Align 2-deoxy-D-ribose dehydrogenase β subunit (characterized)
to candidate SM_b20342 SM_b20342 isoquinoline 1-oxidoreductase
Query= metacyc::MONOMER-20833 (739 letters) >FitnessBrowser__Smeli:SM_b20342 Length = 737 Score = 395 bits (1016), Expect = e-114 Identities = 271/741 (36%), Positives = 395/741 (53%), Gaps = 36/741 (4%) Query: 10 APVNLSRRRFLASTAVGALVIGFGLPLGAGRVQA--ATSAERGTQVPA-----FLEIRPD 62 A SRR+FL +GAL G G+ +G + A A + E T+ + +L I D Sbjct: 14 ARAEASRRQFL----LGALAAGTGVAIGYRILSASPALAGEAATESGSHAFSPYLTIGGD 69 Query: 63 GTVRLLSPFMEGGQGTHTAMAQIVGEELDAD-PATFIVEAAPPGEAY--VVMENGLRITG 119 G V +LS E GQG++ +A +V EELD+D A ++ AA +AY + ++ TG Sbjct: 70 GKVTVLSSQFEMGQGSYNGIATLVAEELDSDWSAIDVIGAAGNIKAYGNIAFGGTMQGTG 129 Query: 120 GSMSVRMSYPTMRRLGALARAMLLQAGAKQWGVPVGELTTQPGRVVHAASGRSLGYGELA 179 GS S+ S+ RR GA ARAML+ A A +WGV E+ + G + H SG+S G+G A Sbjct: 130 GSTSMSTSWERYRRAGAAARAMLVAAAAAEWGVDAAEIAVENGVLSHP-SGKSGGFGAFA 188 Query: 180 SSALDMPVPDPASITLRDPSQFRWIGKP-VKRLDAYDKSTGKALYSIDLKVDNMLHAAVQ 238 + A MPVP A + L++P ++ IG +KR D+ K+ G Y+ID+K+ ML A + Sbjct: 189 AKAATMPVP--ADVKLKEPGDWKLIGNDELKRFDSARKANGTEQYTIDVKLPGMLTAVMI 246 Query: 239 HAPRLGMTVGSLRNQSQVEGMKGVHSVHVLPGAVAVVAERWWHAKRAVEAIQVDWQEAAA 298 H P G S + S +KGV V P +AVV E W A + EA+ V+W E A Sbjct: 247 HPPLFGAKAKSF-DASAARAIKGVVDVVETPRGIAVVGEHMWAAIKGREAVTVEWDETGA 305 Query: 299 DSALRVMPADFSSDKHREFLAAQQGPTRDDENEGDVAGALKGAKTQVEATYHNQYLNHAQ 358 + R P S+ +R+ A + P +GD A A +EAT+ YL HA Sbjct: 306 EK--RGTPELMST--YRDL--AGKSPAAFARKDGDTDAAFTSAAKVIEATFEFPYLAHAA 359 Query: 359 LEPPSALARFNPDGTLEIWLPNQAPDMFRADIAKRTGLDPAQITLHSPLLGGFFGRHFLY 418 LEP +A+AR N DGT+EIW +Q PD+++ ++ G+ ++ L+ GG FGR ++ Sbjct: 360 LEPLNAVARRNDDGTIEIWGGHQLPDVYQNLASEIAGVPVEKVRLNVMKTGGSFGRRAVF 419 Query: 419 DSANPYPQAIALAKAVS--RPIKLIWSREEEFLRDVLRPLAVVKFRAALDDKGLPVAIE- 475 D + +A+ +AKA+ P+K+ W+REE+ RP V + +A +D+ G VA Sbjct: 420 DG-DVVVEAVHVAKALGFRAPVKVQWTREEDTRAGRYRPAYVHRLKAGIDEAGKLVAWSD 478 Query: 476 -AVSATEGPTEALAGKQGDKIDPTAVEGLSGKSYAIPNKRIAQIYVKGAPMLGYWRSVGN 534 V + A G + +DPT+VEG + YAI N+ + + +WRSVG+ Sbjct: 479 HIVGQSIMAKTAWDGMVQNGVDPTSVEGANNLPYAIANQTVGLTTTDVRVPVLWWRSVGS 538 Query: 535 SLNDFFYESFLDELADKGGHDPYELRLHLLRDNPRLTTLLQAAGELSGGWKRGPFTAEDG 594 + F E+FLDE+A+ G DP E RL +L + R T+L+ A E + K P Sbjct: 539 THTAFAAEAFLDEVAEAAGRDPLEFRLSMLEPDSRHATVLKLAAEKAEWQKPLP------ 592 Query: 595 TRRARGVAMASPFGSHTAAIAEVSIENGKVKVHDIWQAIDPGSIVNPAIVEAQVNGAVAL 654 R RGVA+A FGS A IAEVS++ +KV + A+D G +NP V AQV G + Sbjct: 593 EGRFRGVAVAESFGSVVAQIAEVSVDGDGIKVERVVAAVDCGLAINPDQVRAQVEGGIGF 652 Query: 655 GLSQTLLEEAVYVDGKPRARNYDLYPILAPAQMARVHVRVVESGEKMGGIGEPPLPAVAP 714 GLS L EE DGK N+D+Y L M +V V +V S GIGEP +P + P Sbjct: 653 GLSAILGEEITLTDGKVDQGNFDMYTPLRIDAMPKVEVHIVASANPPSGIGEPGVPPIGP 712 Query: 715 AVANAVAQLTGQRVRSLPLSR 735 AVANA + G+R+R +P ++ Sbjct: 713 AVANAAFKALGKRIRVMPFAK 733 Lambda K H 0.317 0.134 0.394 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: 1359 Number of extensions: 84 Number of successful extensions: 11 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: 739 Length of database: 737 Length adjustment: 40 Effective length of query: 699 Effective length of database: 697 Effective search space: 487203 Effective search space used: 487203 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: 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