Align Dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate SM_b20820 SM_b20820 ferredoxin reductase
Query= reanno::pseudo6_N2E2:Pf6N2E2_478 (461 letters) >FitnessBrowser__Smeli:SM_b20820 Length = 409 Score = 72.4 bits (176), Expect = 3e-17 Identities = 77/251 (30%), Positives = 120/251 (47%), Gaps = 24/251 (9%) Query: 66 RHHSQGSALGITVSAPSLDIGKSVEWKDGIVD----RLTTGVAALLKKHKVQVIHG-WAK 120 R G + +T + P L + KDG+ + G AA ++ ++ V+ G A+ Sbjct: 21 REKGFGGEITLTGAEPHLPYERPPLSKDGLAQASLPKFIAG-AARYEEARITVLTGVTAE 79 Query: 121 VIDG--KTVEVGD-TRIQCEHLLLATGSKSVDLPMLPVGGPIISS----TEALA---PTS 170 ID K V + D + + LLLATG++ P +P I + +ALA + Sbjct: 80 SIDRVHKAVTLSDGVSLDYDRLLLATGARPRAFPRVPENAGRIRTLRTHADALAIRGALT 139 Query: 171 VPKHLVVVGGGYIGLELGIAYRKLGAEVSVVEAQERILP-AYDGELTQPVHEALKQLGVK 229 L V+GGG+IGLEL RKLGAEV +VE R+L E+ V E ++ GV+ Sbjct: 140 PGARLAVIGGGFIGLELAATARKLGAEVVLVEGLPRVLSRGVPEEIAVLVAERHRREGVE 199 Query: 230 LYLKHSVEGFDAQASTLQVRDPAGDTLNLDTDRVLVAVGRKPNTQGWNLEALNLAM-NGA 288 + + D ++ D ++++ D ++V +G PNT+ EA LA+ NG Sbjct: 200 IICGAQIAAIDGAGDGARLL--LADGVDIEADLIVVGIGAVPNTE--LAEAAGLAIENGI 255 Query: 289 AVKIDQRCQTS 299 AV D+R TS Sbjct: 256 AV--DERLCTS 264 Score = 29.3 bits (64), Expect = 3e-04 Identities = 26/111 (23%), Positives = 49/111 (44%), Gaps = 17/111 (15%) Query: 174 HLVVVGGGYIGLELGIAYRK--LGAEVSVVEAQERILPAYDGELTQPVHEALKQLGVKLY 231 H+V++G G G A R+ G E+++ A+ LP L++ + L Q + + Sbjct: 3 HIVIIGAGECGARAAFALREKGFGGEITLTGAEPH-LPYERPPLSK---DGLAQASLPKF 58 Query: 232 LKHSVEGFDAQASTL-----------QVRDPAGDTLNLDTDRVLVAVGRKP 271 + + +A+ + L D ++LD DR+L+A G +P Sbjct: 59 IAGAARYEEARITVLTGVTAESIDRVHKAVTLSDGVSLDYDRLLLATGARP 109 Score = 28.9 bits (63), Expect = 3e-04 Identities = 31/109 (28%), Positives = 47/109 (43%), Gaps = 15/109 (13%) Query: 4 TLNTTLLIIGGGPGGYVAAIRAGQLGIPTILVEGQALGGTCLNIGCIPSKALIHVAEQFH 63 T L +IGGG G A A +LG +LVEG L+ G +P + + VAE Sbjct: 139 TPGARLAVIGGGFIGLELAATARKLGAEVVLVEGLP---RVLSRG-VPEEIAVLVAE--- 191 Query: 64 QTRHHSQGSALGITVSAPSLD---IGKSVEWKDGI---VDRLTTGVAAL 106 RH +G + ++D G + DG+ D + G+ A+ Sbjct: 192 --RHRREGVEIICGAQIAAIDGAGDGARLLLADGVDIEADLIVVGIGAV 238 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: 409 Number of extensions: 19 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 461 Length of database: 409 Length adjustment: 32 Effective length of query: 429 Effective length of database: 377 Effective search space: 161733 Effective search space used: 161733 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 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