Align glycerol-3-phosphate dehydrogenase; EC 1.1.5.3 (characterized)
to candidate GFF2721 Psest_2775 Glycerol-3-phosphate dehydrogenase
Query= CharProtDB::CH_091834 (512 letters) >FitnessBrowser__psRCH2:GFF2721 Length = 511 Score = 743 bits (1917), Expect = 0.0 Identities = 364/495 (73%), Positives = 423/495 (85%), Gaps = 1/495 (0%) Query: 10 PLAEVYDVAVVGGGINGVGIAADAAGRGLSVFLCEQHDLAQHTSSASSKLIHGGLRYLEH 69 P++E+YDVAV+GGGINGVGIAADAAGRGLSVFLCE+ DLA HTSSASSKLIHGGLRYLEH Sbjct: 7 PVSELYDVAVIGGGINGVGIAADAAGRGLSVFLCERDDLASHTSSASSKLIHGGLRYLEH 66 Query: 70 YEFRLVREALAEREVLLAKAPHIVKPLRFVLPHRPHLRPAWMIRAGLFLYDHLGKREKLP 129 YEFRLVREALAERE+LLAKAPHIVKP+RFVLPHRPHLRPAWMIRAGLFLYD+LG R+KLP Sbjct: 67 YEFRLVREALAEREMLLAKAPHIVKPMRFVLPHRPHLRPAWMIRAGLFLYDNLGMRKKLP 126 Query: 130 ASRGLRFTGSSPLKAEIRRGFEYSDCAVDDARLVVLNAISAREHGAHVHTRTRCVSARRS 189 ASRGLRF SPLK I RGFEYSDC VDDARLVVLNA++ARE GAH+HTRT+C+SA+R+ Sbjct: 127 ASRGLRFGSESPLKPVITRGFEYSDCWVDDARLVVLNAMAAREKGAHIHTRTQCLSAKRA 186 Query: 190 KGLWHLHLERSDGSLYSIRARALVNAAGPWVARFIQDDLKQKSPYGIRLIQGSHIIVPKL 249 G+WH+ L+R DGS +S+RA+ALVNAAGPWVA+FI ++L+Q+SPYGIRLIQGSHIIVPKL Sbjct: 187 GGIWHVELQREDGSRFSLRAKALVNAAGPWVAQFIGENLQQRSPYGIRLIQGSHIIVPKL 246 Query: 250 YEGEHAYILQNEDRRIVFAIPYLDRFTMIGTTDREYQGDPAKVAISEEETAYLLQVVNAH 309 YEGE AYI+QNEDRRIVFAIPYLDR+TMIGTTDREY+GDPAKV+ISEEE AY+L V N H Sbjct: 247 YEGEQAYIMQNEDRRIVFAIPYLDRYTMIGTTDREYRGDPAKVSISEEEIAYVLGVANTH 306 Query: 310 FKQQLAAADILHSFAGVRPLCDDESDEPSAITRDYTLSLSAGNGEPPLLSVFGGKLTTYR 369 F++QL DI+H+FAGVRPLCDDESD PSA+TRDYTLSL+A + PLLSVFGGKLTTYR Sbjct: 307 FRKQLEPRDIVHTFAGVRPLCDDESDNPSAVTRDYTLSLAAEEKQAPLLSVFGGKLTTYR 366 Query: 370 KLAESALTQLQPFFANLGPAWTAKAPLPGGEQMQSVEALTEQLANRYAWLDRELALRWAR 429 KLAESA+ QL+PFF +G +WTA+A LPGGE M + +ALTE+L + L LA RWA Sbjct: 367 KLAESAMAQLKPFFPAMGGSWTAQAALPGGEDMSTADALTEELVAKVQGLKLPLAKRWAT 426 Query: 430 TYGTRVWRLLDGVNGEADLGEHLGGGLYAREVDYLCKHEWAQDAEDILWRRSKLGLFLSP 489 YG RVWR+L + LGE LG LYA+EV+YL + EWA +DILWRR+KLGL S Sbjct: 427 LYGNRVWRMLGEAHSLDALGEDLGQQLYAQEVEYLRREEWATQVDDILWRRTKLGLAFSE 486 Query: 490 SQQVRLGQYLQSEHP 504 ++ RL +YL +E P Sbjct: 487 PEKARLARYL-AERP 500 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: 895 Number of extensions: 22 Number of successful extensions: 1 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: 511 Length adjustment: 35 Effective length of query: 477 Effective length of database: 476 Effective search space: 227052 Effective search space used: 227052 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