Align mannitol 2-dehydrogenase (EC 1.1.1.67) (characterized)
to candidate BWI76_RS15490 BWI76_RS15490 mannitol dehydrogenase family protein
Query= BRENDA::O08355 (493 letters) >FitnessBrowser__Koxy:BWI76_RS15490 Length = 487 Score = 339 bits (870), Expect = 1e-97 Identities = 190/479 (39%), Positives = 268/479 (55%), Gaps = 8/479 (1%) Query: 11 LAPEVKLPAYTLADTRQGIAHIGVGGFHRAHQAYYTDALMNTGEGLDWSICGVGLRSEDR 70 L LPAY I H+G G FHRAHQA Y D L T G DW V L ++ Sbjct: 6 LTANATLPAYDRNRLIPRIVHLGFGAFHRAHQAVYADILA-TEHGSDWGYTEVNLIGGEQ 64 Query: 71 KARDDLAGQDYLFTLYELGDTDDTEVRVIGSISDMLLAE-DSAQALIDKLASPEIRIVSL 129 + D L QD L+T+ E+ D RV+G + + A+ D ++++ K+ P++ IVSL Sbjct: 65 QIAD-LQKQDLLYTVAEMS-ADAWTARVVGVVKQAMHAQVDGLESVLAKMCEPQVAIVSL 122 Query: 130 TITEGGYCIDDSNGEFMAHLPQIQHDLAHPSSPKTVFGFICAALTQRRAAGIPAFTVMSC 189 TITE GYC ++GE P I DL +P PK+ G + AL +R+AAG+PAF+VMSC Sbjct: 123 TITEKGYCHSPASGELQLDHPLIAADLQNPRQPKSAPGVVVEALARRKAAGLPAFSVMSC 182 Query: 190 DNLPHNGAVTRKALLAFAALHNAELHDWIKAHVSFPNAMVDRITPMTSTAHRLQLHDEHG 249 DN+P NG V R + A+A +A+L +WI +V+FP+ MVDRI P + ++ G Sbjct: 183 DNMPENGHVMRNVICAYARAVDADLAEWITRNVTFPSTMVDRIVPAVTADTLDKIAQLTG 242 Query: 250 IDDAWPVVCEPFVQWVLEDKFVNGRPAWEKVGVQFTDDVTPYEEMKIGLLNGSHLALTYL 309 + D V CEPF QWV+ED FV GRP WEK G + DV P+EEMK+ +LNGSH L YL Sbjct: 243 VRDPAAVACEPFRQWVIEDNFVAGRPQWEKAGAELVSDVLPFEEMKLRMLNGSHSFLAYL 302 Query: 310 GFLKGYRFVHETMNDPLFVAYMRAYMDLDVTPNLAPVPGIDLTDYKQTLVDRFSNQAIAD 369 G+L GY+ +++ M D + M + P L+ V G+DL Y L++R+SN A+ Sbjct: 303 GYLAGYQHINDCMQDANYRRAAHTLMLAEQAPTLS-VKGVDLARYAGLLIERYSNPALKH 361 Query: 370 QLERVCSDGSSKFPKFTVPTINRLIADGRETERAALVVAAWALYLKGVDENGVSYTIPDP 429 + ++ DGS K P+ + +I +ADG + A+ VA W Y+ GVD+ G + I DP Sbjct: 362 RTWQIAMDGSQKLPQRMLDSIRWHLADGGDFPLLAMGVAGWMRYVSGVDDQGQAIEISDP 421 Query: 430 RAEFCQGLVSDDALISQR---LLAVEEIFGTAIPNSPEFVAAFERCYGSLRDNGVTTTL 485 V + +R LL +E IFG ++P FV A R Y SL+ +G T+ Sbjct: 422 MLPVITQTVQNSEDGEERVRALLGIEAIFGLSLPKESRFVNAVVRAYLSLQAHGAKATV 480 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: 602 Number of extensions: 31 Number of successful extensions: 4 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: 487 Length adjustment: 34 Effective length of query: 459 Effective length of database: 453 Effective search space: 207927 Effective search space used: 207927 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