Align Dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate WP_002721120.1 RSPH17029_RS12910 FAD-dependent oxidoreductase
Query= reanno::pseudo6_N2E2:Pf6N2E2_478 (461 letters) >NCBI__GCF_000015985.1:WP_002721120.1 Length = 401 Score = 68.2 bits (165), Expect = 5e-16 Identities = 73/236 (30%), Positives = 102/236 (43%), Gaps = 30/236 (12%) Query: 125 KTVEVGDTRIQCEHLLLATGSKSVDLPMLPVGGPI--------ISSTEALAPT-SVPKHL 175 +TV VG I L L TGS + LP GG + ++ + + P + L Sbjct: 88 RTVTVGGEAIPYGRLALTTGSAARHLPEA-AGGKLDGVYTVRTLADVDRMRPEFQAGRRL 146 Query: 176 VVVGGGYIGLELGIAYRKLGAEVSVVEAQERILPAYDGELTQPVHEALKQL-GVKLYLKH 234 VV+GGGYIGLE KLG V+VVE RIL T AL GV++ Sbjct: 147 VVIGGGYIGLEAAAVGAKLGLAVTVVEMAPRILQRVAAPETADWFRALHAAHGVRI---- 202 Query: 235 SVEGFDAQASTLQVRDPA---GDTLNLDTDRVLVAVGRKPNTQGWNLEALNLAMNGAAVK 291 +EG + T + R D +L D V+ VG +P T+ EA LA++ + Sbjct: 203 -LEGVALERLTGEGRVTGALLADGTHLPADFVIAGVGIRPVTE--LAEAAGLALDN-GIA 258 Query: 292 IDQRCQTSMRNVWAIGDLSGEPMLAHR--------AMAQGEMVAELIAGQHREFNP 339 +D QTS +W+ GD + P R A+ Q E VA + G + P Sbjct: 259 VDALGQTSDPAIWSAGDCASFPWRGGRLRLESVQNAIDQAEAVAANMLGAGAPYLP 314 Score = 25.8 bits (55), Expect = 0.003 Identities = 64/272 (23%), Positives = 104/272 (38%), Gaps = 20/272 (7%) Query: 175 LVVVGGGYIGLELGIAYRKLGAEVSVVEAQERILPAYDGELTQPVHEALKQLGVKLYLKH 234 +VVVG G G L R L E S++ A E P Y + +L+L++ Sbjct: 4 IVVVGAGQAGAALVAKLRALKFEGSILLAGEEPSPPYQRPPLSKAYLLGTMEEERLWLRN 63 Query: 235 SVEGFDAQASTLQVRDPAGDTLNLDTDRVLVAVGRKPNTQGWNLEALNLAMNGAAVKIDQ 294 F A+A +++R A T +D V VG + G L L AA + + Sbjct: 64 --RAFYAEAG-IELRLGAPVTA-IDRAARTVTVGGEAIPYG----RLALTTGSAARHLPE 115 Query: 295 RCQTSMRNVWAIGDLSGEPMLAHRAMAQGEMVAELIAGQHREFNPTAIAAVCFTDPELVV 354 + V+ + L+ + A +V +I G + A+ A +V Sbjct: 116 AAGGKLDGVYTVRTLADVDRMRPEFQAGRRLV--VIGGGYIGLEAAAVGAKLGLAVTVVE 173 Query: 355 VGKTPDEAKAAGLDCIVSSFPFAANG----RAMTLESKSGFVRV---VARRDNHLIVGWQ 407 + + AA AA+G + LE +G RV + HL + Sbjct: 174 MAPRILQRVAAPETADWFRALHAAHGVRILEGVALERLTGEGRVTGALLADGTHLPADFV 233 Query: 408 AVGVG---VSELSTAFGQSLEMGARLEDIAGT 436 GVG V+EL+ A G +L+ G ++ + T Sbjct: 234 IAGVGIRPVTELAEAAGLALDNGIAVDALGQT 265 Lambda K H 0.318 0.135 0.394 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: 411 Number of extensions: 21 Number of successful extensions: 4 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: 461 Length of database: 401 Length adjustment: 32 Effective length of query: 429 Effective length of database: 369 Effective search space: 158301 Effective search space used: 158301 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: 51 (24.3 bits)
This GapMind analysis is from Apr 10 2024. 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