Align L-malate/citrate:H+ symporter (electroneutral) (characterized)
to candidate BWI76_RS04430 BWI76_RS04430 citrate carrier protein
Query= TCDB::P94363 (450 letters) >FitnessBrowser__Koxy:BWI76_RS04430 Length = 446 Score = 204 bits (520), Expect = 4e-57 Identities = 127/432 (29%), Positives = 232/432 (53%), Gaps = 24/432 (5%) Query: 29 MNIKVGIIPLPVYALLFILITVFVMHHDVKSDILTSIAVMAFFGFTFAQIGKSIPIVRS- 87 + K+ +PLP+YA I + + ++ + +DI+ A+M G F +IGK +PI Sbjct: 19 LGFKIFGMPLPLYAFALITLLLSHFYNALPTDIVGGFAIMFIIGAVFGEIGKRLPIFNKY 78 Query: 88 IGGPAILATFIPSAVVYYHLLPNDIVKSTTEFTENSNFLYLFIAGIVVGSILGMKRETLV 147 IGG ++ + + VY + +++ T + SNFL LFIA ++ G+IL + R+ L+ Sbjct: 79 IGGAPVMIFLVAAYFVYAGIFTQKEIEAITNVMDKSNFLNLFIAVLITGAILSVNRKLLL 138 Query: 148 KAFMKIFIPLIVGSVTAAIVGLAVGTLLGLGFQHTLLYIVIPIMAGGVGEGAIPLSIGYS 207 K+ + +++G + A+I G+ +G G+ ++ V+PIM GG G GA+PLS Y Sbjct: 139 KSLLGYIPTILMGILGASIFGILIGLCFGISVDRIMMLYVLPIMGGGNGAGAVPLSEIYH 198 Query: 208 DIMPISQGEAFALVLPSIMLGSLCAIILAGLLNRIGKKKPEWTGNGKVDRSEEESPALEE 267 + S+ E ++ + + + ++ AI+ A LL+ IGKK +G G++ R + S +E+ Sbjct: 199 SVTGRSREEYYSTAIAILTIANIFAIVFAALLDIIGKKHTWLSGEGELVR--KASFKVED 256 Query: 268 SQSGQQMFNLSLFASGGILAVSLYL------------VGMLAHDFFGFPAPVAMLLLAVL 315 + Q+ + A G +LA + +L +G ++ +F + M+L+ Sbjct: 257 DEKAGQITHRET-AVGLVLATTCFLLAYVIAKKILPSIGGVSIHYFAW-----MVLIVAA 310 Query: 316 IKLFRLVPASIENGAFGVSRFFSTAVTYPLLFAIGVSMTPWDKLVAAFNLSNIITILSVV 375 + L I+ GA +S FFS + + L+ +GV T +++ A +N++ I +V+ Sbjct: 311 LNASGLCSPEIKAGAKRLSDFFSKQLLWVLMVGVGVCYTDLQEIIDAITFANVV-IAAVI 369 Query: 376 VTMMAVGFFTGKWL-NMYPIETAI-INACHSGQGGTGDVAILSAAERLELMPFAQVSTRI 433 V VG G WL +PIE+AI C + +GG+GD+ +LSA R+ L+ +AQ+S+R+ Sbjct: 370 VVGAVVGAAVGGWLIGFFPIESAITAGLCMANRGGSGDLEVLSACNRMNLISYAQISSRL 429 Query: 434 GGAITVSLTLLL 445 GG I + + ++ Sbjct: 430 GGGIVLVIASIV 441 Lambda K H 0.326 0.141 0.412 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: 594 Number of extensions: 36 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: 450 Length of database: 446 Length adjustment: 33 Effective length of query: 417 Effective length of database: 413 Effective search space: 172221 Effective search space used: 172221 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 (21.6 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