Align L-lactate permease (characterized)
to candidate WP_043745478.1 AMB_RS20875 L-lactate permease
Query= SwissProt::P33231 (551 letters) >NCBI__GCF_000009985.1:WP_043745478.1 Length = 547 Score = 758 bits (1958), Expect = 0.0 Identities = 375/551 (68%), Positives = 454/551 (82%), Gaps = 4/551 (0%) Query: 1 MNLWQQNYDPAGNIWLSSLIASLPILFFFFALIKLKLKGYVAASWTVAIALAVALLFYKM 60 M W Q YDPAGN+WLSSLIA++PI+FFF AL LKLKG+VA + TV +++AVA++FYKM Sbjct: 1 MQAWMQVYDPAGNLWLSSLIAAIPIIFFFVALAILKLKGHVAGTITVLLSIAVAIVFYKM 60 Query: 61 PVANALASVVYGFFYGLWPIAWIIIAAVFVYKISVKTGQFDIIRSSILSITPDQRLQMLI 120 PVA A+ + V GF +GLWPIAWIII AVF+YK++VKTGQF+IIRSS++SIT DQRLQML+ Sbjct: 61 PVAAAVMAGVQGFLFGLWPIAWIIIGAVFLYKVTVKTGQFEIIRSSVVSITADQRLQMLM 120 Query: 121 VGFCFGAFLEGAAGFGAPVAITAALLVGLGFKPLYAAGLCLIVNTAPVAFGAMGIPILVA 180 +GF FGAFLEGAAGFGAPVAITAALLVGLGF PLYAAGLCLI NTAPVAFGAMGIPI+VA Sbjct: 121 IGFSFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGAMGIPIIVA 180 Query: 181 GQVTGIDSFEIGQMVGRQLPFMTIIVLFWIMAIMDGWRGIKETWPAVVVAGGSFAIAQYL 240 GQV+G+D+F+IG M GRQLP + + V FWI+ IMDG++G++ETWPA++VAGGSFA + Sbjct: 181 GQVSGLDAFKIGAMAGRQLPLLAVFVPFWIIFIMDGFKGVRETWPAILVAGGSFAFGVWF 240 Query: 241 SSNFIGPELPDIISSLVSLLCLTLFLKRWQPVRVFRFGDLGASQVDMTLAHTGYTAGQVL 300 +SN+IGPELPDI S+L+SL+C+T+FLK WQP +FRF + G D +H YT GQV Sbjct: 241 TSNYIGPELPDITSALISLVCITVFLKFWQPKNIFRFKEEGE---DEKHSH-DYTTGQVA 296 Query: 301 RAWTPFLFLTATVTLWSIPPFKALFASGGALYEWVINIPVPYLDKLVARMPPVVSEATAY 360 RAW PFL LTA VT+WS+ PFKA+FA GG L IN VP L LVA++PP+V+ A A Sbjct: 297 RAWAPFLILTAVVTVWSLKPFKAMFAKGGELVFTNINWEVPALHNLVAKVPPIVAAAKAV 356 Query: 361 AAVFKFDWFSATGTAILFAALLSIVWLKMKPSDAISTFGSTLKELALPIYSIGMVLAFAF 420 AV+ + SATGTAIL +A+++I+ L MK S+ + TFG TL EL PIY+IG VLAFA+ Sbjct: 357 PAVYTLNLVSATGTAILISAIITIIMLGMKGSEGLKTFGETLNELKRPIYTIGTVLAFAY 416 Query: 421 ISNYSGLSSTLALALAHTGHAFTFFSPFLGWLGVFLTGSDTSSNALFAALQATAAQQIGV 480 ++N SGLS+TLAL L G + FFSP LGWLGVFLTGSDTSSNALF ALQAT A Q+G+ Sbjct: 417 VANASGLSTTLALLLTGAGDFYPFFSPVLGWLGVFLTGSDTSSNALFGALQATTAHQLGI 476 Query: 481 SDLLLVAANTTGGVTGKMISPQSIAIACAAVGLVGKESDLFRFTVKHSLIFTCIVGVITT 540 SD+L+VAANTTGGVTGKMISPQSIA+ACAAVGLVG E++LFRFT+KHS+ F CI+GVITT Sbjct: 477 SDILMVAANTTGGVTGKMISPQSIAVACAAVGLVGHEANLFRFTLKHSVFFVCIIGVITT 536 Query: 541 LQAYVLTWMIP 551 LQAYVLTWMIP Sbjct: 537 LQAYVLTWMIP 547 Lambda K H 0.328 0.140 0.436 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: 1001 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: 551 Length of database: 547 Length adjustment: 36 Effective length of query: 515 Effective length of database: 511 Effective search space: 263165 Effective search space used: 263165 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 (21.8 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