Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate GFF4004 HP15_3944 alcohol dehydrogenase zinc-binding domain protein
Query= BRENDA::P22144 (363 letters) >FitnessBrowser__Marino:GFF4004 Length = 368 Score = 112 bits (279), Expect = 2e-29 Identities = 105/345 (30%), Positives = 162/345 (46%), Gaps = 34/345 (9%) Query: 30 DVLVQVKKTGICGSDIHFYAHGRIGNFVLTKPMVLGHESAGTVVQVGKGVTSLKVGDNVA 89 ++ +++ G+C SD+ G P+VLGHE+AG VV+VG+GVT+ K GD+V Sbjct: 31 EITIKIAACGVCHSDLS----ATTGKIPYPPPLVLGHEAAGVVVEVGEGVTAFKEGDHVV 86 Query: 90 IEPGIPSRFSDEYKSGHYNLCPHMAFA------ATPNSK--EGEP----NPPGTLCKYFK 137 + G LC + A T +K +GEP G + ++ Sbjct: 87 STFISMCGKCSQCVRGRPVLCENARKAMFNLPDGTVRTKGADGEPLNVFGACGVMAEFAT 146 Query: 138 SPEDFLVKLPDHVSLELGALVE-PLSVGVHA-SKLGSVAFGDYVAVFGAGPVGLLAAAVA 195 D VK+ + V ++ ALV + GV A + G AVFG G VGL A Sbjct: 147 MHVDNCVKVDETVPMQNAALVGCAVMTGVGAVFNTAKLEPGSRAAVFGIGGVGLNAIQGC 206 Query: 196 KTFGAKGVIVVDIFDNKLKMAKDIGAATHTFN-SKTGGSEELIKAFGGNVPNVVLECTGA 254 T GA+ V+ VD KL MAK+ G ATHT N ++ + + +K G V + EC GA Sbjct: 207 VTAGAEMVVAVDSNPAKLAMAKEFG-ATHTVNINEVEDAAKAVKKMTGGV-DYAFECVGA 264 Query: 255 EPCIKLGVDAIAPGGRFVQVGNAAGPVSFPITVFAM--KELTLFGSFRYGF---NDYKTA 309 P ++ ++ GG V VG A +T + E TL GS+ +D+ Sbjct: 265 GPVVEQAYKSLGRGGTAVVVGVADPKDKTSLTTLTLPADERTLKGSWLGSARPQHDFPRI 324 Query: 310 VGIFDTNYQNGRENAPIDFEQLITHRYKFKDAIEAYDLVRAGKGA 354 +G+ Y+ G+ + ++L+T Y ++A +A+D + AGK A Sbjct: 325 LGL----YKAGK----LKLDELVTRTYPIEEAAQAFDDMVAGKNA 361 Lambda K H 0.318 0.138 0.411 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: 343 Number of extensions: 23 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: 363 Length of database: 368 Length adjustment: 30 Effective length of query: 333 Effective length of database: 338 Effective search space: 112554 Effective search space used: 112554 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 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