Align lactose 3-dehydrogenase flavin subunit (EC 1.1.99.13) (characterized)
to candidate H281DRAFT_02427 H281DRAFT_02427 Choline dehydrogenase
Query= metacyc::MONOMER-15712 (579 letters) >FitnessBrowser__Burk376:H281DRAFT_02427 Length = 534 Score = 164 bits (415), Expect = 8e-45 Identities = 163/577 (28%), Positives = 256/577 (44%), Gaps = 66/577 (11%) Query: 11 KNTYDAIVVGSGITGGIAAKELT-EKGLKVLVLERGPMVRHLEDYPTAMLDPWQSKYPQG 69 K D +++GSG +G AA L+ ++ L+++ LE+G + + DYP+ +D Sbjct: 2 KEVADIVIIGSGASGAAAAWSLSRDRSLRIVCLEQGSVTKP-SDYPSTSVD--------- 51 Query: 70 KLPEAELNAHYKVQRRTGYTMTEQTQH----FFVRDDEHPYTEENRFDWIRGYHVGGRSL 125 +++ R Y+ + + + D P + N G+ GG ++ Sbjct: 52 ----------WELSRSGAYSSNPSVRRSAADYPIDDSASPISIAN----FNGF--GGSTI 95 Query: 126 TWGRQSYRHSPIDFEANAREGIAVDWPIRYEDLAPWYEHVERFIGVSGQAEGLPHFPDGH 185 + R P DF +G+ DWP+ +E+L P++ ER +GV+G G P PD Sbjct: 96 LYSAHFPRFHPSDFRTRTLDGVGDDWPLSFEELKPFFTENERMMGVAGLV-GDPANPDYE 154 Query: 186 -YQPPMELNCVEK----AFKARSEARFPERRVTIGRTAHLTDPTEEQLALGRTKCQYRNL 240 PP+ L + + AF +P I H R C Sbjct: 155 SLLPPIPLGPMGRTMAAAFNELGWHWWPSYSA-INTHRHGN----------RGACVNLGP 203 Query: 241 CIRGCPFGAYYSSNSGGLIAAERTGNLVIRPNSIVTELIYDERAGRASGVRILDAETRKD 300 C GC GA S + A + G + +R E+ D R G+A GV +DA+ + Sbjct: 204 CNTGCAQGAKASVDVTYWPVARQQG-VEVRTQCRAREITLDAR-GQADGVLYMDADG-VE 260 Query: 301 EEFHADVIFLCASALNSAWIMMNSTSSRFPNGFGNASDQLGRNVMDHHLGAGATGQAPEF 360 +A V+ + S + + +++NS SS FP+G N + +GRN+M H L A +A Sbjct: 261 HRLNARVVVVACSGVGTPRLLLNSRSSAFPDGLLNDNGLVGRNLMLHPL---AYTEAVFD 317 Query: 361 ADMYFSGRRPNGIYVPRFRNLGDAASKRSDYLRGFGYQGGAGRATWERD-RGQGGRG--F 417 D+ S P+G + + AA + D++RG+ Q G E G R Sbjct: 318 HDVQ-SSIGPHGCCILSQQFYESAAER--DFVRGYTMQVLRGAPPVETAVSGYFMRQVPL 374 Query: 418 GAARKAALSQPGPWTMGLSGFGEMLPYADNRVTLNRDVEDKFGLPTLTMNVTMRDNEMAM 477 GA A ++ T G++ E LP +NRV L+ D D G+P + + + DN M Sbjct: 375 GAEHHAKFNRLFNRTAGIAIITEDLPEPENRVELDPDRCDSSGMPGVKVFYKLGDNTSRM 434 Query: 478 RRDMQAAAAEMLEAAGFQNVRAHDNGFAP--GLGIHEMGTARMGRDPKTSVLNAHNQVHE 535 + + ++ AAG + + + FAP G H MGTARMG DP TSV+N Q H Sbjct: 435 LKHGIEMSKQVFAAAGAKVM----SSFAPVKNTGWHLMGTARMGDDPATSVVNKFGQAHA 490 Query: 536 CKNVYVTDGAAMASASCVNPSLTYMALTARAADHAVR 572 KN+++ D + +A VNP T ALT A DH R Sbjct: 491 VKNLFIVDSSIFVTAGAVNPVATAQALTLMACDHLQR 527 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: 689 Number of extensions: 34 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 579 Length of database: 534 Length adjustment: 36 Effective length of query: 543 Effective length of database: 498 Effective search space: 270414 Effective search space used: 270414 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