Align NADH-dependent phenylglyoxylate dehydrogenase subunit alpha; Phenylglyoxylate:NAD oxidoreductase; Phenylglyoxylate:acceptor oxidoreductase; EC 1.2.1.58 (characterized)
to candidate 8499838 DvMF_0603 2-oxoglutarate ferredoxin oxidoreductase subunit alpha (RefSeq)
Query= SwissProt::Q8L3B1 (417 letters) >FitnessBrowser__Miya:8499838 Length = 382 Score = 112 bits (281), Expect = 1e-29 Identities = 106/355 (29%), Positives = 161/355 (45%), Gaps = 39/355 (10%) Query: 16 RKQKVILAEGNEAAALGVALARPDMVSVYPITPQSSLVEHVAK---LIADGRMDADIVDA 72 RK++ + A GNEA A G LA + YPITP + ++E +A LI DG + Sbjct: 8 RKRRELFALGNEAVAEGALLAGCSFYAGYPITPSTEIMEVMANRLPLIEDGVF----IQM 63 Query: 73 EGEHSVLSVLQGGALAGARTYTATCGPGLAFMFEPYFRTSGMRLPIVLTIVTRDGIT--- 129 E E + + G +LAG + TAT GPG A M E + P+V+ V R G + Sbjct: 64 EDEIASMGATIGASLAGRKAMTATSGPGFALMQEHIGYACMVEAPLVVVNVMRGGPSTGL 123 Query: 130 ---------PQSVWGGHQDAMTVREAGWIQVYCESVQEVLDTTVMAFKIAEHHDVMLPVN 180 + WG H D I + +VQE L+ TV AF AE + PV Sbjct: 124 PTSPAQADVQMARWGTHGDHPI------IVLSASNVQECLEMTVTAFNFAEKY--RTPVI 175 Query: 181 VCLDGNYLSYGASRVELPDQAVVDEFMGEKNVNWHVALDPLRPMAVDPLTG----GTTGK 236 + LD ++ ++ +PD DE V V + +P A D G G Sbjct: 176 LLLD-EVTAHTREKITVPDP---DEVEILSRVEPTVPPEWFKPYA-DTARGVPAMAPIGS 230 Query: 237 GPQTFVRYRKGQCRGMQNAL-SVIEEVHADWAKRIGRSFA--PLVEEYRLDDAEFAIMTL 293 G +T V G +++ ++I + + + +EY LDDAE A++ Sbjct: 231 GYRTHVTGLTHDVMGYPTQRPDEVKDAMLRLFRKIDQYYGDIQMSDEYMLDDAEVAVVAY 290 Query: 294 GSMTGAAKDAVDEAREAGKKIGLIKIKTFSPFPVEALKKALGKVKALGVIDRSVG 348 GS+ +A AV++ARE G K GL+ +KT PFP A++K + + V + ++G Sbjct: 291 GSVARSAHLAVEQARERGAKAGLLTLKTLFPFPRPAVEKLTHRCHTVVVPEMNMG 345 Lambda K H 0.319 0.135 0.403 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: 348 Number of extensions: 24 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 417 Length of database: 382 Length adjustment: 31 Effective length of query: 386 Effective length of database: 351 Effective search space: 135486 Effective search space used: 135486 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 (21.8 bits) S2: 50 (23.9 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