Align Dihydromonapterin reductase; H(2)-MPt reductase; EC 1.5.1.50; Dihydrofolate reductase; DHFR; EC 1.5.1.3 (uncharacterized)
to candidate AZOBR_RS00495 AZOBR_RS00495 dihydrofolate reductase folM
Query= curated2:A8AGY5 (240 letters) >FitnessBrowser__azobra:AZOBR_RS00495 Length = 242 Score = 156 bits (394), Expect = 4e-43 Identities = 91/234 (38%), Positives = 129/234 (55%), Gaps = 5/234 (2%) Query: 9 ILITGGGRRIGLAIAWHFLNQKQPVIVSYRTHYPAIDGLTQAGALCIQADFSTDDGVLAF 68 +L+TG GRR+GL +A + PVI YRT ++ L AGA+C+Q D + DG Sbjct: 10 VLVTGAGRRVGLHLAERMMALGHPVIAHYRTPTDGVERLRAAGAVCLQGDLADPDGGPRL 69 Query: 69 AEKIKTHTPGLRAILHNASAWMAEAPGTPLSDVLACM---MQIHVNTPYLLNHALERLLR 125 AE ++ LRA++HNASA+ AP T +D L + +HV P+ LN L LL Sbjct: 70 AEAVRAVAGSLRAVIHNASAFEVTAPDT--ADALRQLDVFHAVHVRAPFALNRELAPLLD 127 Query: 126 GHGHAATDIIHFTDYVVERGSDKHIAYAASKAALDNMTRSFARKLAPEVKVNAIAPSLIL 185 DI+H TD + + AY ASKA L N+ SFA++LAP+VKVN + P IL Sbjct: 128 ACSARRADIVHITDIYADNPNPAFDAYCASKAGLQNLALSFAKRLAPKVKVNVVQPGPIL 187 Query: 186 FNENDDAEYRQQALNKSLMKTAPGEKEVIDLVDYLLTSCFVTGRSFAVDGGRHL 239 F E E R + L+++L+ G + + V+ +L + + TG AVDGGR L Sbjct: 188 FKEWHGPEARARVLSETLLGEEGGVEAIGMAVEAILRNHYQTGAVVAVDGGRRL 241 Lambda K H 0.321 0.136 0.406 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: 170 Number of extensions: 7 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: 242 Length adjustment: 23 Effective length of query: 217 Effective length of database: 219 Effective search space: 47523 Effective search space used: 47523 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