Align glycerol-3-phosphate dehydrogenase (EC 1.1.5.3) (characterized)
to candidate RR42_RS13815 RR42_RS13815 FAD-dependent oxidoreductase
Query= BRENDA::Q06B39 (650 letters) >FitnessBrowser__Cup4G11:RR42_RS13815 Length = 534 Score = 366 bits (939), Expect = e-105 Identities = 219/567 (38%), Positives = 306/567 (53%), Gaps = 48/567 (8%) Query: 53 EQYQRLASHTKNNPFDVLVIGGGATGAGCAFDAQTRGLQTALIEREDFASGTSSRSTKLV 112 E+ LA+ + +DV+VIGGGATG G A DA +RG +T L+E DFA GTSS++TKLV Sbjct: 12 ERATLLATLEREPKWDVIVIGGGATGLGTAVDAASRGYRTLLVEAADFAKGTSSKATKLV 71 Query: 113 HGGVRYLEKAVFNLDYDQLKLVYEALHERDRLLSNASHLAHPLPILTPCYNWWEVPYYWA 172 HGGVRYL + + LV EALHER L NA HL PL + P Y ++ P+Y Sbjct: 72 HGGVRYLAQG-------NISLVREALHERGLLARNAPHLVWPLGFVVPAYQLFDQPFYGI 124 Query: 173 GMKMYDLVAGTSTLVPSKFLTSLETLTYLPTMSKNIGGKSLKGSIMYYDGQFNDSRMNVA 232 G+K+YD++AG L S++L ETL PT+++++GG+ L+G +Y+DGQF+D+R+ +A Sbjct: 125 GLKLYDMLAGGLNLSGSRWLNHRETLAAAPTLAEHVGGRPLRGGNLYFDGQFDDARLAIA 184 Query: 233 LACSSAAAGATVMNYTECKQLIKDDQGKVIGARCRDRATGAETDVYARVLINATGAFADD 292 L + G T +NY L G + G +D A D+ A +INATG + D Sbjct: 185 LMRTLFDVGGTAINYLRVSGL-SQRNGVIDGVTVQDVLGDASFDLKASCVINATGVWVDA 243 Query: 293 VRRYSEPDAQQTVMASSGAHVTLPDFYGSARTGMIIPKTKDGRVIFMLPFQGHVIAGTTD 352 VR+ + A+ V S G H+TLP + ++IPKT DGRV+F++P+ GH I GTTD Sbjct: 244 VRQMEDGQARSMVAPSQGVHLTLPRSFLPGDRAILIPKTDDGRVLFVVPWNGHTIIGTTD 303 Query: 353 TPIK-ATSRPRSSEEDIDFILATLSDFLDVRVSRGDVLSTWCGIRPLPAPKKNTTSENVV 411 TP K PR+ +D+DFIL T + +L +R DV S W G+RPL ++ ++ Sbjct: 304 TPRKDLPLEPRAGADDVDFILETATRYLSRAPTRADVTSVWAGLRPLVKATGEASTASLS 363 Query: 412 RDHVIFEDKDGLLNVTGGKWTTYRAMAEQAIDLAMASGKLPKSAKPCQTANYKLLGATNY 471 R+H I K GL+ VTGGKWTTYR MAE + A+ LP A PC TA+ L GA Sbjct: 364 REHTILVSKAGLITVTGGKWTTYRKMAEDVVGTAIQRQMLP--AAPCVTADLPLHGAQGL 421 Query: 472 TYTLMAELAQQHGMPQRYFGKNSSKERNSNGSPRVAMDTEIAHHLSTAYGDNAMRVIAMA 531 L A G P RY+G A L T G++ M Sbjct: 422 PANLP---APGSGSPDRYYGNE-------------------AGMLHTLPGNDEM------ 453 Query: 532 EEEGLGKRLIAGHPILEAEVMYTAKHEYCLTIEDFIDRRSRLAFLDVKATEAALPRIAEI 591 L+ G + A V + A+ E +ED + RR+R FL+ A AA PR+AEI Sbjct: 454 --------LVPGAGLTAAHVRFAARFELARRVEDVLARRNRALFLEASAASAAAPRVAEI 505 Query: 592 MGNTLGWNDKQRTSAITAAVKHLQENF 618 + G +D +A A+ + L + Sbjct: 506 LAEEHG-HDAAWQAAEVASFRELASGY 531 Lambda K H 0.317 0.132 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: 851 Number of extensions: 43 Number of successful extensions: 6 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: 650 Length of database: 534 Length adjustment: 37 Effective length of query: 613 Effective length of database: 497 Effective search space: 304661 Effective search space used: 304661 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: 53 (25.0 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