Align Proton/sodium-glutamate symport protein; Glutamate-aspartate carrier protein (characterized)
to candidate HSERO_RS19090 HSERO_RS19090 C4-dicarboxylate ABC transporter
Query= SwissProt::P24943 (421 letters) >FitnessBrowser__HerbieS:HSERO_RS19090 Length = 431 Score = 327 bits (837), Expect = 6e-94 Identities = 174/428 (40%), Positives = 278/428 (64%), Gaps = 15/428 (3%) Query: 2 RKIGLAWQIFIGLILGIIVGAIFYGN------PKVATYLQPIGDIFLRLIKMIVIPIVIS 55 ++I A IF ++LGI+VG + + + ++A Y+ D+FLRLIKM++ P+V S Sbjct: 3 KRIPQAAYIFAAMLLGILVGYLIFSHNDKAQAKELAGYISIASDLFLRLIKMVIAPLVFS 62 Query: 56 SLVVGVASVGDLKKLGKLGGKTIIYFEIITTIAIVVGLLAANIFQPGTGVNMKSLEKTDI 115 +LVVG+A +GD K +G++ GK++ +F I + +++ +G++ AN+ QPG GV +L D Sbjct: 63 TLVVGIAHMGDAKSVGRIFGKSLAWFFIASLVSLALGMIMANLLQPGAGV---ALPSPDA 119 Query: 116 QSYVDTTNEVQHHSMVETFVNIVPKNIFESLTKGDMLPIIFFSVMFGLGVAAIGEKGKPV 175 T++ ++ E F ++VPK+I E++ + ++L ++ FS+ FG+ +A++GE+GK + Sbjct: 120 AGAGLATSKF---TVKEFFNHLVPKSIVEAMAQNEVLQVVVFSMFFGIALASLGERGKHL 176 Query: 176 LQFFQGTAEAMFYVTNQIMKFAPFGVFALIGVTVSKFGVESLIPLSKLVIVVYATMVFFI 235 L + M +T +MKFAP VFA + TV+ G+E L+ + + Y ++V + Sbjct: 177 LAVIDDLSHTMLKITVYVMKFAPVAVFAAMAATVAVNGLEILVSFAVFMRDFYFSLVL-L 235 Query: 236 FVVLGGVAKLF-GINIFHIIKILKDELILAYSTASSETVLPKIMEKMENFGCPKAITSFV 294 +V+L V +F IFH++ ++K+ +LA++TASSE PK+++ ++ FG + I+SFV Sbjct: 236 WVILIAVGFIFLKKRIFHLLALIKEAFLLAFATASSEAAYPKLLDALDRFGVKRKISSFV 295 Query: 295 IPTGYSFNLDGSTLYQALAAIFIAQLYGIDMPISQQISLLLVLMVTSKGIAGVPGVSFVV 354 +P GYSFNLDGS +Y A +FIAQ YGI MPIS QI+++LVLM+TSKGIAGVP S VV Sbjct: 296 MPMGYSFNLDGSMIYCTFATLFIAQAYGIHMPISTQITMMLVLMLTSKGIAGVPRASLVV 355 Query: 355 LLATLGTVGIPIEGLAFIAGIDRILDMARTAVNVIGNSLAAIIMSKWE-GQYNEEKGKQY 413 + ATL IP GL I GID LDM R+A N +GNS+A+ +++KWE G EE+ + Sbjct: 356 IAATLHQFNIPEAGLLVILGIDTFLDMGRSATNAVGNSIASAVVAKWEGGLMTEEEAARA 415 Query: 414 IAQLQQSA 421 +++Q A Sbjct: 416 EVEIEQEA 423 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: 415 Number of extensions: 14 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: 431 Length adjustment: 32 Effective length of query: 389 Effective length of database: 399 Effective search space: 155211 Effective search space used: 155211 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