Align Proton/sodium-glutamate symport protein; Glutamate-aspartate carrier protein (characterized)
to candidate RR42_RS33745 RR42_RS33745 C4-dicarboxylate transporter
Query= SwissProt::P24943 (421 letters) >FitnessBrowser__Cup4G11:RR42_RS33745 Length = 452 Score = 327 bits (839), Expect = 3e-94 Identities = 153/402 (38%), Positives = 256/402 (63%), Gaps = 5/402 (1%) Query: 9 QIFIGLILGIIVGAIFYGNPKVATYLQPIGDIFLRLIKMIVIPIVISSLVVGVASVGDLK 68 Q+ I + GI++G P + + L+P+GDIF+RLIKM+ PI+ +++V+G+A + +K Sbjct: 12 QVLIAVAAGILLGIFM---PHIGSALKPLGDIFIRLIKMVFAPIIFATVVLGIAKMESMK 68 Query: 69 KLGKLGGKTIIYFEIITTIAIVVGLLAANIFQPGTGVNMKSLEKTDIQSYVDTTNEVQHH 128 LG++G + ++YFE+++T A+++G++ N+ QPG G+N+ D +S T +V+H Sbjct: 69 DLGRVGWRALLYFEVLSTFALLLGVIVVNVVQPGHGMNVDPAT-LDTKSIAAYTAQVKHE 127 Query: 129 SMVETFVNIVPKNIFESLTKGDMLPIIFFSVMFGLGVAAIGEKGKPVLQFFQGTAEAMFY 188 +++ +N+VP +I ++L K D+L I+ FSV G+ +A +GE+GKP + A AMF Sbjct: 128 GIMDFLLNLVPMSIMDALAKNDILQILVFSVFMGVALAHLGERGKPFVAALDSFANAMFA 187 Query: 189 VTNQIMKFAPFGVFALIGVTVSKFGVESLIPLSKLVIVVYATMVFFIFVVLGGVAKLFGI 248 + IM+ AP F + TV K+G S+ L KLV +Y T F+ +VLG + ++ G Sbjct: 188 IVGMIMRVAPVAAFGAMSFTVGKYGFGSIASLGKLVATMYGTCALFVLIVLGAICRICGF 247 Query: 249 NIFHIIKILKDELILAYSTASSETVLPKIMEKMENFGCPKAITSFVIPTGYSFNLDGSTL 308 +F+ +K +KDE++ T+SSE+V+P++M K+EN G K + V+P G +FN DG + Sbjct: 248 GLFNFLKYIKDEILTVLGTSSSESVIPQLMRKLENVGVSKPVVGLVVPAGLTFNPDGQCI 307 Query: 309 YQALAAIFIAQLYGIDMPISQQISLLLVLMVTSKGIAGVPGVSFVVLLATLGTVG-IPIE 367 Y +AAIFIAQ + ++ Q +L VL++TSKG AG+ G F+ L ATL ++G IP+ Sbjct: 308 YYTMAAIFIAQATNTPLTLTDQFVVLGVLLLTSKGSAGITGSGFITLAATLASLGKIPVA 367 Query: 368 GLAFIAGIDRILDMARTAVNVIGNSLAAIIMSKWEGQYNEEK 409 G+ + G+DR + AR N IGN++A + ++KW G +E++ Sbjct: 368 GMVLLLGVDRFMSEARAITNTIGNAVATMAIAKWVGALDEDR 409 Lambda K H 0.326 0.143 0.404 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: 439 Number of extensions: 30 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: 421 Length of database: 452 Length adjustment: 32 Effective length of query: 389 Effective length of database: 420 Effective search space: 163380 Effective search space used: 163380 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