Align 2-deoxy-D-ribose dehydrogenase β subunit (characterized)
to candidate N515DRAFT_4011 N515DRAFT_4011 isoquinoline 1-oxidoreductase, beta subunit
Query= metacyc::MONOMER-20833 (739 letters) >FitnessBrowser__Dyella79:N515DRAFT_4011 Length = 769 Score = 279 bits (713), Expect = 4e-79 Identities = 234/774 (30%), Positives = 367/774 (47%), Gaps = 62/774 (8%) Query: 9 DAPVNLSRRRFLASTA--VGALVIGFGLP-LGAGRVQAATSAERGTQVPAFLEIRPDGTV 65 + P RRRFL A GAL++G G V A + + A++ I DG V Sbjct: 5 NTPALPQRRRFLQVLAGTAGALIVGVRYAEAGDAPVPPAMLGDTLYGLGAYVRIDADGNV 64 Query: 66 RLLSPFMEGGQGTHTAMAQIVGEELDADPATFIVEAAPPGEAYVVMENGL---------R 116 + + + G G TA+ +I+ +ELDAD A V P G + +ENG + Sbjct: 65 LIGARDPDTGTGVATALPRILADELDADWAR--VSVVPLG---LGVENGNGEPRWIYGHQ 119 Query: 117 ITGGSMSVRMSYPTMRRLGALARAMLLQAGAKQWGVPVGELTTQPGRVVHAASGRSLGYG 176 + G S+ ++ +R+ GALAR +L+QA A++ GVP L TQ G V+ + GR YG Sbjct: 120 VGGTGSSIPAAWHDLRQAGALARWLLMQAAARRLGVPADRLRTQGGAVI-SPDGRRFDYG 178 Query: 177 ELASSALDMPVPDPASITLRDPSQFRWIGKPVKRLDAYDKSTGKALYSIDLKVDNMLHAA 236 LA +A + P A + ++ P ++ IG+P +DA TG+A ++ID + L A Sbjct: 179 SLAEAASKV-APPTAPVPVKTPDRYTLIGQPAGDVDARAIVTGQAQFAIDNYFGDALVAV 237 Query: 237 VQHAPRLGMTVGSLRNQSQVEGMKGVHSV-------HVLPG------AVAVVAERWWHAK 283 + H P + T+ ++ + E +KGV + +LPG +VAV+AE W A Sbjct: 238 LVHCPWVDGTLAD-KDFHEAEAVKGVVKIVELKPEPGLLPGETPLAPSVAVLAEDTWSAL 296 Query: 284 RAVEAIQVDWQEAAADS----ALRVMPADFSSDKH--------REFLAAQQGPTRDDENE 331 +A ++++W+ + S AL D + + ++ A PT N+ Sbjct: 297 QARAKLKLEWKPGPSGSESSAALEQQANDLVNPREATAKGAAAKDAAARDNTPTMRVRND 356 Query: 332 GDVAGALKGAKTQVEATYHNQYLNHAQLEPPSALARFNPDGTLEIWLPNQAPDMFRADIA 391 GDV G K A +V+ATY +L HA EP + LAR + D + + P QAP + + Sbjct: 357 GDVDGMAKKAARRVDATYVQPWLAHATAEPMNCLARVDKDRAVLV-APTQAPQRAWSVVQ 415 Query: 392 KRTGLDPAQITLHSPLLGGFFGRHFLYDSANPYPQAIALAKAVSRPIKLIWSREEEFLRD 451 + TG P QI + P +GG +GR +D +A+ LAK RP++L+W+REE+ D Sbjct: 416 RLTGFKPDQIEIRVPRVGGGYGRRLDHDFV---AEAVMLAKLADRPVRLLWTREEDLAHD 472 Query: 452 VLRPLAVVKFRAALDDKGLPVAIEAVSATEGPTEALAGKQGDKIDPTAVEGLSGKSYAIP 511 RP +V + A LD K V + A+ A G ++ + V+ + +P Sbjct: 473 FYRPASVHRLSATLDRKRQIVTWDQRMASASAL-ARRGTPEQRLWTSEVDVNQLPAGLVP 531 Query: 512 NKRIAQIYVKGAPMLGYWRSVGNSLNDFFYESFLDELADKGGHDPYELRLHLLRDNPRLT 571 N R ++ A G R + + N F ESF+DE+A+ DP RL LL + + Sbjct: 532 NYRSDWYALQSALPRGPHRGMPHVSNAFAVESFVDEIANALKEDPLVTRLRLLGEAREVP 591 Query: 572 TLLQAAGELSGGWKRGPFTA-------EDGTRRARGVAMASPF--GSHTAAIAEVSIENG 622 LQ G G + R G+ MA G++ A E S++ Sbjct: 592 --LQGGGSFDTGRLINVLKLVADRIEWRNWLRTVNGLGMACWHMDGAYVAHAIETSLQGE 649 Query: 623 KVKVHDIWQAIDPGSIVNPAIVEAQVNGAVALGLSQTLLEEAVYVDGKPRARNYDLYPIL 682 K+ + + A+D G ++NP +E Q+ GA LS L + DG+P+ R+Y YP+ Sbjct: 650 KLNIERVVCAVDVGRVINPLGLEGQIAGATLDALSAALNLAITFKDGQPQQRSYKDYPLA 709 Query: 683 APAQMA-RVHVRVVESGEKMGGIGEPPLPAVAPAVANAVAQLTGQRVRSLPLSR 735 + AQ+ V V +V +P APA+ANAV +++ RVR LPL + Sbjct: 710 SMAQLPDAVDVIIVPGDRDPAAASFLAMPTAAPALANAVFRVSAVRVRRLPLMK 763 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: 1448 Number of extensions: 70 Number of successful extensions: 10 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: 769 Length adjustment: 40 Effective length of query: 699 Effective length of database: 729 Effective search space: 509571 Effective search space used: 509571 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