Align glycerol-3-phosphate dehydrogenase; EC 1.1.5.3 (characterized)
to candidate H281DRAFT_04228 H281DRAFT_04228 homodimeric glycerol 3-phosphate dehydrogenase (quinone)
Query= CharProtDB::CH_091834 (512 letters) >FitnessBrowser__Burk376:H281DRAFT_04228 Length = 509 Score = 543 bits (1399), Expect = e-159 Identities = 277/480 (57%), Positives = 347/480 (72%), Gaps = 5/480 (1%) Query: 15 YDVAVVGGGINGVGIAADAAGRGLSVFLCEQHDLAQHTSSASSKLIHGGLRYLEHYEFRL 74 YD+ VVGGGING GIA DAAGRGLSV LCEQ DLA HTSSAS+KLIHGGLRYLE+ EF L Sbjct: 7 YDLLVVGGGINGAGIARDAAGRGLSVLLCEQDDLAAHTSSASTKLIHGGLRYLEYREFGL 66 Query: 75 VREALAEREVLLAKAPHIVKPLRFVLPHRPHLRPAWMIRAGLFLYDHLGKREKLPASRGL 134 VR+AL ERE LL APHI+ PLRFV+PH P LRPAW+IRAGLFLYDHL +RE LP SRG+ Sbjct: 67 VRKALQERETLLRAAPHIMWPLRFVMPHMPDLRPAWLIRAGLFLYDHLARRELLPGSRGI 126 Query: 135 RFT---GSSPLKAEIRRGFEYSDCAVDDARLVVLNAISAREHGAHVHTRTRCVSARRSKG 191 PL I+RGF YSD V+DARLVVLNA+ A EHGA + TRTR +SA R+ G Sbjct: 127 VMRDHPAGVPLVESIKRGFVYSDGWVNDARLVVLNALDAAEHGAKILTRTRLLSAVRAGG 186 Query: 192 LWHLHLERSDGSLYSIRARALVNAAGPWVARFIQDDLKQKSPYGIRLIQGSHIIVPKLYE 251 W L R+DG+ +RA ++ NAAGPWV +Q L + + + +RL++GSHI+ +L+E Sbjct: 187 EWRAQLRRADGTTVDVRAASIANAAGPWVGELLQGALGRAASHSVRLVKGSHIVTRRLFE 246 Query: 252 GEHAYILQNEDRRIVFAIPYLDRFTMIGTTDREYQGDPAKVAISEEETAYLLQVVNAHFK 311 ++AYI QN D+RI+FAIPY +T+IGTTD EY+GDPAKVAIS +ET YL +N +FK Sbjct: 247 HDYAYIFQNPDKRIIFAIPYEHDYTLIGTTDLEYRGDPAKVAISADETQYLCDSINRYFK 306 Query: 312 QQLAAADILHSFAGVRPLCDDE-SDEPSAITRDYTLSLSAGNGEPPLLSVFGGKLTTYRK 370 Q+++ AD+ +++GVRPL ++E +D PSA+TRDY+L L A GE PLLSVFGGK+TT+RK Sbjct: 307 QKISPADVRWTYSGVRPLLEEEGADNPSAVTRDYSLELDAPAGEAPLLSVFGGKITTFRK 366 Query: 371 LAESALTQLQPFFANLGPAWTAKAPLPGGEQMQ-SVEALTEQLANRYAWLDRELALRWAR 429 LAE A+ +L P + P+WTA APLPGG+ Q + E L ++AWL +LA R AR Sbjct: 367 LAEEAVDKLAPALGSDAPSWTAGAPLPGGDIPQANFERFLAGLKQQHAWLPADLAHRLAR 426 Query: 430 TYGTRVWRLLDGVNGEADLGEHLGGGLYAREVDYLCKHEWAQDAEDILWRRSKLGLFLSP 489 YGTRV ++ A LG+ GLY E+ YL EWA+ A D+LWRRSKLGL + P Sbjct: 427 AYGTRVKNVIGDARSLAGLGQAFAPGLYEAELTYLRDTEWARSAHDVLWRRSKLGLHVEP 486 Lambda K H 0.321 0.136 0.415 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: 786 Number of extensions: 24 Number of successful extensions: 4 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: 512 Length of database: 509 Length adjustment: 35 Effective length of query: 477 Effective length of database: 474 Effective search space: 226098 Effective search space used: 226098 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