Align Dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate Synpcc7942_0842 Synpcc7942_0842 glutathione reductase
Query= reanno::Smeli:SMc03204 (464 letters) >FitnessBrowser__SynE:Synpcc7942_0842 Length = 446 Score = 214 bits (546), Expect = 4e-60 Identities = 146/449 (32%), Positives = 222/449 (49%), Gaps = 19/449 (4%) Query: 8 LLVLGAGPGGYVAAIRAGQLGVNTVIVEKAKAGGTCLNVGCIPSKALIHA---ADEYHRL 64 LLV+GAG GG A+ RA G I E GGTC+ GC+P K +++A A +YH Sbjct: 7 LLVIGAGSGGLAASKRAASYGAKVAIAETDLVGGTCVIRGCVPKKLMVYASSFASQYHYA 66 Query: 65 RAAASGKGPLGLSLSAPAIDLRRTIAWKDGIVGRLNGGVTGLLKKAGVKAVIGEGRFVDG 124 A G S P + IA D V RL+ LL+KAGV ++G +FVD Sbjct: 67 EA-------YGWSAVQPQFSWPKLIAAIDAEVNRLSRLHISLLEKAGVDLILGHAQFVDE 119 Query: 125 KTVDVETETGLQRIRAEAIVIATGSAPVELPDLPFGGSVISSTQALALTDVPQTLAVIGG 184 + V G +++ A I+IA G P++LP +P G I+S + L + PQ AVIGG Sbjct: 120 HRLQV----GDRQVTAAKILIAAGGRPIKLP-IPGGELAITSREMFHLPEQPQRFAVIGG 174 Query: 185 GYIGLELGTAFAKLGSKVTVLEALDRILPQYDADLSKPVMKRLGELGVEVFTRTAAKRLS 244 GYIG E LGS+VT + DRIL +D +L + V + + GV+ T +R+ Sbjct: 175 GYIGCEFAGILRSLGSEVTQIIRRDRILQGFDQELREAVQTGMSQHGVQFRTGVTVERID 234 Query: 245 ADRRGLLAEENGRAFEVPAEKVLVTVGRRPVTDGWGLEEIDLDHSGRFIRIDDQCRTSMR 304 GL + + ++ ++VL+ GR P +G L+ + GR I +D RT+ Sbjct: 235 QTETGLQLSYSDGSQQI-VDQVLMATGREPWLEGLNLDAAGVAIEGRRIAVDAWSRTNQP 293 Query: 305 GVYAIGDVTGEPMLAHRAMAQGEMVAEIVAGHK-RSWDKRCIPAVCFTDPEIVGAGLSPE 363 ++A+GD T L A+A+G A+ G K R I + F+ PE GLS E Sbjct: 294 HIFAVGDCTDRVNLTPVAIAEGRAFADTEFGQKPRQISYENIASAVFSQPEACSVGLSEE 353 Query: 364 EARAAGID--VKIGQFPFQANGRAMTTLSEDGFVRVIARADNHLVLGIQAVGHGVSELSA 421 A+A + +++ + F+ + E ++++ ++ VLG VG +E+ Sbjct: 354 AAKAEYGEERIRVYRSRFRPMFYTLPQAEERVLMKLVVETESDRVLGAHMVGKDAAEIIQ 413 Query: 422 TFALAIEMGARLEDIAGTIHAHPTQSEAF 450 + A+A+ MGA D T+ HPT +E F Sbjct: 414 SVAIAVTMGATKADFDATMALHPTSAEEF 442 Lambda K H 0.319 0.137 0.396 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: 464 Number of extensions: 28 Number of successful extensions: 8 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: 464 Length of database: 446 Length adjustment: 33 Effective length of query: 431 Effective length of database: 413 Effective search space: 178003 Effective search space used: 178003 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 (21.7 bits) S2: 51 (24.3 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