Align L-lactate and D-lactate permease (lctP family) (characterized)
to candidate WP_041376782.1 PNAP_RS17340 L-lactate permease
Query= reanno::pseudo5_N2C3_1:AO356_07550 (564 letters) >NCBI__GCF_000015505.1:WP_041376782.1 Length = 553 Score = 500 bits (1288), Expect = e-146 Identities = 268/564 (47%), Positives = 363/564 (64%), Gaps = 16/564 (2%) Query: 4 WQQLYSPLGSLGLSALAAVIPIVFFFLALAVFRLKGHVAGSITLALAIAVAIFAFNMPAD 63 WQQ+Y P G++ +S L A IP+V + L +K H+A + L AI VA+FA+ MPAD Sbjct: 3 WQQIYDPFGNMFISTLLAAIPVVVMLVCLGFLHIKAHIAAGLGLIAAILVAVFAYGMPAD 62 Query: 64 MAFAAAGYGFAYGLWPIAWIIVAAVFLYKLTVKSGQFEVIRSSVLSITDDQRLQVLLIGF 123 MA AA YG GL PI WI++ +FL +L ++G F++++ S+ IT D+RLQ+LLI F Sbjct: 63 MAGRAALYGGFTGLLPIGWIVLNIIFLQQLAEQNGSFKILQDSLSGITADRRLQLLLIAF 122 Query: 124 CFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGALGIPIIVAGQV 183 CFGAF EGAAGFG PVA+TA +L+GLGF+PL A+GL LIANTAPVAFGALG P+I +V Sbjct: 123 CFGAFFEGAAGFGTPVAVTAGILIGLGFSPLAASGLSLIANTAPVAFGALGTPVITLAKV 182 Query: 184 TGIDAFKIGAMTGRQLPLLSLFVPFWLVFMMDGLRGVRETWPAALVAGLSFAITQYFTSN 243 G D ++ AM GRQLPL SL VPFWL++ G + + E WPA LV GLSFAI QY SN Sbjct: 183 HGYDLMEVTAMIGRQLPLFSLMVPFWLIWAFAGRKAMMEIWPAILVTGLSFAIPQYLVSN 242 Query: 244 FIGPELPDITSALASLISLTLFLKVWQPKRT-AGAQIAGATSSATVTASVGGFGQPRSTV 302 FIGPEL DI +A+ S++SL LFL+VWQPK+ + G SA +P + + Sbjct: 243 FIGPELVDIIAAIVSMVSLVLFLRVWQPKKIWTSPSLKGHDVSAHE-------AKPPAPI 295 Query: 303 ASPYSLGEIIKAWSPFLILTVLVTIWTLKPFKAMFAAGGSMYGWVFNFAIPHLDQMVIKV 362 + +I+AW+P++IL+V V +W L P KA S++ +F + L ++ KV Sbjct: 296 VI-HDRAALIRAWTPWVILSVFVFVWGLPPVKAWL---NSIF--APSFPMAGLHNLIEKV 349 Query: 363 APIVINPTAIPAVFKLDPISATGTAIFFSALISMLVLKINIKTGLTTFKETLFELRWPIL 422 P+V P AV+ L+ +SATGT I SA+IS L++K N TF TL+ +R+ +L Sbjct: 350 PPVVPTPHKESAVYVLNLLSATGTGILISAIISALIMKYNPIEIAKTFFRTLWLVRYSLL 409 Query: 423 SIGMVLAFAFVTNYSGMSSTMALVLAGTGAAFPFFSPFLGWLGVFLTGSDTSSNALFSSL 482 +I ++LA +T YSG +T+ L A +G +PFF +GW+GV +TGSDT+SN LF + Sbjct: 410 TIVLMLALGTLTRYSGTDTTLGLAFANSGVFYPFFGTLMGWIGVAMTGSDTASNVLFGGM 469 Query: 483 QATTAHQIGVNDTLLVAANTSGGVTGKMISPQSIAVACAATGLVGKESDLFRFTLKHSLF 542 Q A Q+G++ L+ AAN+SGGV GKMI QSI VA AT E D+ R+ HS+ Sbjct: 470 QRVAAEQLGLSPNLMGAANSSGGVMGKMIDAQSIVVASTATKWFNHEGDILRYVFIHSVV 529 Query: 543 FATIVGLITLAQAY-W-FTGMLVH 564 A +VGL QAY W FT M+VH Sbjct: 530 LACLVGLFVSLQAYVWPFTLMVVH 553 Lambda K H 0.327 0.139 0.422 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: 826 Number of extensions: 37 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: 564 Length of database: 553 Length adjustment: 36 Effective length of query: 528 Effective length of database: 517 Effective search space: 272976 Effective search space used: 272976 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