Align The aerobic dicarboxylate (succinate (Km, 30 μM), fumarate (Km, 79 (characterized)
to candidate WP_011913625.1 PST_RS12610 anion transporter
Query= TCDB::A4QAL6 (527 letters) >NCBI__GCF_000013785.1:WP_011913625.1 Length = 482 Score = 440 bits (1132), Expect = e-128 Identities = 227/486 (46%), Positives = 323/486 (66%), Gaps = 26/486 (5%) Query: 36 GLVLAALVYLLF-PSNSVETVMQSSGVDPETEYTNNAMRLTAAVTILMAVWWMTEAIPLA 94 G VLAA + L+ P + ++ DP + A LT + LMAVWW TEAIP+ Sbjct: 9 GAVLAAWIGLILGPLLLLACIL----TDPPGGLSEKAW-LTVGLAALMAVWWSTEAIPIP 63 Query: 95 ATALIPLVAFPAFQVVDFGKAAAPYANPTIFLFLGGFLMALGLQKWNLHRRMALAVVLAV 154 AT+L+P++ P + KA APYANPTIFLFLGGFL+ L +Q+WNLH+R+ALA +LAV Sbjct: 64 ATSLLPILLIPLLDIDTLAKATAPYANPTIFLFLGGFLLGLAMQRWNLHKRIALATLLAV 123 Query: 155 GTKPKQLVLGFMVATGFLSMWVSNTATAVVMLPIGMSVLALTAETVGGMKNQK--KFATG 212 G +P + + GFM+AT F+SMWVSNTAT+++MLPIG+SV+ L + G + ++ +FA Sbjct: 124 GNQPSRQIAGFMIATAFISMWVSNTATSIMMLPIGLSVIGL---LIAGSEEKEGARFAVA 180 Query: 213 LMLSIAYSASIGSLGTLIGTPPNALLAAYMSESHDIHIGFGQWMILGVPIAVVFTIIAWL 272 L+L IAYSAS+G + TLIGTPPNALLAA+M E++D+ IGFGQWM+LG+P+++ + W Sbjct: 181 LLLGIAYSASVGGIATLIGTPPNALLAAFMRENYDVQIGFGQWMLLGLPLSIGMLVFIWW 240 Query: 273 VLTTVFKPEMKEIPGG--RELIKREIAEMGPWTAPQVTVGVIFAAAALAWVFIPLTLDWT 330 LT + GG R L+++E+A +GP + + V V+F AA AW+F PL D+ Sbjct: 241 SLTR----GGFRLAGGDSRGLLEKEMAALGPMSRAEKMVAVVFVLAAAAWIFQPLLADYI 296 Query: 331 GSQLSINDSLIGIAAGLLMFIVPANFKTGERILDWRTAGELPWDVLLLFGGGLSLSAMFT 390 +ND+ I +AA + +F++P + ++DW A + PW VLLLFGGGLSL+ + Sbjct: 297 D---GVNDTSIAMAAAIALFLIPVDLHKRVFLMDWEQANKAPWGVLLLFGGGLSLAGIIG 353 Query: 391 STGLSLWIGELAKGLDALPIFILIFAIAVLVLFLTEFTSNTATAATFLPIMGGVAVGIGL 450 ++GL+ WI DALP+ +I + +++FLTE TSNTATAA FLP++G +AV GL Sbjct: 354 ASGLAEWIASSLGAFDALPLLAMIALVVTVIIFLTEITSNTATAAAFLPLLGALAVAQGL 413 Query: 451 TAGGEQNVLLLTIPVALSATCAFMLPVATPPNAIAFGSGYIKIGEMVKGGLWLNIIAVIL 510 + +L IP A++A+CAFM+PVATPPNAI FG+G + I M+K G LN+ V+L Sbjct: 414 SPE------MLAIPAAVAASCAFMMPVATPPNAIVFGTGQLPIQAMIKAGFVLNLFGVLL 467 Query: 511 ISISTY 516 +S+ Y Sbjct: 468 VSLLCY 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: 845 Number of extensions: 45 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 Sep 24 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