Align D-mannonate oxidoreductase (EC 1.1.1.57) (characterized)
to candidate BPHYT_RS23425 BPHYT_RS23425 mannitol dehydrogenase
Query= ecocyc::MANNONOXIDOREDUCT-MONOMER (486 letters) >FitnessBrowser__BFirm:BPHYT_RS23425 Length = 496 Score = 389 bits (998), Expect = e-112 Identities = 213/476 (44%), Positives = 282/476 (59%), Gaps = 8/476 (1%) Query: 14 PSWDHSRLESRIVHLGCGAFHRAHQALYTHHLLESTDSDWGICEVNLMPGNDRVLIENLK 73 P W R+ IVHLG G FHRAHQALYT + + DWGIC V L D + L Sbjct: 25 PLWQEPRIG--IVHLGIGNFHRAHQALYTEEAMLAAGGDWGICGVTLQ--GDVGKRDALM 80 Query: 74 KQQLLYTVAEKGAESTELKIIGSMKEALHPEIDGCEGILNAMARPQTAIVSLTVTEKGYC 133 +QQ LY+V E+G ++ ++ +++E L D + +A P IVSLTVTEKGYC Sbjct: 81 EQQGLYSVVERGPHGAKVTVVRALREVLAMPHDQA-ALFARLADPAVRIVSLTVTEKGYC 139 Query: 134 ADAASGQLDLNNPLIKHDLENPTAPKSAIGYIVEALRLRREKGL-KAFTVMSCDNVRENG 192 D +G++ L+NP + HDL +P P++ G +V ALR R + + FTV+SCDN+ NG Sbjct: 140 RDPRTGEVALDNPAVAHDLASPFEPRTVPGILVAALRQRHDDARGQPFTVLSCDNLSHNG 199 Query: 193 HVAKVAVLGLAQARDPQLAAWIEENVTFPCTMVDRIVPAATPETLQEIADQLGVYDPCAI 252 + V A+ DP LA WI +V FP TMVDRIVPA T +A + D + Sbjct: 200 AALRQVVCSFARQLDPALADWIAAHVAFPSTMVDRIVPATTHAESVTVAHAIVYQDAAPV 259 Query: 253 ACEPFRQWVIEDNFVNGRPDWDKVGAQFVADVVPFEMMKLRMLNGSHSFLAYLGYLGGYE 312 CEPFRQWVIED F GRP WD VGAQ V DV PFE+ KLRMLNG+HS LAYL LGG+E Sbjct: 260 PCEPFRQWVIEDRFPAGRPAWDAVGAQLVDDVTPFELAKLRMLNGTHSTLAYLSMLGGFE 319 Query: 313 TIADTVTNPAYRKAAFALMMQEQAPTLSMPEGTDLNAYATLLIERFSNPSLRHRTWQIAM 372 TI ++ P R A+M +E APTL+MP DL+AY L+ER++NP+L+HR QIAM Sbjct: 320 TIDAAISYPPMRNLIHAMMTEEIAPTLTMPASFDLSAYRDALLERYANPALKHRCSQIAM 379 Query: 373 DGSQKLPQRLLDPVRLHLQNGGSWRHLALGVAGWMRYTQGVDEQGNAIDVVDPMLAEFQ- 431 DGSQK+P RLLD + + G S+ L L VA WM + +G + G ++ DP+ + Sbjct: 380 DGSQKIPPRLLDTIAARIDAGQSFTRLVLAVAAWMMFLRGHADDGTRYEISDPLASRLHA 439 Query: 432 -KINAQYQGADRVKALLGLSGIFADDLPQNADFVGAVTAAYQQLCERGARECVAAL 486 ++A + ALL + +F DL +F A+ A + L E GAR +AAL Sbjct: 440 LAVSAHDDPQALMDALLSVREVFPADLTAFPEFREALLRALRLLREEGARGAIAAL 495 Lambda K H 0.320 0.135 0.408 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: 664 Number of extensions: 27 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 486 Length of database: 496 Length adjustment: 34 Effective length of query: 452 Effective length of database: 462 Effective search space: 208824 Effective search space used: 208824 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: 52 (24.6 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