Align lactose 3-dehydrogenase flavin subunit (EC 1.1.99.13) (characterized)
to candidate Ga0059261_0546 Ga0059261_0546 Choline dehydrogenase and related flavoproteins
Query= metacyc::MONOMER-15712 (579 letters) >FitnessBrowser__Korea:Ga0059261_0546 Length = 560 Score = 509 bits (1312), Expect = e-149 Identities = 274/563 (48%), Positives = 359/563 (63%), Gaps = 16/563 (2%) Query: 12 NTYDAIVVGSGITGGIAAKELTEKGLKVLVLERGPMVRHLEDYPTAMLDPWQSKYPQGKL 71 N +DAIV+GSG++GG AAKELTEKGL+VL+L+RG MV H EDY T P + + Sbjct: 5 NRFDAIVIGSGVSGGFAAKELTEKGLRVLMLDRGVMVEHGEDY-TYDGKPAYEVPARNIM 63 Query: 72 PEAELNAHYKVQRRTGYTMTEQTQHFFVRDDEHPYT--EENRFDWIRGYHVGGRSLTWGR 129 P+ + + Y + + GY + + F+ D +PY E ++F WIR VGG+SL WGR Sbjct: 64 PKPLIESDYFIAKN-GY-VAPSNRRFYNDDRLNPYAHDEGSKFFWIRPGAVGGKSLIWGR 121 Query: 130 QSYRHSPIDFEANAREGIAVDWPIRYEDLAPWYEHVERFIGVSGQAEGLPHFPDGHYQPP 189 S+R S DFEAN REGI DWPIRY+D+APWY VE +IGVSG E LP PD +QPP Sbjct: 122 WSFRWSADDFEANKREGIDGDWPIRYDDIAPWYSKVENYIGVSGSRENLPQLPDSEFQPP 181 Query: 190 MELNCVEKAFKARSEARFPERRVTIGRTAHLTDPTEEQLALGRTKCQYRNLCIRGCPFGA 249 M +N EK K R E +FP R++ R ++LT+ EQ RTKCQ RN C GC FGA Sbjct: 182 MPMNIAEKWVKQRLETQFPGRKLINARLSNLTEDKPEQ---NRTKCQMRNQCGNGCSFGA 238 Query: 250 YYSSNSGGLIAAERTGNLVIRPNSIVTELIYDERAGRASGVRILDAETRKDEEFHADVIF 309 Y+S+ + L AA TG L +R +++VT L YD R +GVR +DA TR+ E +AD++F Sbjct: 239 YFSTQAVTLPAARATGRLTLRSDAVVTNLEYDPVRKRVTGVRFVDARTRQAEVVNADLVF 298 Query: 310 LCASALNSAWIMMNSTSSRFPNGFGNASDQLGRNVMDHHLGAGATGQAPEFADMYFSGRR 369 LCASA+ S I+MNS ++ ++S LG+ VMDH G G+ P ++ GRR Sbjct: 299 LCASAMASTQILMNSRAAGSGRSHFDSSGTLGKYVMDHIFRVGIEGEIPGMSEYIEYGRR 358 Query: 370 PNGIYVPRFRNLGDAASKRSDYLRGFGYQGGAGRATWERDRGQGGRGFGAARKAALSQPG 429 P GIY+PRFRN+G A + + RG+GYQGGA R GFGA+ K + + Sbjct: 359 PGGIYIPRFRNIG--ADENLGFKRGYGYQGGAHRDV------APPVGFGASMKHGMRKYA 410 Query: 430 PWTMGLSGFGEMLPYADNRVTLNRDVEDKFGLPTLTMNVTMRDNEMAMRRDMQAAAAEML 489 PW +S FGE LPY DN V+L+ D D+FG+P + +V R+NE+ M D + ML Sbjct: 411 PWKFHISAFGECLPYRDNSVSLHADKVDRFGVPLMRFDVRFRENELRMMADARTQGEAML 470 Query: 490 EAAGFQNVRAHDNGFAPGLGIHEMGTARMGRDPKTSVLNAHNQVHECKNVYVTDGAAMAS 549 +AAG +VR+ + PG IHEMG ARMG DP++SVLN+ +Q H+ N+YVTDGA MAS Sbjct: 471 KAAGLGSVRSWEGEHVPGDAIHEMGGARMGADPRSSVLNSWSQAHDASNLYVTDGAQMAS 530 Query: 550 ASCVNPSLTYMALTARAADHAVR 572 SCVNPSLT+MALT RAADHAVR Sbjct: 531 VSCVNPSLTFMALTVRAADHAVR 553 Lambda K H 0.319 0.135 0.414 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: 837 Number of extensions: 36 Number of successful extensions: 5 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: 579 Length of database: 560 Length adjustment: 36 Effective length of query: 543 Effective length of database: 524 Effective search space: 284532 Effective search space used: 284532 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 (21.8 bits) S2: 53 (25.0 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