: 415 TVPMVRILINSGVNGAEL-----ASMPIVMARYVADSVGSIYPLLAPAVGALGAFLAGSN 469 +V +V I SG+ A L SMP+ +A V+ G +P+ A VG LG+F+ GSN Sbjct: 420 SVSIVSIFKGSGIVDAALNPNNYPSMPLALAEAVSGLAGQTWPMFASFVGGLGSFITGSN 479 Query: 470 TVSNMMFSQFQFGVAQSLGISGAMVVATQAVGAAAGNMVAIHNVVAASATVGLLGREGST 529 TVS+++F++FQ+GVA SLG+ +++A Q VG A GNM+ IHN+VA A GL GREG+ Sbjct: 480 TVSDLLFAEFQWGVASSLGLPHQIIIAAQGVGGAMGNMICIHNIVAVCAVAGLSGREGAI 539 Query: 530 LRKTIWPTLYYVLFTGVIGLIAIYV 554 L++T P L Y L G++ + +V Sbjct: 540 LKRTALPFLIYGLVVGIMVYLMSFV 564 Lambda K H 0.326 0.140 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: 1088 Number of extensions: 65 Number of successful extensions: 7 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: 564 Length of database: 570 Length adjustment: 36 Effective length of query: 528 Effective length of database: 534 Effective search space: 281952 Effective search space used: 281952 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