Align 6,7-dihydropteridine reductase (EC 1.5.1.34) (characterized)
to candidate Ga0059261_2819 Ga0059261_2819 Short-chain dehydrogenases of various substrate specificities
Query= BRENDA::P09417 (244 letters) >FitnessBrowser__Korea:Ga0059261_2819 Length = 222 Score = 97.4 bits (241), Expect = 2e-25 Identities = 65/194 (33%), Positives = 99/194 (51%), Gaps = 6/194 (3%) Query: 13 VLVYGGRGALGSRCVQAFRARNWWVASVDVVENEEASASIIVKMTDSFTEQADQVTAEVG 72 V+V GG G LG V ++R V +VD+ + + +I + + +E Sbjct: 4 VIVTGGLGGLGRAVVTTLKSRGHRVVAVDIASGQSDADRVIAGVDLADETAVATAFSEAA 63 Query: 73 KLLGEEKVDAILCVAGGWAGGNAKSKSLFKNCDLMWKQSIWTSTISSHLATKHLKEGGLL 132 LGE +DA++ VAGG+ ++ S+ + D M++ ++ T+ ISS HLK G ++ Sbjct: 64 GALGE--IDALVNVAGGFTWEPVETGSM-ASWDAMYRINLRTAAISSRAVLPHLKSGAIV 120 Query: 133 TLAGAKAALDGTPGMIGYGMAKGAVHQLCQSLAGKNSGMPPGAAAIAVLPVTLDTPMNRK 192 + A +A G GM Y +K V L +SLA + G G A+LP LDTP NRK Sbjct: 121 NVGAAASAAPGM-GMAPYAASKAGVMALTESLAEELRGR--GIRVNAILPTILDTPANRK 177 Query: 193 SMPEADFSSWTPLE 206 MP+AD + W LE Sbjct: 178 DMPDADPAGWVSLE 191 Lambda K H 0.316 0.129 0.390 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: 130 Number of extensions: 9 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: 244 Length of database: 222 Length adjustment: 23 Effective length of query: 221 Effective length of database: 199 Effective search space: 43979 Effective search space used: 43979 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 (21.6 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