Align glycerol-3-phosphate dehydrogenase [NAD(P)+] (EC 1.1.1.94) (characterized)
to candidate SM_b20499 SM_b20499 glycerol-3-phosphate dehydrogenase
Query= BRENDA::P13035 (501 letters) >FitnessBrowser__Smeli:SM_b20499 Length = 577 Score = 186 bits (473), Expect = 1e-51 Identities = 154/503 (30%), Positives = 235/503 (46%), Gaps = 46/503 (9%) Query: 5 DLIVIGGGINGAGIAADAAGRGLSVLMLEAQDLACATSSASSKLIHGGLRYLEHYEFRLV 64 D+ V+GGGING + + A +G+ VL++E D S+A S+++HGGLRYLE+ EF LV Sbjct: 17 DVCVLGGGINGLSVFRELALQGVRVLLVEKHDYCSGASAALSRMVHGGLRYLENGEFTLV 76 Query: 65 SEALAEREVLLKMAPHIAFPMRFRLP-------------------HRPHLRPAWMIRIGL 105 E+L ER+ LL+ APH+ P+ +P RP R A I+ GL Sbjct: 77 KESLVERDRLLRNAPHLVSPLATTVPVFDIFSGLANGIVRFLGLSRRPSRRGAIAIKAGL 136 Query: 106 FMYDHLGKRTSLPGSTGLR-----FGANSVLKPEIKRGFEYSDCWVD-DARLVLANAQMV 159 +YD L ++ +L R L P+I+ Y D WV R+ + Q Sbjct: 137 SIYDLLTRKRALMPRHRFRGRRATLAKWPALNPKIRSSATYYDAWVSHPERIGMELLQDG 196 Query: 160 VRKGGEVLTRTRATSARRENGLWIVEAEDIDTGKKYSWQARGLVNATGPWVKQFFDDGMH 219 + E A R E G +I+ A+D++ G + +VNATG W+ +G Sbjct: 197 LSASTEAAALNYAELRRNEAGTYII-ADDVE-GVSVEIEPSLIVNATGGWID--ITNGAL 252 Query: 220 LPSPYGIRLI----KGSHIVVPRVHTQ----KQAYILQNEDKRIVFVIPWMDEFSIIGTT 271 LP + + KGSH+++ VH + +NED RI + P+ + ++G+T Sbjct: 253 LPPDHRSAPLMGGTKGSHLIIDNVHLRDALGDHMIYYENEDGRICILFPYFGKV-LVGST 311 Query: 272 DVEYKGDPKAVKIEESEINYLLNVYNTHFKK-QLSRDDIVWTYSGVRPLCDDESDSPQAI 330 D+ DP V+ EE E +Y+L ++ ++IV+ +SGVRPL I Sbjct: 312 DIRV-DDPGTVRCEEEERDYILQSLAFVLPGIEIGPEEIVYKFSGVRPLPASSDSFTGRI 370 Query: 331 TRDYTLDIHDENGKAPLLSVFGGKLTTYRKLAEHALEKLTPYYQGIGPAWTKESVLPGG- 389 RD+ + + G P+L + GGK TT+R E A + + T + + GG Sbjct: 371 PRDHFCTMIESAG-TPVLCMIGGKWTTFRSFGELAADTVLERLGLPRRTSTADRAIGGGR 429 Query: 390 AIEGDRDDYAARLRRRYPFLTESLARHYARTYGSNSELLLGNAGTVSDLG-EDFGHEFYE 448 DR+ + A L R +A ++R YG+ +E L G SD GH Sbjct: 430 RFPADRESWIAALAARCGLPPPHVAELFSR-YGTEAEALAAFIGQGSDAAIPGAGHTM-- 486 Query: 449 AELKYLVDHEWVRRADDALWRRT 471 EL +L+ +E V DD L RRT Sbjct: 487 RELLFLIRNEAVEHLDDLLLRRT 509 Lambda K H 0.320 0.137 0.417 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: 600 Number of extensions: 32 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: 501 Length of database: 577 Length adjustment: 35 Effective length of query: 466 Effective length of database: 542 Effective search space: 252572 Effective search space used: 252572 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: 52 (24.6 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