Align L-lactate permease (characterized, see rationale)
to candidate GFF926 Psest_0955 L-lactate transport
Query= uniprot:A0KZB2 (547 letters) >FitnessBrowser__psRCH2:GFF926 Length = 564 Score = 449 bits (1155), Expect = e-130 Identities = 243/550 (44%), Positives = 337/550 (61%), Gaps = 14/550 (2%) Query: 4 LQLLASLTPVISVMIFLVLLRMPASKAMPISMIITALAAVFIWQMDTTLLAASVLEGLLS 63 L L + TP++ I L+ LR PAS+AMP+ + TA +F+W M + AS L+GL+ Sbjct: 5 LLALFAFTPILLAAIMLIGLRWPASRAMPLVFLFTAAIGLFVWDMSVNRIIASTLQGLVI 64 Query: 64 AITPLTIIFGAVFLLNTLKYSGAMDTIRAGFTNISADARVQVIIICWLFGAFIEGSAGFG 123 + L IIFGA+ LLNTLK+SG + IRAGFT IS D R+Q III WLFG FIEG++GFG Sbjct: 65 TLGLLWIIFGAILLLNTLKHSGGITAIRAGFTTISPDRRIQAIIIAWLFGCFIEGASGFG 124 Query: 124 TPAAIGAPLLVLLGVPPVAAAVVALIADSACVSFGAIGLPVLFGMEQGLTQGGVSLAAEQ 183 TPAAI APLLV +G P +AA ++ ++ S VSFGA+G P++ G+ GL + Q Sbjct: 125 TPAAIAAPLLVAVGFPAMAAVLLGMLVQSTPVSFGAVGTPIVVGINSGLDTATI---GAQ 181 Query: 184 FAAHGGSYVGYARFIVMHMITIDLITGTLIPLVMVTILTGFFGRNKSFKEGLAIWKFAIF 243 A G S+ Y + I + I GT++PLVMV +LT FFG+ KS+K G + FAIF Sbjct: 182 LVAQGSSWNAYLQQITSSVAITHAIVGTVMPLVMVLMLTRFFGKEKSWKAGFEVLPFAIF 241 Query: 244 AGLAFTVPAWIINYLAGPEFPSVIGSLVGMALVIPVARKGYLLPKTPWNDFAENDSQEGA 303 AGLAFT+P GPEFPS++G LVG+A+V AR +L PKT W DFA+ Sbjct: 242 AGLAFTLPYAATGIFLGPEFPSLLGGLVGLAIVTTAARFKFLTPKTTW-DFADAKEWPAE 300 Query: 304 KIET---------TAKFSQIAAWTPYIIMAALLVLSRTVAPLKAWLSSFNISWTGLMG-T 353 + T S AW PY+++ A+LV+SR + A L S +I++ ++G T Sbjct: 301 WLGTIEMKLDEMAARPMSAFRAWLPYVLVGAILVISRVFPQVTAALKSVSIAFANILGET 360 Query: 354 ELKASFATLYAPGAFFVAVCILGFFLFKMKSPAIKQSIGVSCKSMLPTIISLGASVPMVK 413 + A LY PG V V ++ FFL M+ +K ++ S +L L +VPMV+ Sbjct: 361 GINAGIEPLYLPGGILVMVVLITFFLHGMRVSELKAAVKESSGVLLSAGFVLLFTVPMVR 420 Query: 414 IFLNSGVNGAGLASMPVALADMLGQSMGAVWAWMAPIVGIFGAFLSGSATFSNMMFSSLQ 473 I +NSGVNGA LASMP+ +A + S+G+++ +AP VG GAFL+GS T SNMMFS Q Sbjct: 421 ILINSGVNGAELASMPIVMARYVADSVGSIYPLLAPAVGALGAFLAGSNTVSNMMFSQFQ 480 Query: 474 YSVADNIGMNHTLVLALQGIGANAGNMMCVMNVVAAATVVGMAGRESEIIRKTMPVAIGY 533 + VA ++G++ +V+A Q +GA AGNM+ + NVVAA+ VG+ GRE +RKT+ + Y Sbjct: 481 FGVAQSLGISGAMVVATQAVGAAAGNMVAIHNVVAASATVGLLGREGSTLRKTIWPTLYY 540 Query: 534 ALLAGTIATL 543 L G I + Sbjct: 541 VLFTGVIGLI 550 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: 919 Number of extensions: 53 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: 564 Length adjustment: 36 Effective length of query: 511 Effective length of database: 528 Effective search space: 269808 Effective search space used: 269808 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 17 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