Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate Pf1N1B4_5582 Quinate/shikimate dehydrogenase [Pyrroloquinoline-quinone] (EC 1.1.99.25)
Query= BRENDA::D4P700 (796 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5582 Length = 807 Score = 603 bits (1555), Expect = e-176 Identities = 341/819 (41%), Positives = 467/819 (57%), Gaps = 35/819 (4%) Query: 1 MGKNSSSFSVVRF--LTVLFAVLT-GAFMLIGGIWLATIGGSWYYIIGGAAMLLTAFLLW 57 M K+ S SV R+ V F VL G F GG +LAT+GGSWY+++ G ++++A LL+ Sbjct: 1 MTKSRPSASVSRWPIWVVAFGVLVFGLFFATGGGYLATLGGSWYFLLAGFGLIVSAVLLF 60 Query: 58 RRNSAALVVYALLLLATLAWGVWEVGTDFWALAPRTDVLVIFGVWLVLPFVYRGLYQPGK 117 ++ ++A +++ T+ W + +VG +FW L R L + +++ L +Y L + Sbjct: 61 KQRLQGAWLFAAVMVLTVIWALADVGLNFWPLISRLFALGVLSLFVAL--IYPHLRKANS 118 Query: 118 GALGAMGVALVASAAVLTYSVFNDPQVVNGALPATADNAPQAQPLSNIADGDWPAYARDQ 177 A G G AL A+ + V + + T D A +W Y D+ Sbjct: 119 LASGRSGYALSGVLAIAVVAGGAGMFVPHAPVSPTGDGPGLTTVDPAKAQKNWEHYGNDE 178 Query: 178 QGTRFSPLKQINHDNVKELQVAWQFQTGDMKRPSDPGEITDEVTPIKIRDTLYLCTPHQI 237 G+RF+ L QIN NV +L AW + TGD+ SD D++TP+++ D +++CTPH Sbjct: 179 GGSRFAALDQINRSNVSKLVPAWTYNTGDIAI-SDGNGAEDQMTPLQVGDKVFICTPHNN 237 Query: 238 LFALDAATGKQKWKFDPGLKTNPTFQHVTCRGVSYHEFPAA-----------KDASNTQP 286 L ALDA TGKQ WK + KT +Q CRGV+Y + AA K S Sbjct: 238 LIALDADTGKQLWKNEINAKTR-VWQR--CRGVAYFDATAALAQPADGSTPVKPVSIPAG 294 Query: 287 ALCSRRIYLPVNDGRLFALDAETGERCPAFGNNGELDLQHKQPVTTPGMYEPTSPPVITD 346 A C RR+ D RL A+DA+TGE C FGNNG++DL+ Y+ +S P++ Sbjct: 295 ANCQRRLLTNTIDARLIAVDADTGEFCQGFGNNGQVDLKAGLGDVPDSYYQLSSAPLMAG 354 Query: 347 TTIVMAGAVTDNFSTREPSGAIRGFDVNTGKLLWVFDPGAKDPNAIPADEHTFTMNSPNS 406 TT+V+ G V DN T P G IRGFDV TG++ W FDPG + PA T+ ++PNS Sbjct: 355 TTVVVGGRVADNVQTDMPGGVIRGFDVVTGEMRWAFDPGNPEDKQAPAAGSTYVRSTPNS 414 Query: 407 WAPAVYDPKLDIVYLPMGVTTPDIWGGNRTPEQERYASSVLALNATTGKLVWSYQTVHHD 466 WAP YDP ++ V+LPMG ++ DI+G RT +Y +SVLALNATTG+ W YQTVH+D Sbjct: 415 WAPMSYDPAMNTVFLPMGSSSTDIYGVERTALNHKYGASVLALNATTGEEKWVYQTVHND 474 Query: 467 LWDMDLPSQPTLADITDKDGNTVPVIYAPAKTGNIFVLDRRTGKTVVPAPETPVPQGAAK 526 LWD DLP QP+L D T DG+ VP + K G IFVLDR TGK + E PV Sbjct: 475 LWDFDLPMQPSLIDFTKADGSKVPAVVIGTKAGQIFVLDRATGKPLTKVEEVPVKTSNIP 534 Query: 527 GDHVSATQPYS-ELTFRPKQNLTDKDMWGATMYDQLVCRVIFKRLRYEGPFTPPSEQGTL 585 + S TQP S + Q LT+ DMWGAT +DQL+CR+ FK++RY+G +T P +L Sbjct: 535 NEPYSLTQPKSVGMPEIGAQTLTESDMWGATPFDQLLCRISFKKMRYDGLYTAPGTDISL 594 Query: 586 VFPGNLGMFEWGGISVDPHRQIAIANPMALPFVSKLIPRGPGNPEEPPKGATGGSGTETG 645 FPG+LG WGGIS DP N M L ++I ++ K ++GG TG Sbjct: 595 SFPGSLGGMNWGGISTDPVHGFIFVNDMRLGLWIQMIA-----AKKDAKASSGGEALNTG 649 Query: 646 I--QPQYGVPYGVELNPFLSPFGLPCKQPAWGYVSAVDLKTNEVVWKQRIGTVRDSSP-- 701 + P G PY V N FLS G+PC+ P +G ++A+D+KT +V W+ +GTV+D+ P Sbjct: 650 MGAVPLKGTPYAVNKNRFLSVAGIPCQAPPFGTLTAIDMKTQKVAWQVPVGTVQDTGPLG 709 Query: 702 --VPLPFKMGMPMLGGPVATAGKVFFIGATADNYLRAFSTDTGELLWQARLPAGGQATPM 759 + LP +GMP LGG ++T G + FI T D YLRAF++ G+ W+ARLP G Q PM Sbjct: 710 IKMHLPLPIGMPTLGGTLSTQGGLVFIAGTQDYYLRAFNSANGKEAWKARLPVGSQGGPM 769 Query: 760 TY--EVNGKQYVVIAAGGHGSFGTKLGDYVIAYALPDQK 796 TY GKQYVVI AGG + GDYVIAYALPD + Sbjct: 770 TYVSPKTGKQYVVITAGGARQSPDR-GDYVIAYALPDSQ 807 Lambda K H 0.319 0.137 0.433 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: 2205 Number of extensions: 144 Number of successful extensions: 17 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: 796 Length of database: 807 Length adjustment: 41 Effective length of query: 755 Effective length of database: 766 Effective search space: 578330 Effective search space used: 578330 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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