Align L-lactate permease (characterized, see rationale)
to candidate WP_090447327.1 BLS63_RS18840 L-lactate permease
Query= uniprot:A0KZB2 (547 letters) >NCBI__GCF_900100495.1:WP_090447327.1 Length = 566 Score = 438 bits (1126), Expect = e-127 Identities = 238/553 (43%), Positives = 342/553 (61%), Gaps = 16/553 (2%) Query: 2 TILQLLASLTPVISVMIFLVLLRMPASKAMPISMIITALAAVFIWQMDTTLLAASVLEGL 61 T+L +LA P++ + L+ R PA AMP+ ++TAL + W M + AS L+GL Sbjct: 4 TLLSILA-FVPLVLAGVLLIGFRWPAKYAMPVIFLLTALIGLTAWDMSLNRVIASSLQGL 62 Query: 62 LSAITPLTIIFGAVFLLNTLKYSGAMDTIRAGFTNISADARVQVIIICWLFGAFIEGSAG 121 + L IIFGA+ LLNTLK+SG + IR GF+ IS D RVQ +I+ WLFG FIEG++G Sbjct: 63 ILTAAILWIIFGAILLLNTLKHSGGIAAIRRGFSTISPDRRVQALIVAWLFGCFIEGASG 122 Query: 122 FGTPAAIGAPLLVLLGVPPVAAAVVALIADSACVSFGAIGLPVLFGMEQGLTQGGVSLAA 181 FGTPAA+ APLLV LG P +AA V+ ++ S VSFGA+G P+L G+ GL + G+S Sbjct: 123 FGTPAAVAAPLLVALGFPALAAVVLGMMVQSTPVSFGAVGTPILVGVAGGLDKTGMS--- 179 Query: 182 EQFAAHGGSYVGYARFIVMHMITIDLITGTLIPLVMVTILTGFFGRNKSFKEGLAIWKFA 241 Q S+ + I + + G L+PL+MV I+T FFG+N+S+KEGLA+ FA Sbjct: 180 AQLLTLDSSWEIFFHLIFSRVAITHGLIGVLMPLIMVMIMTRFFGKNQSWKEGLAVAPFA 239 Query: 242 IFAGLAFTVPAWIINYLAGPEFPSVIGSLVGMALVIPVARKGYLLPKTPWNDFAEND--- 298 IF L+F +P GPEFPS+IG++VG+A+V+P A+ G+LLPK W DFAE Sbjct: 240 IFTALSFVLPYMAAGVFLGPEFPSMIGAMVGLAIVVPAAKAGFLLPKQTW-DFAEAKDWP 298 Query: 299 ----SQEGAKIETTAKFSQIA---AWTPYIIMAALLVLSRTVAPLKAWLSSFNISWTGLM 351 + K++ A + I+ AW PY+++A LVLSR LKA L S + W ++ Sbjct: 299 VEWMGKIEMKLDDVAGKTPISVPMAWAPYLLLAVFLVLSRIFPQLKAALLSISFGWKDIL 358 Query: 352 G-TELKASFATLYAPGAFFVAVCILGFFLFKMKSPAIKQSIGVSCKSMLPTIISLGASVP 410 G T + + LY PG V + FFL +M+ +K ++G S +++L L ++P Sbjct: 359 GETGISGTLEPLYLPGGILCMVVLATFFLHRMRFAELKAAVGESSRTLLGAGFVLIFTIP 418 Query: 411 MVKIFLNSGVNGAGLASMPVALADMLGQSMGAVWAWMAPIVGIFGAFLSGSATFSNMMFS 470 MV+I +NSGVNGA L SMPVA+A ++ S+G V+ AP VG GAF++GS T SN+M S Sbjct: 419 MVRILINSGVNGADLMSMPVAMAQLVADSVGGVYPMFAPAVGALGAFIAGSNTVSNLMLS 478 Query: 471 SLQYSVADNIGMNHTLVLALQGIGANAGNMMCVMNVVAAATVVGMAGRESEIIRKTMPVA 530 Q++ A +G++ +++A Q +GA AGNM+ + NVVAA+ VG+ GRE +RKTM Sbjct: 479 QFQFNAAGLLGVSGAMMVAAQSVGAAAGNMIAIHNVVAASATVGLLGREGITLRKTMLPT 538 Query: 531 IGYALLAGTIATL 543 + Y L AG++ + Sbjct: 539 LYYLLAAGSLTMI 551 Lambda K H 0.326 0.138 0.413 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: 964 Number of extensions: 55 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: 547 Length of database: 566 Length adjustment: 36 Effective length of query: 511 Effective length of database: 530 Effective search space: 270830 Effective search space used: 270830 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