Align The aerobic dicarboxylate (succinate (Km, 30 μM), fumarate (Km, 79 (characterized)
to candidate GFF1761 Psest_1800 anion transporter
Query= TCDB::A4QAL6 (527 letters) >FitnessBrowser__psRCH2:GFF1761 Length = 482 Score = 439 bits (1128), Expect = e-127 Identities = 216/457 (47%), Positives = 315/457 (68%), Gaps = 17/457 (3%) Query: 62 DPETEYTNNAMRLTAAVTILMAVWWMTEAIPLAATALIPLVAFPAFQVVDFGKAAAPYAN 121 +P + + A LT + LMAVWW TEAIP+ AT+L+P++ P + KA APYAN Sbjct: 32 EPPADLSRTAW-LTVGMAALMAVWWSTEAIPIPATSLLPILLIPVLGIDTLAKATAPYAN 90 Query: 122 PTIFLFLGGFLMALGLQKWNLHRRMALAVVLAVGTKPKQLVLGFMVATGFLSMWVSNTAT 181 PTIFLFLGGFL+ L +Q+WNLH+R+ALA +LAVG+ P + + GFM+AT F+SMWVSNTAT Sbjct: 91 PTIFLFLGGFLLGLAMQRWNLHKRIALATLLAVGSAPSRQIAGFMIATAFISMWVSNTAT 150 Query: 182 AVVMLPIGMSVLALTAETVGGMKNQKKFATGLMLSIAYSASIGSLGTLIGTPPNALLAAY 241 +++MLPIG+SV++L ++ ++FA L+L IAY+AS+G + TLIGTPPNALLAA+ Sbjct: 151 SIMMLPIGLSVISLLV-AGSDKRDGERFAIALLLGIAYAASVGGIATLIGTPPNALLAAF 209 Query: 242 MSESHDIHIGFGQWMILGVPIAVVFTIIAWLVLTTVFKPEMKEIPGG--RELIKREIAEM 299 + E++D+HIGFGQWM+LG+P+++ + W LT + GG R ++++E+A + Sbjct: 210 LRENYDVHIGFGQWMLLGLPVSLGMLLFIWWWLTR----GGFTLSGGDSRAMLEKEMAAL 265 Query: 300 GPWTAPQVTVGVIFAAAALAWVFIPLTLDWTGSQLSINDSLIGIAAGLLMFIVPANFKTG 359 GP + + V V+F+ AALAW+F PL +ND+ I +AA L +F++P + + Sbjct: 266 GPMSKAEKMVAVVFSLAALAWIFQPLLAKHVN---GVNDTSIAMAAALSLFLIPVDLRQR 322 Query: 360 ERILDWRTAGELPWDVLLLFGGGLSLSAMFTSTGLSLWIGELAKGLDALPIFILIFAIAV 419 ++DW A + PW VLLLFGGGLSL+ + ++GL+ WI + G ALP+ ++I +A+ Sbjct: 323 VFLMDWEQANKAPWGVLLLFGGGLSLAGVIGASGLAQWIAQSLGGFGALPLILMIGLVAL 382 Query: 420 LVLFLTEFTSNTATAATFLPIMGGVAVGIGLTAGGEQNVLLLTIPVALSATCAFMLPVAT 479 ++ FLTE TSNTATAA FLP++G +AV GL+ +L IP A++A+CAFM+PVAT Sbjct: 383 VITFLTEITSNTATAAAFLPLLGALAVAQGLSPE------MLAIPAAIAASCAFMMPVAT 436 Query: 480 PPNAIAFGSGYIKIGEMVKGGLWLNIIAVILISISTY 516 PPNAI FG+G + I M+K G +N+ V L+++ Y Sbjct: 437 PPNAIVFGTGQMHIQSMIKAGFAINLFGVALVTLLCY 473 Lambda K H 0.324 0.139 0.418 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: 824 Number of extensions: 46 Number of successful extensions: 7 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: 527 Length of database: 482 Length adjustment: 34 Effective length of query: 493 Effective length of database: 448 Effective search space: 220864 Effective search space used: 220864 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. 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