Align glycerol-3-phosphate dehydrogenase; EC 1.1.5.3 (characterized)
to candidate WP_086509596.1 BZY95_RS08920 glycerol-3-phosphate dehydrogenase
Query= CharProtDB::CH_091834 (512 letters) >NCBI__GCF_002151265.1:WP_086509596.1 Length = 500 Score = 611 bits (1575), Expect = e-179 Identities = 309/489 (63%), Positives = 367/489 (75%), Gaps = 4/489 (0%) Query: 16 DVAVVGGGINGVGIAADAAGRGLSVFLCEQHDLAQHTSSASSKLIHGGLRYLEHYEFRLV 75 D+ ++GGGING GIA DAAGRGLSV LCEQ DLA TSSASSKLIHGGLRYLEH+EFRLV Sbjct: 10 DLFIIGGGINGTGIANDAAGRGLSVSLCEQGDLAGATSSASSKLIHGGLRYLEHHEFRLV 69 Query: 76 REALAEREVLLAKAPHIVKPLRFVLPHRPHLRPAWMIRAGLFLYDHLGKREKLPASRGLR 135 EAL EREVLL KAPHI+ PLRF+LPHR HLRPAWMIRAGLFLYDHLGKR+ LP SR +R Sbjct: 70 GEALREREVLLRKAPHIIWPLRFILPHRSHLRPAWMIRAGLFLYDHLGKRKMLPGSRSVR 129 Query: 136 FTGSSPLKAEIRRGFEYSDCAVDDARLVVLNAISAREHGAHVHTRTRCVSARRSKGLWHL 195 F SPL+ I+RGFEYSDC VDDARLVVLNA+ ARE GA + RTRC+ A+ G+W + Sbjct: 130 FAADSPLQEGIKRGFEYSDCWVDDARLVVLNALQAREGGAEILVRTRCIGAKEENGIWRI 189 Query: 196 HLER-SDGSLYSIRARALVNAAGPWVARFIQDDLKQKSPYGIRLIQGSHIIVPKLYEGEH 254 LE G + +AR LVNAAGPWV R +++ + S Y IR+IQGSH+IVP+L + Sbjct: 190 ELEDVRSGERFERQARTLVNAAGPWVERVVREQAARSSRYSIRMIQGSHLIVPRLNGDDR 249 Query: 255 AYILQNEDRRIVFAIPYLDRFTMIGTTDREYQGDPAKVAISEEETAYLLQVVNAHFKQQL 314 AYILQN DRRIVF +PY D F++IGTTDR YQGDP + AISEEE YLL VVNAHF++QL Sbjct: 250 AYILQNSDRRIVFVLPYEDDFSLIGTTDRRYQGDPTQAAISEEEIDYLLGVVNAHFRRQL 309 Query: 315 AAADILHSFAGVRPLCDDESDEPSAITRDYTLSLSAGNGEPPLLSVFGGKLTTYRKLAES 374 +D++ SF+GVRPLCDDES EPSA+TRDYTL+ + PLLSVFGGK+TTYRKLAE+ Sbjct: 310 QRSDVISSFSGVRPLCDDESAEPSAMTRDYTLAFD--DQGAPLLSVFGGKITTYRKLAEA 367 Query: 375 ALTQLQPFFANLGPAWTAKAPLPGGEQMQSVEALTEQLANRYAWLDRELALRWARTYGTR 434 AL QL+P +GP+WTA+A LPGGE + + E +L + Y WL A R+AR+YG+ Sbjct: 368 ALKQLKPVLPAMGPSWTAEAALPGGE-IGNQENFMARLLHDYPWLGEARARRFARSYGSL 426 Query: 435 VWRLLDGVNGEADLGEHLGGGLYAREVDYLCKHEWAQDAEDILWRRSKLGLFLSPSQQVR 494 R L G DLGEH G GL A E DYL HEWA EDILWRR+KLGL L+P Q R Sbjct: 427 CLRFLAGTQCAEDLGEHFGAGLTAAEADYLVDHEWATTVEDILWRRTKLGLRLTPRQVER 486 Query: 495 LGQYLQSEH 503 L ++++ H Sbjct: 487 LQAHVEAHH 495 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: 802 Number of extensions: 28 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: 500 Length adjustment: 34 Effective length of query: 478 Effective length of database: 466 Effective search space: 222748 Effective search space used: 222748 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 24 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