Align Na(+)-malate symporter; Sodium-dependent malate transporter (characterized)
to candidate BWI76_RS04430 BWI76_RS04430 citrate carrier protein
Query= SwissProt::O05256 (448 letters) >FitnessBrowser__Koxy:BWI76_RS04430 Length = 446 Score = 262 bits (669), Expect = 2e-74 Identities = 149/438 (34%), Positives = 243/438 (55%), Gaps = 11/438 (2%) Query: 14 QKDSQEKNLFQKIWSWEIGVIPLPLYTVLAVIIILAAYYNELPANMLGGFAIIMILGVFL 73 Q S EK I ++I +PLPLY + ++L+ +YN LP +++GGFAI+ I+G Sbjct: 6 QAPSAEKKGVSDILGFKIFGMPLPLYAFALITLLLSHFYNALPTDIVGGFAIMFIIGAVF 65 Query: 74 GDIGQRIPIL-KDIGGPAILSLFVPSFLVFYNVLNSTSLDAVTNLMKTSNFLYFYIACLV 132 G+IG+R+PI K IGG ++ V ++ V+ + ++A+TN+M SNFL +IA L+ Sbjct: 66 GEIGKRLPIFNKYIGGAPVMIFLVAAYFVYAGIFTQKEIEAITNVMDKSNFLNLFIAVLI 125 Query: 133 VGSILGMNRIVLIQGFIRMFVPLVAGTIAAVAAGILVGFIFGYSAYDSFFFVVVPIIAGG 192 G+IL +NR +L++ + ++ G + A GIL+G FG S V+PI+ GG Sbjct: 126 TGAILSVNRKLLLKSLLGYIPTILMGILGASIFGILIGLCFGISVDRIMMLYVLPIMGGG 185 Query: 193 IGEGILPLSIAYSQILGSSADVFVSQLVPAAIIGNVFAIICAALMKKLGDKRPDLNGNGR 252 G G +PLS Y + G S + + S + I N+FAI+ AAL+ +G K L+G G Sbjct: 186 NGAGAVPLSEIYHSVTGRSREEYYSTAIAILTIANIFAIVFAALLDIIGKKHTWLSGEGE 245 Query: 253 LVKSKKANEIFNQKEAEAKIDFKLMGAGVLLACTFFIFGGLLEKFIF--IPGAIL----- 305 LV +KA+ E +I + G++LA T F+ ++ K I I G + Sbjct: 246 LV--RKASFKVEDDEKAGQITHRETAVGLVLATTCFLLAYVIAKKILPSIGGVSIHYFAW 303 Query: 306 MIISAAAVKYANILPKKMEEGAYQLYKFISSSFTWPLMVGLGILFIPLDDVASVISIPFV 365 M++ AA+ + + +++ GA +L F S W LMVG+G+ + L ++ I+ V Sbjct: 304 MVLIVAALNASGLCSPEIKAGAKRLSDFFSKQLLWVLMVGVGVCYTDLQEIIDAITFANV 363 Query: 366 IICISVVIAMIGSGYFVGKLMNMYPVESAIVT-CCHSGLGGTGDVAILSASGRMGLMPFA 424 +I +V+ + G L+ +P+ESAI C + GG+GD+ +LSA RM L+ +A Sbjct: 364 VIAAVIVVGAVVGAAVGGWLIGFFPIESAITAGLCMANRGGSGDLEVLSACNRMNLISYA 423 Query: 425 QISTRLGGAGTVICATVL 442 QIS+RLGG ++ A+++ Sbjct: 424 QISSRLGGGIVLVIASIV 441 Lambda K H 0.328 0.145 0.427 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: 627 Number of extensions: 35 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: 448 Length of database: 446 Length adjustment: 33 Effective length of query: 415 Effective length of database: 413 Effective search space: 171395 Effective search space used: 171395 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 (21.7 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