Align 2-deoxy-D-ribose dehydrogenase β subunit (characterized)
to candidate RR42_RS25790 RR42_RS25790 acylaldehyde oxidase
Query= metacyc::MONOMER-20833 (739 letters) >FitnessBrowser__Cup4G11:RR42_RS25790 Length = 748 Score = 346 bits (888), Expect = 2e-99 Identities = 243/748 (32%), Positives = 381/748 (50%), Gaps = 44/748 (5%) Query: 12 VNLSRRRFLASTAVGALVIGFGLPLGAGRVQAATSAERGT-----QVPAFLEIRPDGTVR 66 V +RR L +AV L I L V + + GT +V ++ I P G Sbjct: 15 VKSPQRRRLLKSAVALLAIPAAGSLAIPVVYSLSEKHSGTPAAEVEVSDWIWIEPSGHTI 74 Query: 67 LLSPFMEGGQGTHTAMAQIVGEELDADPATFIVEAAPPGEAY---VVMENGLRITGGSMS 123 + E GQG +T + Q++ +E+DAD V+ +AY E + TG SMS Sbjct: 75 IGVSQCEFGQGIYTGLPQVLADEMDADWENISVKFVTARDAYRNDAGDEPLQQYTGASMS 134 Query: 124 VRMSYPTMRRLGALARAMLLQAGAKQWGVPVGELTTQPGRVVHAASGRSLGYGELASSAL 183 + + MR GA AR +LL+AGA++ GV + TT+ GRV+H A+GRS+GYGE+ + A+ Sbjct: 135 MTYFFERMRLAGAQARDVLLRAGAQRLGVRSSQCTTRTGRVIHPATGRSIGYGEVVADAI 194 Query: 184 DMPV-PDPASITLRDPSQFRWIGKPVKRLDAYDKSTGKALYSIDLKVDNMLHAAVQHAPR 242 + + P P ++ PS+ IGK ++R+D K G A++ +D++V ML AV+ AP Sbjct: 195 KLRINPHPR---MKVPSEHSLIGKNLRRVDTPPKVDGSAVFGMDVEVPGMLIGAVRMAPS 251 Query: 243 LGMTVGSLRNQSQVEGMKGVHSVHVLP-------GAVAVVAERWWHAKRAVEAIQVDWQE 295 + ++ +RN++++ +GV ++ V V VVA +W AK+A++A+ +++ Sbjct: 252 VTGSIVRIRNEAEIRKREGVKAIVVTSLWPVPTRNTVIVVANSYWTAKQALDALDIEFDA 311 Query: 296 AAADSALRVMPADFSSDKHREFLAAQQGPT-RDDENEGDVAGALKGAKTQVEATYHNQYL 354 AA R +D + E L ++ P R N ++ G + V A YH Y+ Sbjct: 312 GAA----RNTSSDLIRKQFVEGLDSKDAPVARRIGNPEEILNG-PGKRVVVSADYHTPYV 366 Query: 355 NHAQLEPPSALARFNPDGTLEIWLPNQAPDMFRADIAKRTGLDPAQITLHSPLLGGFFGR 414 HA +EP A +G +E W P Q D R ++ K GL P ++T+H+ LGG FGR Sbjct: 367 AHATMEPVVATVDVR-EGEIEAWGPFQGQDFLRGELGKAFGLPPDKVTVHTVYLGGSFGR 425 Query: 415 HFLYDSANPYPQAIALAKAVSRPIKLIWSREEEFLRDVLRPLAVVKFRAALDDKGLPVAI 474 +L D A A A +KAV +P+K+I SRE++ RP A +FRA L D G+P+A+ Sbjct: 426 KYLPDFAL---HAAAASKAVGKPVKVIRSREDDTRHSYYRPGAAGRFRAVLGDGGMPLAL 482 Query: 475 EAVSATEGPTEALAGKQGDKI---DPTAVEGLSGKSYAIPNKRIAQIYVKGAPMLGYWRS 531 A + + + + + D T VE + Y +P+ + + VK L + RS Sbjct: 483 HARISGQSLYGVIKQDKMAAVGGWDETMVESIYDLIYRVPHLLVDAVDVKQPIPLSFLRS 542 Query: 532 VGNSLNDFFYESFLDELADKGGHDPYELRLHLLRDNPRLTTLLQAAGELSGGWKRGPFTA 591 VG++ + FF ESF+ ELA G D Y+ R LL + P +L A + + W+R Sbjct: 543 VGSTSSVFFLESFVSELAHAAGADDYQYRRKLLAEQPLALRVLDATAK-AAQWER----- 596 Query: 592 EDGTRRARGVAM------ASPFGSHTAAIAEVSIENGKVKVHDIWQAIDPGSIVNPAIVE 645 E G RG+A F ++ A + E+ + G+VK+ +D G VNP +++ Sbjct: 597 EAGPGVFRGMAFNVYTGRGEGFQTYVALVIELEVVQGRVKLKRAVCGVDAGRAVNPGLIK 656 Query: 646 AQVNGAVALGLSQTLLEEAVYVDGKPRARNYDLYPILAPAQMARVHVRVVESGEKMGGIG 705 A + G + L+ T E + G R ++ YP+L A+M V V ++ES G G Sbjct: 657 ANMEGGIGFALTNTFKSELTFDKGAIRQSSFHDYPLLQLAEMPNVEVTILESDRPPQGCG 716 Query: 706 EPPLPAVAPAVANAVAQLTGQRVRSLPL 733 E L APAVA+A+ TG R RS+PL Sbjct: 717 EVVLGPTAPAVASAMFHATGTRFRSMPL 744 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: 1259 Number of extensions: 69 Number of successful extensions: 9 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: 748 Length adjustment: 40 Effective length of query: 699 Effective length of database: 708 Effective search space: 494892 Effective search space used: 494892 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