Align Glycolate permease, GlcA or YghK (substrates: L-lactate, D-lactate and glycolate) (characterized)
to candidate WP_034994427.1 DL88_RS07750 L-lactate permease
Query= TCDB::Q46839 (560 letters) >NCBI__GCF_000745425.1:WP_034994427.1 Length = 567 Score = 486 bits (1252), Expect = e-142 Identities = 260/567 (45%), Positives = 351/567 (61%), Gaps = 25/567 (4%) Query: 4 WTQMYMPMGGLGLSALVALIPIIFFFVALAVLRLKGHVAGAITLILSILIAIFAFKMPID 63 W Q+Y P G LS ++A +PI +A ++K H A L L+ L+A F MP Sbjct: 2 WQQIYDPFGNRLLSTVIASLPIFCLLGLIAFSKVKAHFAALTALALAYLVATLGFTMPAI 61 Query: 64 MAFAAAGYGFIYGLWPIAWIIVAAVFLYKLTVASGQFDIIRSSVISITDDQRLQVLLIGF 123 MA AA G + GL+PI WII+ +FLY+LTV +G F I++ S+ ++T D+RLQ+LL+ + Sbjct: 62 MAGKAALLGALTGLFPIGWIIINVIFLYRLTVENGSFAILQDSIANVTADRRLQLLLVAY 121 Query: 124 SFGALLEGAAGFGAPVAITGALLVGLGFKPLYAAGLCLIANTAPVAFGALGVPILVAGQV 183 +FGA EGAAGFG PVA+TGA+L+GLGF PL A+GL LIANTAPVAFGALG P++ V Sbjct: 122 AFGAFFEGAAGFGTPVAVTGAILIGLGFSPLAASGLSLIANTAPVAFGALGAPVVTLAAV 181 Query: 184 TGIDPFHIGAMAGRQLPFLSVLVPFWLVAMMDGWKGVKETWPAALVAGGSFAVTQFFTSN 243 T +D + AM GRQLP SV+VPFW+VA G +G E WPA LV G SFA+ QF SN Sbjct: 182 THLDLGQVTAMVGRQLPIFSVMVPFWVVAAFAGLRGTLEVWPAVLVTGLSFAIPQFLVSN 241 Query: 244 YIGPELPDITSALVSIVSLALFLKVWRPKNTETAISMG---------QSAGAMVVNKPSS 294 + GP L D+ +ALV + L F+++W+P+ T + QS GA V + S Sbjct: 242 FHGPWLVDVIAALVCMACLIGFMRIWQPRRIWTNPNFANRHDISLRPQSVGAAVADPVPS 301 Query: 295 GGPVPSE---YSLGQIIRAWSPFLILTVLVTIWTMKPFKA----LFAPGGAFYSLVINFQ 347 +E Y+ Q+I+AW P+LIL V+V IW + FK LF P F+ Sbjct: 302 TAHTNAERPAYTRAQLIKAWMPWLILCVIVFIWGTESFKIPVNNLFLP---------KFE 352 Query: 348 IPHLHQQVLKAAPIVAQPTPMDAVFKFDPLSAGGTAIFIAAIISIFILGVGIKKGIGVFA 407 I LH+ V K P+ A PT AVF F+ L+ GT I +A I+S ++G G I + Sbjct: 353 IDGLHRLVQKMPPVAAAPTIESAVFSFNILTMSGTGILLAGILSGLLMGYGPLSLIKQYG 412 Query: 408 ETLISLKWPILSIGMVLAFAFVTNYSGMSTTLALVLAGTGVMFPFFSPFLGWLGVFLTGS 467 TL ++ +++I +LA +T Y+G+ TL L AGTGV++PFF+ LGWLGV LTGS Sbjct: 413 RTLYVVRNSLITIAAMLALGTLTRYAGLDATLGLAFAGTGVVYPFFAALLGWLGVALTGS 472 Query: 468 DTSSNALFGSLQSTTAQQINVSDTLLVAANTSGGVTGKMISPQSIAVACAATGMVGRESE 527 DT+SN LFG LQ+ TAQQ+ +S L+ AAN+SGGV GKM+ QSI VA AT G E Sbjct: 473 DTASNVLFGGLQTVTAQQLGLSPILMAAANSSGGVMGKMVDAQSIVVASTATNWFGHEGA 532 Query: 528 LFRYTVKHSLIFASVIGIITLLQAYVF 554 + R+ HS++ A ++GI +LQ YVF Sbjct: 533 ILRFVFPHSIVLACLVGIFIMLQVYVF 559 Lambda K H 0.327 0.141 0.424 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: 907 Number of extensions: 42 Number of successful extensions: 3 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: 560 Length of database: 567 Length adjustment: 36 Effective length of query: 524 Effective length of database: 531 Effective search space: 278244 Effective search space used: 278244 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