Align L-malate/citrate:H+ symporter (electroneutral) (characterized)
to candidate RR42_RS29530 RR42_RS29530 malate permease
Query= TCDB::P94363 (450 letters) >FitnessBrowser__Cup4G11:RR42_RS29530 Length = 451 Score = 512 bits (1318), Expect = e-149 Identities = 258/427 (60%), Positives = 329/427 (77%), Gaps = 6/427 (1%) Query: 22 ENWFAKAMNIKVGIIPLPVYALLFILITVFVMHHDVKSDILTSIAVMAFFGFTFAQIGKS 81 E W+ K M ++GIIPLPVY +L LI F + V +I +IAV+AFFGFT A+IGK Sbjct: 25 EGWW-KLMEFRIGIIPLPVYVILLALIAGFAVTGKVPGEISMAIAVLAFFGFTCAEIGKR 83 Query: 82 IPIVRSIGGPAILATFIPSAVVYYHLLPNDIVKSTTEFTENSNFLYLFIAGIVVGSILGM 141 +PI+R+IG AI ATFIPSA+ YYHLLP I+ TTEFT+++NFLYLFIA I+VGSIL M Sbjct: 84 LPIIRNIGAAAIFATFIPSALTYYHLLPKPILSLTTEFTKSTNFLYLFIASIIVGSILSM 143 Query: 142 KRETLVKAFMKIFIPLIVGSVTAAIVGLAVGTLLGLGFQHTLLYIVIPIMAGGVGEGAIP 201 R L++ F+KIFIPL VGS+ A IVG AVGT LGLG HT YIV+PIMAGGVGEGAIP Sbjct: 144 DRRVLIQGFIKIFIPLAVGSIAAGIVGTAVGTALGLGAHHTFFYIVVPIMAGGVGEGAIP 203 Query: 202 LSIGYSDIMPISQGEAFALVLPSIMLGSLCAIILAGLLNRIGKKKPEWTGNGKVDRSEEE 261 LSIGYS+I+ + QG+ FA VLP +MLGSL AIIL+G+L+++GK+ P TG G++ EE+ Sbjct: 204 LSIGYSEILHLPQGDLFAQVLPPVMLGSLTAIILSGVLDKVGKRFPHLTGEGRLQVGEED 263 Query: 262 --SPALEESQSGQQMFNLSLFASGGILAVSLYLVGMLAHDFFGFPAPVAMLLLAVLIKLF 319 P EE + +++ A+ GI A++LYL+G++ + FG PAPVAML LAVL+K+ Sbjct: 264 EMDPVQEEIRG---HIDVTHIAAAGITAITLYLLGLMCRNLFGLPAPVAMLFLAVLVKIT 320 Query: 320 RLVPASIENGAFGVSRFFSTAVTYPLLFAIGVSMTPWDKLVAAFNLSNIITILSVVVTMM 379 R V ++ GAF V +FFSTAVTYPLLFAIGV+MTPWDKL+AAF L+NI+TI++ V T+M Sbjct: 321 RAVSPPLQEGAFVVYKFFSTAVTYPLLFAIGVAMTPWDKLIAAFTLANIVTIVATVTTLM 380 Query: 380 AVGFFTGKWLNMYPIETAIINACHSGQGGTGDVAILSAAERLELMPFAQVSTRIGGAITV 439 GF + L M+PI+TAI+NACHSGQGGTGDVAIL+AA R+ LMPFAQ++TRIGGAI V Sbjct: 381 GTGFVVARMLKMHPIDTAIVNACHSGQGGTGDVAILTAANRMTLMPFAQIATRIGGAIVV 440 Query: 440 SLTLLLL 446 +LTL++L Sbjct: 441 TLTLIVL 447 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: 663 Number of extensions: 32 Number of successful extensions: 2 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: 451 Length adjustment: 33 Effective length of query: 417 Effective length of database: 418 Effective search space: 174306 Effective search space used: 174306 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