Align Proton/sodium-glutamate symport protein; Glutamate-aspartate carrier protein (characterized)
to candidate Pf1N1B4_4413 Aerobic C4-dicarboxylate transporter for fumarate, L-malate, D-malate, succunate
Query= SwissProt::P24943 (421 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4413 Length = 451 Score = 320 bits (820), Expect = 6e-92 Identities = 153/402 (38%), Positives = 250/402 (62%), Gaps = 5/402 (1%) Query: 9 QIFIGLILGIIVGAIFYGNPKVATYLQPIGDIFLRLIKMIVIPIVISSLVVGVASVGDLK 68 Q+ I +ILG IVG P+ T L+P+GD F++LIKM++ P++ ++V G+A + ++K Sbjct: 11 QVLIAVILGAIVGVFV---PETGTALKPLGDAFIKLIKMLLAPVIFLTVVTGIARMENMK 67 Query: 69 KLGKLGGKTIIYFEIITTIAIVVGLLAANIFQPGTGVNMKSLEKTDIQSYVDTTNEVQHH 128 +LG++G + +IYFE+++T+A+VVGL+ ++F+PG G+N+ + D S T V+H Sbjct: 68 ELGRVGFRALIYFEVVSTLALVVGLVVVDVFKPGAGMNI-DVASLDTSSLATYTTAVKHA 126 Query: 129 SMVETFVNIVPKNIFESLTKGDMLPIIFFSVMFGLGVAAIGEKGKPVLQFFQGTAEAMFY 188 S ++ +NI+P I ++ KG++L I+ FS++ G+ +A +G + K + + MF Sbjct: 127 SFMDFVMNIIPDTIVDAFAKGNVLQILLFSILLGVALAHVGPRAKVFVDTLDSLMQGMFR 186 Query: 189 VTNQIMKFAPFGVFALIGVTVSKFGVESLIPLSKLVIVVYATMVFFIFVVLGGVAKLFGI 248 + N +M+ AP G F I T+ K+G SL L KL+ VY T F+ VLG + + G Sbjct: 187 IVNMVMRLAPIGAFGAIAFTIGKYGFGSLFSLGKLMACVYLTCAVFVIFVLGPICRYSGF 246 Query: 249 NIFHIIKILKDELILAYSTASSETVLPKIMEKMENFGCPKAITSFVIPTGYSFNLDGSTL 308 +++ +K +K+EL T+SSE+VLP+++ KME G K + +IP+G +FN DG + Sbjct: 247 SLWKFLKFIKEELFTVLGTSSSESVLPQMISKMEKAGVSKPVAGMIIPSGLTFNPDGQAI 306 Query: 309 YQALAAIFIAQLYGIDMPISQQISLLLVLMVTSKGIAGVPGVSFVVLLATLGTVG-IPIE 367 Y +AAIFIAQ + ++ Q+ +L VLM TSKG AGV G F++L ATL ++G IP+ Sbjct: 307 YYTIAAIFIAQATNTPLTLTDQLIVLAVLMFTSKGSAGVTGSGFIILAATLSSLGTIPVA 366 Query: 368 GLAFIAGIDRILDMARTAVNVIGNSLAAIIMSKWEGQYNEEK 409 G+ + G+DR + AR N IGN + + ++KW G + K Sbjct: 367 GMVLLLGVDRFMSEARAITNTIGNGVGTMAIAKWVGALDTVK 408 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: 410 Number of extensions: 23 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: 421 Length of database: 451 Length adjustment: 32 Effective length of query: 389 Effective length of database: 419 Effective search space: 162991 Effective search space used: 162991 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