Align lactose 3-dehydrogenase flavin subunit (EC 1.1.99.13) (characterized)
to candidate GFF1393 Psest_1430 Choline dehydrogenase and related flavoproteins
Query= metacyc::MONOMER-15712 (579 letters) >FitnessBrowser__psRCH2:GFF1393 Length = 525 Score = 174 bits (442), Expect = 6e-48 Identities = 164/574 (28%), Positives = 256/574 (44%), Gaps = 86/574 (14%) Query: 17 IVVGSGITGGIAAKELTEKGLKVLVLERGPMVRH-LEDYPTAMLDPWQSKYPQGKLPEAE 75 +++GSG GG A L ++ ++ +VLE G RH LED D W L Sbjct: 13 VIIGSGAGGGTLANALAKQKIRSVVLEAGK--RHTLEDIEN---DEWAMFKKISWLD--- 64 Query: 76 LNAHYKVQRRTGYTMTEQTQHFFVRDDEHPYTEENRFDWI-RGYHVGGRSLTWGRQSYRH 134 K Q G+ +TE WI +G VGG ++ W + R Sbjct: 65 -----KRQAAGGWHLTENNPTLPA--------------WIVKG--VGGSTVHWAGIALRF 103 Query: 135 SPIDFEANAREG-IA----VDWPIRYEDLAPWYEHVERFIGVSGQAEGLPHFPDGHYQPP 189 +F+ + G IA +DWP+ E++APWYE E+ +GV+G + G+ + P Sbjct: 104 RDFEFKMQSINGDIAGANLLDWPVTLEEMAPWYEKAEKHMGVTGPSTGMDYHP------- 156 Query: 190 MELNCVEKAFK--ARSEARFPERRVTIGRTAHLTDPTEEQLALGRTKCQYRNLCIRGCPF 247 +FK A R + + G A T+P ++ R CQ C++GC Sbjct: 157 -----WHNSFKVLATGAKRVGYKEILSGPMAINTEPYDD-----RAACQQLGFCMQGCKM 206 Query: 248 GAYYSSNSGGLIAAERTGNLVIRPNSIVTELIYDERAGRASGVRILDAETRKDEEFHADV 307 GA +S+ + AE +G +RP S+V + +D + GRA+ V DA + A V Sbjct: 207 GAKWSTLYTDIPRAEASGYCEVRPQSMVLRIEHDAK-GRANAVVYADASGTIQRQ-KARV 264 Query: 308 IFLCASALNSAWIMMNSTSSRFPNGFGNASDQLGRNVMDHHLGAGATGQAPEFADMYFSG 367 + + +++ S +++NS S+ FP+G N+S Q+GRN M H AG P+ +M+ G Sbjct: 265 VCVAGNSIESPRLLLNSASAMFPDGLANSSGQVGRNYMT-HTTAGIFAVMPKPVNMH-RG 322 Query: 368 RRPNGIYVPRFRNLGDAASKRSDYLRGF--GYQ------GGAGRATWERDRGQG-GRGFG 418 G+ N D RGF GY+ G + + +G G+ F Sbjct: 323 TTCAGVISDESYN---------DPSRGFVGGYRLEILALGLPFLSAFLDPTPKGWGKQFT 373 Query: 419 AARKAALSQPGPWTMGLSGFGEMLPYADNRVTLNRDVEDKFGLPTLTMNVTMRDNEMAMR 478 + + G W GE LP NR+TL+ +D++GLP + + + AMR Sbjct: 374 SRMEKYNHMSGVWLC-----GEDLPLESNRITLHDSEKDQYGLPIPVVTKSDHPMDAAMR 428 Query: 479 RDMQAAAAEMLEAAGFQNVRAHDNGFAPGLGIHEMGTARMGRDPKTSVLNAHNQVHECKN 538 + AA A EAAG ++ P H MGT RM + V+N Q H+ N Sbjct: 429 KHGVAATARCYEAAGATDIIE----LPPYPASHNMGTNRMSAMARDGVVNKWGQSHDIPN 484 Query: 539 VYVTDGAAMASASCVNPSLTYMALTARAADHAVR 572 ++V+DG+ ++ NP+LT +AL R A+ R Sbjct: 485 LFVSDGSQFTTSGGQNPTLTIVALALRQAEQIGR 518 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: 703 Number of extensions: 36 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 579 Length of database: 525 Length adjustment: 36 Effective length of query: 543 Effective length of database: 489 Effective search space: 265527 Effective search space used: 265527 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