Align Monocarboxylic acid transporter (characterized)
to candidate WP_011386681.1 AMB_RS21920 cation acetate symporter
Query= SwissProt::Q8NS49 (551 letters) >NCBI__GCF_000009985.1:WP_011386681.1 Length = 554 Score = 397 bits (1021), Expect = e-115 Identities = 232/537 (43%), Positives = 319/537 (59%), Gaps = 31/537 (5%) Query: 23 ISVFVVFIIVTMTVVLRVGKSTSESTDFYTGGASFSGTQNGLAIAGDYLSAASFLGIVGA 82 I +FV F+++T+ + K T + DFYT G +G QNGLAIAGD++SAASFLG+ Sbjct: 41 ILMFVGFVLLTLGITWWASKRTKSAADFYTAGGGITGFQNGLAIAGDFMSAASFLGVTAL 100 Query: 83 ISLNGYDGFLYSIGFFVAWLVALLLVAEPLRNVGRFTMADVLSFRLRQKPVRVAAACGTL 142 + G DG +Y++G V W + L L+AEPLRN+G++T ADV+++RL + PVR AA +L Sbjct: 101 LYGTGLDGMVYAVGVVVGWPLMLFLIAEPLRNLGKYTFADVVAYRLAKVPVRTYAAFSSL 160 Query: 143 AVTLFYLIAQMAGAGSLVSVLLDIHEFKWQAVVVGIVGIVMIAYVLLGGMKGTTYVQMIK 202 V +FYLIAQM GAG L+ +L + ++ + +VG G++MI YV GGM TT+VQ+IK Sbjct: 161 TVVVFYLIAQMVGAGQLIKLLFGM-DYLYALFLVG--GLMMI-YVTFGGMAATTWVQIIK 216 Query: 203 AVLLVGGVAIMTVLTFVKVSGGLTTLLNDAVEKHAASDYAATKGYDPTQILEPGLQYGAT 262 AVLL+ G M + + AV+ KG I+ PGL + Sbjct: 217 AVLLLSGATFMAGAVLSRFGFSPEAMFAKAVQ---------VKG--SNAIMSPGLLF--- 262 Query: 263 LTTQLDFISLALALCLGTAGLPHVLMRFYTVPTAKEARKSVTWAIVLIGAFYLMTLVLGY 322 +D ISLA+AL GTAGLPH+LMRF+TVP AKEARKSV +A IG FY++ +V+G Sbjct: 263 -KDPIDTISLAMALAFGTAGLPHILMRFFTVPDAKEARKSVFYATAFIGFFYVLAVVIGI 321 Query: 323 GAAALVGPDRVIAAPGAA-----NAAAPLLAFELGGSIFMALISAVAFATVLAVVAGLAI 377 GA ALV D A G A N AA LA +GG +F+ ISAVAFAT+LAVVAGL + Sbjct: 322 GAIALVATDPTYLADGKALKGGGNMAAVWLAHAVGGDLFLGFISAVAFATILAVVAGLTL 381 Query: 378 TASAAVGHDIYNAVIRNGQSTEAEQVRVSRITVVVIGLISIVLGILAMTQNVAFLVALAF 437 ++A+ HD+Y V G + E ++R+SR+ + +G+I+I+LG+L QN+A+L L Sbjct: 382 AGASAISHDLYANVFARGHAKEETELRISRLASLALGVIAIILGMLFEKQNIAYLAGLTL 441 Query: 438 AVAASANLPTILYSLYWKKFNTTGAVAAIYTGLISALLLIFLSPAVSGNDSAMVPGADWA 497 A+AASAN P +L S+ W + GA+ GL+SA++L L PAV V G Sbjct: 442 AIAASANFPLLLLSMLWPGLTSRGAILGGVAGLVSAVVLTVLGPAV----WKAVLGNPQP 497 Query: 498 IFPLKNPGLVSIPLAFIAGWIGTLVGKPDNMDDLAAEME---VRSLTGVGVEKAVDH 551 IFP NP L S+ F A W ++ + AE VRS TG+G E H Sbjct: 498 IFPWGNPALFSVAAGFAATWFFSVTDGSERAVREKAEFNAQFVRSQTGLGAEGVSAH 554 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: 700 Number of extensions: 32 Number of successful extensions: 7 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: 554 Length adjustment: 36 Effective length of query: 515 Effective length of database: 518 Effective search space: 266770 Effective search space used: 266770 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 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