Align gluconate 5-dehydrogenase (EC 1.1.1.69); D-sorbitol dehydrogenase (acceptor) (subunit 1/2) (EC 1.1.99.21) (characterized)
to candidate Pf1N1B4_5582 Quinate/shikimate dehydrogenase [Pyrroloquinoline-quinone] (EC 1.1.99.25)
Query= BRENDA::Q70JN9 (743 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5582 Length = 807 Score = 481 bits (1239), Expect = e-140 Identities = 268/697 (38%), Positives = 375/697 (53%), Gaps = 52/697 (7%) Query: 65 GPSPYAPQAPGVNAANLPDIGSMDPNDVPQMAPQQSASPASGDWAAYGHDDSQMRYSPLS 124 G + P AP + P + ++DP + A +W YG+D+ R++ L Sbjct: 140 GAGMFVPHAPVSPTGDGPGLTTVDP------------AKAQKNWEHYGNDEGGSRFAALD 187 Query: 125 EITPQNADQLKVAFVYHTGSYPRPGQTNKWAAETTPIKVGDGLYMCSAQNDIMKIDPATG 184 +I N +L A+ Y+TG N + TP++VGD +++C+ N+++ +D TG Sbjct: 188 QINRSNVSKLVPAWTYNTGDIAI-SDGNGAEDQMTPLQVGDKVFICTPHNNLIALDADTG 246 Query: 185 KEIWRHNINEKYEAIPYTAACKGVTYFTSS----------------QVPEGQPCHNRILE 228 K++W++ IN K C+GV YF ++ +P G C R+L Sbjct: 247 KQLWKNEINAKTRV---WQRCRGVAYFDATAALAQPADGSTPVKPVSIPAGANCQRRLLT 303 Query: 229 GTLDMRLIAVDAATGNLCEGFGNGGQVNLMQGLGESVPGFVSMTTPPPVVNGVVVVNHEV 288 T+D RLIAVDA TG C+GFGN GQV+L GLG+ + +++ P + VVV V Sbjct: 304 NTIDARLIAVDADTGEFCQGFGNNGQVDLKAGLGDVPDSYYQLSSAPLMAGTTVVVGGRV 363 Query: 289 LDGQRRWAPSGVIRGYDAESGKFLWAWDVNRPNDHSQPTGNNHYSRGTPNSWAAMTGDNA 348 D + P GVIRG+D +G+ WA+D P D P + Y R TPNSWA M+ D A Sbjct: 364 ADNVQTDMPGGVIRGFDVVTGEMRWAFDPGNPEDKQAPAAGSTYVRSTPNSWAPMSYDPA 423 Query: 349 LGLVYVPTGNSASDYYSALRSPEENKVSSAVVALDVKTGSPRWVFQTVHKDVWDYDIGSQ 408 + V++P G+S++D Y R+ +K ++V+AL+ TG +WV+QTVH D+WD+D+ Q Sbjct: 424 MNTVFLPMGSSSTDIYGVERTALNHKYGASVLALNATTGEEKWVYQTVHNDLWDFDLPMQ 483 Query: 409 ATLMDMPGQDGQPVPALIMPTKRGQTFVLDRRDGKPILPVEERPAPSPGVIPGDPRSPTQ 468 +L+D DG VPA+++ TK GQ FVLDR GKP+ VEE P + IP +P S TQ Sbjct: 484 PSLIDFTKADGSKVPAVVIGTKAGQIFVLDRATGKPLTKVEEVPVKTSN-IPNEPYSLTQ 542 Query: 469 PWSTGMPALRVPDLKETDMWGMSPIDQLFCRIKFRRANYTGEFTPPSVDKPWIEYPGYNG 528 P S GMP + L E+DMWG +P DQL CRI F++ Y G +T P D + +PG G Sbjct: 543 PKSVGMPEIGAQTLTESDMWGATPFDQLLCRISFKKMRYDGLYTAPGTDIS-LSFPGSLG 601 Query: 529 GSDWGSVSYDPQSGILIANWNITPMYDQLVTRKKADELGLMPIDDPNYKPGGGGAE-GNG 587 G +WG +S DP G + N ++ Q++ KK D GG G G Sbjct: 602 GMNWGGISTDPVHGFIFVNDMRLGLWIQMIAAKK----------DAKASSGGEALNTGMG 651 Query: 588 A--MDGTPYGIVVTPFWDQYTGMMCNRPPYGMITAIDMKHGQKVLWQHPLGTARANGPWG 645 A + GTPY + F G+ C PP+G +TAIDMK QKV WQ P+GT + GP G Sbjct: 652 AVPLKGTPYAVNKNRFL-SVAGIPCQAPPFGTLTAIDMK-TQKVAWQVPVGTVQDTGPLG 709 Query: 646 LPTGLPWEIGTPNNGGSVVTAGGVVFIAAATDNQIRAIDEHTGKVVWSAVLPGGGQANPM 705 + LP IG P GG++ T GG+VFIA D +RA + GK W A LP G Q PM Sbjct: 710 IKMHLPLPIGMPTLGGTLSTQGGLVFIAGTQDYYLRAFNSANGKEAWKARLPVGSQGGPM 769 Query: 706 TYEA--NGHQYVAIMAGGHHFMMTPVSDQLVVYALPD 740 TY + G QYV I AGG D ++ YALPD Sbjct: 770 TYVSPKTGKQYVVITAGGAR-QSPDRGDYVIAYALPD 805 Lambda K H 0.315 0.134 0.428 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: 1988 Number of extensions: 121 Number of successful extensions: 8 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: 743 Length of database: 807 Length adjustment: 41 Effective length of query: 702 Effective length of database: 766 Effective search space: 537732 Effective search space used: 537732 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 55 (25.8 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