Align 2-deoxy-D-ribose dehydrogenase β subunit (characterized)
to candidate BPHYT_RS24635 BPHYT_RS24635 aldehyde dehydrogenase
Query= metacyc::MONOMER-20833 (739 letters) >FitnessBrowser__BFirm:BPHYT_RS24635 Length = 750 Score = 418 bits (1075), Expect = e-121 Identities = 265/747 (35%), Positives = 403/747 (53%), Gaps = 55/747 (7%) Query: 14 LSRRRFL------ASTAVGALVIGFGLPLGAGRVQAATSAERGTQVPA----------FL 57 LSRR FL + A G L++GF +P + +A S G V A F+ Sbjct: 25 LSRRTFLKFGVTVGAAAGGGLLLGFSMPAASQDQKAGKSVIGGDGVEAPQSGVFAPNAFI 84 Query: 58 EIRPDGTVRLLSPFMEGGQGTHTAMAQIVGEELDADPATFIVEAAPPGEA-YVVMENGLR 116 +I G V L+ P +E GQG +T++ ++ EEL+ + ++ APP E ++ G + Sbjct: 85 QIDTAGKVTLVIPKVEMGQGVYTSIPMLIAEELEVPLDSITIDHAPPNEKLFMDPLLGGQ 144 Query: 117 ITGGSMSVRMSYPTMRRLGALARAMLLQAGAKQWGVPVGELTTQPGRVVHAASGRSLGYG 176 +TGGS S+R ++ MR+ GA AR +L+ A A+QW V Q G+V+H AS RS+ YG Sbjct: 145 LTGGSTSIRYAWEPMRKAGATARTVLISAAAQQWQVDPASCHAQGGQVIHEASKRSVSYG 204 Query: 177 ELASSALDMPVPDPASITLRDPSQFRWIGKPVKRLDAYDKSTGKALYSIDLKVDNMLHAA 236 EL ++A +P P ++ L+DP F+ IG VKRLD+ +K G A++ +D++V +M++AA Sbjct: 205 ELVTAAAGLPAPQ--NVKLKDPKDFKLIGTAVKRLDSPEKVDGTAMFGLDVRVPDMVYAA 262 Query: 237 VQHAPRLGMTVGSLRNQSQVEGMKGVHSVHVLPGAVAVVAERWWHAKRAVEAIQVDWQEA 296 + + P G T+ S+ + + + + GV V + AVAV+ + W AKR V+A+ + W E Sbjct: 263 IANCPVFGGTLASV-DDTNAKKIPGVRQVIKIDNAVAVIGDHTWAAKRGVQALVIKWNEG 321 Query: 297 A-ADSALRVMPADFSSDKHREFLAAQQGPTRDDENEGDVAGALKGAKTQVEATYHNQYLN 355 A A+ +++ + D ++ R+ A++ +GDV A AKT+V+A Y +L Sbjct: 322 AGANLSMKQIVDDLANASQRDGAVARK--------DGDVGNAFSNAKTRVDAVYQQPFLA 373 Query: 356 HAQLEPPSALARFNPDGTLEIWLPNQAPDMFRADIAKRTGLDPAQITLHSPLLGGFFGRH 415 HA +EP + PDG ++WL +Q P A TGL +I +H+ L+GG FGR Sbjct: 374 HATMEPINCTVHVRPDGC-DVWLGSQVPTRVVDAAAAVTGLPADKIVVHNHLIGGGFGRR 432 Query: 416 FLYDSANPYPQAIALAKAVSRPIKLIWSREEEFLRDVLRPLAVVKFRAALDDKGLPVAIE 475 +D QA+ +AK VS P+K++W+REE+ D+ RP K A LD G PVA + Sbjct: 433 LEFDMVT---QAVKVAKQVSTPVKVVWTREEDIQHDMYRPYYYDKISAGLDANGKPVAWQ 489 Query: 476 ------AVSATEGPTEALAGKQGDKIDPTAVEGLSGKSYAIPNKRIAQIYVKGAPML--- 526 +V A P A K G IDP AVE + Y +PN+ I YV+ P Sbjct: 490 HRIVGSSVMARFAPP---AFKNG--IDPDAVEVAADLPYDLPNQLID--YVRQEPHTVPT 542 Query: 527 GYWRSVGNSLNDFFYESFLDELADKGGHDPYELRLHLLRDNPRLTTLLQAAGELSGGWKR 586 +WR VG + F ESF+DELA + DP + R LL PR ++L A + + Sbjct: 543 AFWRGVGPTRGTFVVESFIDELAAQAKVDPVKYRQDLLGKTPRALSVLNVATQAANWGSA 602 Query: 587 GPFTAEDGTRRARGVAMASPFGSHTAAIAEVSIENGKVKVHDIWQAIDPGSIVNPAIVEA 646 P + RGV++ FGS A + +V++E G+V V + A+D G +VNP +EA Sbjct: 603 VP------KGQGRGVSVMHAFGSFFAIVVDVAVEQGEVAVKRVVCAVDCGMVVNPNTIEA 656 Query: 647 QVNGAVALGLSQTLLEEAVYVDGKPRARNYDLYPILAPAQMARVHVRVVESGEKMGGIGE 706 QV G + G++ L E DG+ N+ Y +L Q + V +V+S E GGIGE Sbjct: 657 QVQGGIIFGITAALYGEITIKDGRVEQNNFTDYRMLRIDQTPPIEVHIVKSSEAPGGIGE 716 Query: 707 PPLPAVAPAVANAVAQLTGQRVRSLPL 733 P A+APA+ NA+ TG+R+R LP+ Sbjct: 717 PGTAALAPALTNAIYAATGKRLRQLPV 743 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: 1341 Number of extensions: 73 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: 750 Length adjustment: 40 Effective length of query: 699 Effective length of database: 710 Effective search space: 496290 Effective search space used: 496290 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