Align dihydromonapterin reductase (EC 1.5.1.50) (characterized)
to candidate GFF3777 HP15_3719 short-chain dehydrogenase/reductase SDR
Query= BRENDA::P0AFS3 (240 letters) >FitnessBrowser__Marino:GFF3777 Length = 235 Score = 251 bits (640), Expect = 1e-71 Identities = 129/232 (55%), Positives = 164/232 (70%), Gaps = 1/232 (0%) Query: 8 PILITGGGRRIGLALAWHFINQKQPVIVSYRTHYPAIDGLINAGAQCIQADFSTNDGVMA 67 PILITG G+RIGLA A +++ QP+IV+YRT+ PAID L AGA C+ ADF+TN G+ Sbjct: 4 PILITGAGQRIGLAFARACLDRGQPIIVTYRTYRPAIDALQKAGAVCLHADFATNAGIDD 63 Query: 68 FADEVLKSTHGLRAILHNASAWMAEKPGAPLADVLACMMQIHVNTPYLLNHALERLLRGH 127 F + T LRAI+HNAS W+ E + ADV+ MMQIHV TPY +N +L Sbjct: 64 FIQALKSRTDTLRAIIHNASDWIPESEDSDPADVMNAMMQIHVMTPYRINLTCRSMLEQE 123 Query: 128 GHAASDIIHFTDYVVERGSDKHIAYAASKAALDNMTRSFARKLAPEVKVNSIAPSLILFN 187 G + +DIIH TDYVVE+GS KHIAYAASKAAL N+T SFAR LAP VKVN++APSLI+FN Sbjct: 124 G-STTDIIHMTDYVVEKGSAKHIAYAASKAALTNLTLSFARLLAPRVKVNAVAPSLIMFN 182 Query: 188 EHDDAEYRQQALNKSLMKTAPGEKEVIDLVDYLLTSCFVTGRSFPLDGGRHL 239 + D YR++ L KSLM PG + + + +LL + ++TGR+ PLDGGRHL Sbjct: 183 QGDSQAYREKTLKKSLMGIEPGAEVAVATLQFLLDNPYITGRTLPLDGGRHL 234 Lambda K H 0.322 0.136 0.407 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: 186 Number of extensions: 6 Number of successful extensions: 2 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: 240 Length of database: 235 Length adjustment: 23 Effective length of query: 217 Effective length of database: 212 Effective search space: 46004 Effective search space used: 46004 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 (21.9 bits) S2: 46 (22.3 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