Align mannitol 2-dehydrogenase (EC 1.1.1.67) (characterized)
to candidate BPHYT_RS16075 BPHYT_RS16075 D-arabinitol 4-dehydrogenase
Query= BRENDA::O08355 (493 letters) >FitnessBrowser__BFirm:BPHYT_RS16075 Length = 470 Score = 245 bits (626), Expect = 2e-69 Identities = 153/446 (34%), Positives = 226/446 (50%), Gaps = 9/446 (2%) Query: 29 IAHIGVGGFHRAHQAYYTDALMNT---GEGLDWSICGVGLRSEDRKARDDLAGQDYLFTL 85 I HIG G FHRAHQA+Y L GE WS+ +RS+ + LA Q+ ++TL Sbjct: 14 ILHIGAGSFHRAHQAWYLHRLNEAKVAGEP-HWSLTVGNIRSDMNAVLEALAAQNGVYTL 72 Query: 86 YELGDTDDTEVRVIGSISDMLLAEDSAQALIDKLASPEIRIVSLTITEGGYCIDDSNGEF 145 + + I SI ++ +S ALI+ A P +I++ T+TEGGY +D+ + E Sbjct: 73 ETVTPQGERAYETIRSIERVVPWTESLDALIEAGADPACKIIAFTVTEGGYYLDEQD-EL 131 Query: 146 MAHLPQIQHDLAHPSSPKTVFGFICAALTQRRAAGIPAFTVMSCDNLPHNGAVTRKALLA 205 P + DL T++G + A L R AG T+ +CDNL NG + Sbjct: 132 DTANPDLAADLE--GGHTTIYGALAAILDARMKAGAGPVTLQTCDNLRSNGERFHAGMSE 189 Query: 206 FAALHNA-ELHDWIKAHVSFPNAMVDRITPMTSTAHRLQLHDEHGIDDAWPVVCEPFVQW 264 F A EL W + + P++MVDRITP + R ++ G+DDA PV+ E F+QW Sbjct: 190 FLERRGASELAQWFDDNTASPSSMVDRITPRPTPDVRERVKAATGVDDAVPVMGEAFIQW 249 Query: 265 VLEDKFVNGRPAWEKVGVQFTDDVTPYEEMKIGLLNGSHLALTYLGFLKGYRFVHETMND 324 V+ED F+ GRPAWEKVG + D V PYEE KI +LN +H + + G L G ++HE D Sbjct: 250 VIEDNFIAGRPAWEKVGAELVDSVMPYEEAKIRILNATHSCIAWAGTLVGLNYIHEGTLD 309 Query: 325 PLFVAYMRAYMDLDVTPNLAPVPGIDLTDYKQTLVDRFSNQAIADQLERVCSDGSSKFPK 384 + Y+ DV P L P P +DL Y+ +++RFSN I D +RV +DG SK P Sbjct: 310 ADINKFAYEYVTEDVIPCLTPSP-LDLERYRDVVLERFSNPYIQDTNQRVAADGFSKLPG 368 Query: 385 FTVPTINRLIADGRETERAALVVAAWALYLKGVDENGVSYTIPDPRAEFCQGLVSDDALI 444 F PT++ G A++ A + +L + + YT D + +A Sbjct: 369 FIAPTLSECFERGVTPAATAMLPALFFRFLDRWNAGKLPYTYQDGVMDERVARAFFEAPD 428 Query: 445 SQRLLAVEEIFGTAIPNSPEFVAAFE 470 + A + + ++ +PE +A E Sbjct: 429 PLKAFAADRLLWGSMAQTPELESALE 454 Lambda K H 0.321 0.137 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: 595 Number of extensions: 31 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: 493 Length of database: 470 Length adjustment: 34 Effective length of query: 459 Effective length of database: 436 Effective search space: 200124 Effective search space used: 200124 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