Align Uncharacterized protein (characterized, see rationale)
to candidate Ga0059261_0201 Ga0059261_0201 Na+/H+-dicarboxylate symporters
Query= uniprot:A0A0C4Y5S4 (436 letters) >FitnessBrowser__Korea:Ga0059261_0201 Length = 455 Score = 442 bits (1137), Expect = e-128 Identities = 227/432 (52%), Positives = 305/432 (70%), Gaps = 11/432 (2%) Query: 5 RLPTLIFIAMLLGVLAGTAAHH-----YAPDPAAA----KSIADHLSILTDVFLRMIKMI 55 +L T I IA++ G + G H+ + D A A K++A + SI+T +FLR+IKMI Sbjct: 4 KLTTFILIALVAGAIVGLGLHYGIHNSFGADSAGAEAELKTVAGYFSIVTTIFLRLIKMI 63 Query: 56 IGPLVFATLVSGIASMGDGKAVGRIGMKAMAWFIAASITSLLLGLLMANLLRPGDGMNLA 115 I PLVFATLV+GIA MGD A+GR+G +A+AWFI AS+ SL LGL++ NL +PG G+N Sbjct: 64 IAPLVFATLVAGIAHMGDTAALGRVGGRAVAWFICASLVSLTLGLILVNLFQPGVGLNFP 123 Query: 116 LPAADAASNLKTGALNLREFIAHMFPKSFVEAMATNEILQIVVFSLFFGFALGTLKDGIG 175 LP DA S ++ A NL++F H+FP S +EAMA NEILQIV+FSLF G A+ + + Sbjct: 124 LPPVDATSGVEKAAFNLKDFFTHVFPASGIEAMAKNEILQIVIFSLFIGVAITAVGEK-A 182 Query: 176 KPVLAGIEGLSHVMLKITNYVMAFAPVGVFGAVAAVITAEGLGVLVVYAKLLGAVYLSLA 235 KP+++ +E L HVML++TNYVM FAP+ VF AVA + G ++ A +G Y+++ Sbjct: 183 KPLVSAVEALVHVMLQVTNYVMRFAPIAVFAAVAGTLAERGPAIIGNLAYFMGTFYIAMF 242 Query: 236 LLWVALIAGGYFFLGRDVFRLLKMVRAPLMIGFATASSESAYPKVIEQLGRFGVKERITG 295 LW LI Y +G+ L++ +R PL++ F+TASSE+AYP+ +E L RFGV RI Sbjct: 243 TLWALLIGVCYLIVGKRTGLLVRYIRDPLLLAFSTASSEAAYPRTLEALDRFGVPPRIAS 302 Query: 296 FVLPLGYSFNLDGSIMYTSFAALFVAQVYGIHLSLSQQVTMLLVLLVTSKGIAGVPRASL 355 FVLPLGYSFNLDGS++Y +FA +F+AQ YGI L+L Q++TMLLVL++TSKGIAGVPRASL Sbjct: 303 FVLPLGYSFNLDGSMIYMTFATIFIAQAYGIDLTLGQEITMLLVLMITSKGIAGVPRASL 362 Query: 356 VVVAAVLPMFGLPEAGILLVLGIDHVLDMGRTVTNVLGNAIATTVVAKSEGAIGAPV-PE 414 VV+AA L F +PEAG+LL+LGIDH LDMGR+ TNV+GNA+A+ VVAK EG P+ P Sbjct: 363 VVIAATLGFFDIPEAGLLLILGIDHFLDMGRSATNVVGNAVASAVVAKWEGGRLDPIEPA 422 Query: 415 EADDPAADGNRG 426 + + P A G Sbjct: 423 DIEPPHAPTGGG 434 Lambda K H 0.325 0.141 0.401 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: 488 Number of extensions: 16 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: 436 Length of database: 455 Length adjustment: 32 Effective length of query: 404 Effective length of database: 423 Effective search space: 170892 Effective search space used: 170892 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 (21.6 bits) S2: 51 (24.3 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