Align Proton/glutamate-aspartate symporter; Glutamate-aspartate carrier protein; Proton-glutamate-aspartate transport protein (characterized)
to candidate GFF3718 PS417_19030 sodium:dicarboxylate symporter
Query= SwissProt::P21345 (437 letters) >FitnessBrowser__WCS417:GFF3718 Length = 425 Score = 467 bits (1201), Expect = e-136 Identities = 227/412 (55%), Positives = 315/412 (76%), Gaps = 5/412 (1%) Query: 1 MKNIKFSLAWQILFAMVLGILLGSYLHYHSDSRDWLVVNLLSPAGDIFIHLIKMIVVPIV 60 M + +L WQI+ ++ GI +G+ LH +SR WLV NLL PAGDIFI L+KMIVVPIV Sbjct: 1 MHTPRIALVWQIMIGLLAGIAIGALLHQLPESRPWLVDNLLQPAGDIFIKLMKMIVVPIV 60 Query: 61 ISTLVVGIAGVGDAKQLGRIGAKTIIYFEVITTVAIILGITLANVFQPGAGVDMSQLATV 120 + +VVGIAG GD K LGRIGA+++ YF ITT+AII+G+ L N+ +PGAG ++S L Sbjct: 61 FACMVVGIAGHGDGKSLGRIGARSLGYFFCITTLAIIVGLVLGNLLKPGAGTELSSLHAA 120 Query: 121 DISKYQSTTEAVQSSSHGIMGTILSLVPTNIVASMAKGEMLPIIFFSVLFGLGLSSLPAT 180 I T + H + I+ ++P N++++MA+G +L ++FF+V+FGLG++ LPA Sbjct: 121 SI-----TLPTSSGAGHSLGQIIVGIIPDNVISAMAQGSLLSVLFFAVMFGLGVARLPAE 175 Query: 181 HREPLVTVFRSISETMFKVTHMVMRYAPVGVFALIAVTVANFGFSSLWPLAKLVLLVHFA 240 ++P++ + R +S+ MFKVT M+M Y+P+GVF +IAVTVANFGF SL PLAKL+++ + + Sbjct: 176 RKDPVIALLRGVSDAMFKVTSMIMAYSPIGVFGMIAVTVANFGFGSLLPLAKLIMVSYVS 235 Query: 241 ILFFALVVLGIVARLCGLSVWILIRILKDELILAYSTASSESVLPRIIEKMEAYGAPVSI 300 I FF LVVL +VARLCG++++ L+R +KDELILA+STASS SV+P++++K+E YG S+ Sbjct: 236 IAFFVLVVLNLVARLCGINLFALMRHIKDELILAFSTASSASVMPQLMKKLETYGVSPSL 295 Query: 301 TSFVVPTGYSFNLDGSTLYQSIAAIFIAQLYGIDLSIWQEIILVLTLMVTSKGIAGVPGV 360 SFVVP GYSFNLDG++L+ I +F+AQLYGIDLS+ + +LV+T+++TSKG AGVPG Sbjct: 296 VSFVVPVGYSFNLDGASLFLGIGTLFVAQLYGIDLSLGDQALLVVTMVLTSKGAAGVPGF 355 Query: 361 SFVVLLATLGSVGIPLEGLAFIAGVDRILDMARTALNVVGNALAVLVIAKWE 412 FV+L ATL S G+PLEG+AFIAGV R+++M TALNV+GNALA LVIAKWE Sbjct: 356 MFVILSATLASAGLPLEGIAFIAGVYRLMEMPTTALNVLGNALAPLVIAKWE 407 Lambda K H 0.326 0.141 0.403 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: 558 Number of extensions: 18 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: 437 Length of database: 425 Length adjustment: 32 Effective length of query: 405 Effective length of database: 393 Effective search space: 159165 Effective search space used: 159165 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