Align L-lactate permease (characterized, see rationale)
to candidate WP_086511817.1 BZY95_RS20890 L-lactate permease
Query= uniprot:A0KZB2 (547 letters) >NCBI__GCF_002151265.1:WP_086511817.1 Length = 610 Score = 456 bits (1174), Expect = e-133 Identities = 246/555 (44%), Positives = 350/555 (63%), Gaps = 20/555 (3%) Query: 2 TILQLLASLTPVISVMIFLVLLRMPASKAMPISMIITALAAVFIWQMDTTLLAASVLEGL 61 T L LLA TP+I + L+ RM A AMPI ++TA+ A+F W+M + AS +GL Sbjct: 4 TTLALLA-FTPLILAGVLLIGFRMAAKTAMPIVYLVTAVIALFAWEMSFNRVLASTFQGL 62 Query: 62 LSAITPLTIIFGAVFLLNTLKYSGAMDTIRAGFTNISADARVQVIIICWLFGAFIEGSAG 121 + + L IIFGA+ LLNTLK+SG + IR GF+ IS D RVQ II+ WLFG FIEG++G Sbjct: 63 ILTASILWIIFGAILLLNTLKHSGGITAIRNGFSGISPDRRVQAIIVAWLFGCFIEGASG 122 Query: 122 FGTPAAIGAPLLVLLGVPPVAAAVVALIADSACVSFGAIGLPVLFGMEQGLTQGGVSLAA 181 FGTPAA+ APL+V LG P +AA VV ++ S VSFGA+G P++ G+ G+ Q ++ Sbjct: 123 FGTPAAVAAPLMVALGFPALAAVVVGMMIQSTPVSFGAVGTPIVVGVTGGINQSAIT--- 179 Query: 182 EQFAAHGGSYVGYARFIVMHMITIDLITGTLIPLVMVTILTGFFGRNKSFKEGLAIWKFA 241 EQ A G +++ Y R I + + I G L+PL+MV I+ FFG NKS+KEGL+I FA Sbjct: 180 EQLEAGGYTWLEYFRLIAAEVAIVHGIIGILMPLIMVVIMVKFFGANKSWKEGLSITPFA 239 Query: 242 IFAGLAFTVPAWIINYLAGPEFPSVIGSLVGMALVIPVARKGYLLPKTPWNDFAENDSQE 301 +FAG+AF VP + L GPEFPS+IG++VG+A+V+P AR+G+L+PK W DF E S Sbjct: 240 LFAGVAFVVPYMLAGVLLGPEFPSMIGAMVGLAIVVPAARRGFLIPKDTW-DFPERSSWP 298 Query: 302 G---AKIETTAKFSQIA---------AWTPYIIMAALLVLSRTVAPLKAWLSSFNISWTG 349 KIE K IA W PY+++A LV SRT+ PL+ L+++ W Sbjct: 299 DNWIGKIE--IKIDDIAGKTPLSTWMGWLPYVLLAVFLVASRTIEPLREALNAWTFGWNN 356 Query: 350 LMG-TELKASFATLYAPGAFFVAVCILGFFLFKMKSPAIKQSIGVSCKSMLPTIISLGAS 408 ++G + S A LY PG + V ++ L +M++ +K + G S +++ L + Sbjct: 357 ILGEAGVSGSLAPLYLPGGILLMVVLVTAVLHRMRAGELKAAFGESSRTIFGAGFVLIFT 416 Query: 409 VPMVKIFLNSGVNGAGLASMPVALADMLGQSMGAVWAWMAPIVGIFGAFLSGSATFSNMM 468 +PMV+I +NSGVN L SMPVA+A + +G V+ + AP VG GAF++GS T +N+M Sbjct: 417 IPMVRILINSGVNAGDLVSMPVAMAQFVADGVGDVYPFFAPAVGGLGAFIAGSNTAANLM 476 Query: 469 FSSLQYSVADNIGMNHTLVLALQGIGANAGNMMCVMNVVAAATVVGMAGRESEIIRKTMP 528 + Q++VA +G++ ++ALQ +GA AGNM+ + NVVAA+ VG+ GRE E IRKT+ Sbjct: 477 LAEFQFNVAQQLGLSTAFMVALQAVGAAAGNMIAIHNVVAASATVGLLGREGETIRKTIL 536 Query: 529 VAIGYALLAGTIATL 543 I Y + AG IA + Sbjct: 537 PTIYYLVFAGAIAMI 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: 992 Number of extensions: 66 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: 610 Length adjustment: 36 Effective length of query: 511 Effective length of database: 574 Effective search space: 293314 Effective search space used: 293314 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