Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate PfGW456L13_3453 Short-chain dehydrogenase/reductase SDR
Query= metacyc::MONOMER-16231 (254 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3453 Length = 272 Score = 143 bits (360), Expect = 4e-39 Identities = 90/254 (35%), Positives = 139/254 (54%), Gaps = 11/254 (4%) Query: 1 MKLLEGKTVLVTGASTGIGRAAAIGAAQHGADVAINYAHSDGPAQSCVAEIEALGQRAIA 60 +K L+GK ++TGA +GIGRA+A+ A+ GA V + ++ AQ+ AEI G A+ Sbjct: 5 LKRLDGKVCVITGAGSGIGRASALRFAREGATVVVTDLFAES-AQAVAAEI---GVNALV 60 Query: 61 VKGDVADPQTAQDFVAKAVETFGKVDVMVSNA-----GICPFHAFLDMPVDVVERTFKVN 115 ++ DV ++ V + V TFG++DV+ +NA F++ ++ +VN Sbjct: 61 LQVDVGQEDALREMVEQTVRTFGRIDVLFNNAVYRNPATTRDIDFINFNTELFHNCMRVN 120 Query: 116 LHGAYFMVQAAAQQMVRQGHGGSIVAVSSISALVGGEYQTHYTPTKAGVHSLMQSTAIAL 175 + G + A M+ QG GSI+ SS S++ G Q Y +KA ++ +Q+ A Sbjct: 121 VLGGVLACKYALPHMLAQG-SGSILFTSSTSSIAGEISQFSYGASKAALNWYVQTIAATF 179 Query: 176 GKHGIRCNSVLPGTILTEINKDDLADQEKREYMEARTPLGRLGAPEDLAGPIVFLASDMA 235 GK GIRCN +LPG I T + + K +++ + + +LG PED+A FLASD A Sbjct: 180 GKRGIRCNGILPGVIRTPAMESWANEAMKSAFLDLQN-VPQLGEPEDIAAMAAFLASDDA 238 Query: 236 AYVTGAALLVDGGM 249 AYV G + VDGGM Sbjct: 239 AYVNGTLMRVDGGM 252 Lambda K H 0.318 0.133 0.379 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: 135 Number of extensions: 4 Number of successful extensions: 3 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: 254 Length of database: 272 Length adjustment: 25 Effective length of query: 229 Effective length of database: 247 Effective search space: 56563 Effective search space used: 56563 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: 47 (22.7 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