Align Monocarboxylic acid transporter (characterized)
to candidate WP_035949051.1 N798_RS12935 cation acetate symporter
Query= SwissProt::Q8NS49 (551 letters) >NCBI__GCF_000768675.1:WP_035949051.1 Length = 551 Score = 630 bits (1625), Expect = 0.0 Identities = 334/561 (59%), Positives = 415/561 (73%), Gaps = 20/561 (3%) Query: 1 MNSTILLAQDAVSEGVGNPILNISVFVVFIIVTMTVVLRVGKSTSESTDFYTGGASFSGT 60 M S + A + VG+P LNI++F F++VT+ V++++ + +FYT FSG Sbjct: 1 MTSFLSAGLPAEATKVGSPALNIAIFAGFVLVTLVVIVKLASGKKSAGEFYTASGGFSGR 60 Query: 61 QNGLAIAGDYLSAASFLGIVGAISLNGYDGFLYSIGFFVAWLVALLLVAEPLRNVGRFTM 120 QNG+AIAGDYLSAASFLGI GAI+L GYDGFLYSIGF VAWLVALLLVAE +RN GR TM Sbjct: 61 QNGIAIAGDYLSAASFLGIAGAIALQGYDGFLYSIGFLVAWLVALLLVAELMRNTGRLTM 120 Query: 121 ADVLSFRLRQKPVRVAAACGTLAVTLFYLIAQMAGAGSLVSVLLDIHEFKWQAVVVGIVG 180 ADVLS+RL+Q+PVR+A A LAV+ FYL+AQMAGAG LVS+LL + Q +V+ +VG Sbjct: 121 ADVLSYRLKQRPVRIATATSVLAVSFFYLLAQMAGAGGLVSLLLGVEGEGAQNIVIAVVG 180 Query: 181 IVMIAYVLLGGMKGTTYVQMIKAVLLVGGVAIMTVLTFVKVSGGLTTLLNDAVEKHAASD 240 IVMIAYVL+GGM+GTT+VQ+IKAVLL+ AIMTV K L+ L + A++ + Sbjct: 181 IVMIAYVLIGGMRGTTWVQIIKAVLLIAATAIMTVWVLGKYGFNLSGLFDAAIQNNPKVG 240 Query: 241 YAATKGYDPTQILEPGLQYGATLTTQLDFISLALALCLGTAGLPHVLMRFYTVPTAKEAR 300 ++LEPG++YG + TT++DFISL+LAL LGTAGLPHVL RFYTVPT+K+AR Sbjct: 241 ---------EKLLEPGVKYGVSTTTKIDFISLSLALVLGTAGLPHVLQRFYTVPTSKQAR 291 Query: 301 KSVTWAIVLIGAFYLMTLVLGYGAAALVGPDRVIAAPGAANAAAPLLAFELGGSIFMALI 360 KSV WAI LIG FYL+TLV+GYGA ALVG + + APG ANAAAPLLAFELGGS F+ ++ Sbjct: 292 KSVEWAIWLIGGFYLLTLVVGYGAGALVGAEEINKAPGKANAAAPLLAFELGGSPFLGIV 351 Query: 361 SAVAFATVLAVVAGLAITASAAVGHDIYNAVIRNGQSTEAEQVRVSRITVVVIGLISIVL 420 S +AFAT+LAVVAGL ITASA HDIY VI+ G +T +VRV+RI+ V IG+I+I+ Sbjct: 352 SGIAFATILAVVAGLTITASATFAHDIYKEVIKRGDTTSDNEVRVARISAVAIGIIAILG 411 Query: 421 GILAMTQNVAFLVALAFAVAASANLPTILYSLYWKKFNTTGAVAAIYTGLISALLLIFLS 480 G+ A +QN+AFLVALAFAVAASANLPTILYSL+WK+FNT GA+ +IY GLIS + LI S Sbjct: 412 GMFAKSQNIAFLVALAFAVAASANLPTILYSLFWKRFNTRGALWSIYGGLISTIGLIIFS 471 Query: 481 PAVSGN--------DSAMV--PGADWAIFPLKNPGLVSIPLAFIAGWIGTLVGKPDNMDD 530 P VSG +M+ P D++ FPL NPGLV+IPLAF GW+GT+ N Sbjct: 472 PVVSGKAPLPGTTVSPSMITNPDIDFSWFPLDNPGLVTIPLAFFLGWLGTVTSSEYNAQK 531 Query: 531 LAAEMEVRSLTGVGVEKAVDH 551 AEMEVRSLTG GV KA+DH Sbjct: 532 Y-AEMEVRSLTGHGVAKALDH 551 Lambda K H 0.324 0.138 0.393 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: 754 Number of extensions: 33 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: 551 Length of database: 551 Length adjustment: 36 Effective length of query: 515 Effective length of database: 515 Effective search space: 265225 Effective search space used: 265225 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.5 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