Align glycerol-3-phosphate dehydrogenase; EC 1.1.5.3 (characterized)
to candidate HSERO_RS23645 HSERO_RS23645 glycerol-3-phosphate dehydrogenase
Query= CharProtDB::CH_091834 (512 letters) >FitnessBrowser__HerbieS:HSERO_RS23645 Length = 534 Score = 540 bits (1390), Expect = e-158 Identities = 283/513 (55%), Positives = 345/513 (67%), Gaps = 17/513 (3%) Query: 15 YDVAVVGGGINGVGIAADAAGRGLSVFLCEQHDLAQHTSSASSKLIHGGLRYLEHYEFRL 74 YDV VVGGGING GIA DAAGRGLSV LCEQHDLAQHTSS+SSKLIHGGLRYLEHYEF L Sbjct: 15 YDVLVVGGGINGAGIARDAAGRGLSVALCEQHDLAQHTSSSSSKLIHGGLRYLEHYEFGL 74 Query: 75 VREALAEREVLLAKAPHIVKPLRFVLPHRPHLRPAWMIRAGLFLYDHLGKREKLPASRGL 134 VR+AL EREVLL APHI+ PLRFV+PH RPAW+IR G+FLYDHL +RE LP SR L Sbjct: 75 VRKALIEREVLLRSAPHIMWPLRFVMPHDQGQRPAWLIRLGMFLYDHLARRELLPGSRAL 134 Query: 135 ---RFTGSSPLKAEIRRGFEYSDCAVDDARLVVLNAISAREHGAHVHTRTRCVSARRSKG 191 R +PLKA+ RGF YSD VDDARLVVLNA+ A E GAH+ TRTRC S R Sbjct: 135 DLRRHASGAPLKAQFTRGFVYSDGWVDDARLVVLNAMDAAEKGAHIMTRTRCESLTRQDN 194 Query: 192 LWHLHLERSDGSLYSIRARALVNAAGPWVARFIQDDLKQKSPYGIRLIQGSHIIVPKLYE 251 W L R DG +RAR +VNAAGPWVA+F+ S +RL++GSHI+VP+L+E Sbjct: 195 GWQAVLRREDGHAMQVRARCVVNAAGPWVAQFLGGAAHVHSSKSVRLVKGSHIVVPRLFE 254 Query: 252 GEHAYILQNEDRRIVFAIPYLDRFTMIGTTDREYQGDPAKVAISEEETAYLLQVVNAHFK 311 +HAYI QN D RIVFAIPY FT+IGTTD EYQG VAIS +ETAYL Q+ N +F+ Sbjct: 255 HDHAYIFQNPDGRIVFAIPYEQDFTLIGTTDIEYQGRVEDVAISADETAYLCQLANRYFE 314 Query: 312 QQLAAADILHSFAGVRPLCDDESDEPSAITRDYTLSLSAGNGEPPLLSVFGGKLTTYRKL 371 + + D++ S++GVRPL +D + + SA+TRDY L L+ PLLS+FGGK+TT+RKL Sbjct: 315 KPITPDDVVWSYSGVRPLLEDAAADASAVTRDYQLDLNLQGA--PLLSIFGGKITTFRKL 372 Query: 372 AESALTQLQPFFANLGPAWTAKAPLPGGE---------QMQSVEALTEQLANRYAWLDRE 422 AE A+ + P N AWT LPGG+ ++ + + L +Y WL Sbjct: 373 AEEAVDMIAPVLGNQRGAWTEHGCLPGGDLYGAQPSNRSVRQFDQYVQGLQQQYPWLPAA 432 Query: 423 LALRWARTYGTRVWRLLDGVNGEADLGEHLGGGLYAREVDYLCKHEWAQDAEDILWRRSK 482 L R+AR YG+R LL+G ++GE + GLYA EVDYL +HEWA +A DILWRRSK Sbjct: 433 LLQRYARAYGSRTHTLLEGRQNVEEMGEEILDGLYAAEVDYLLRHEWASNAADILWRRSK 492 Query: 483 LGLFLSPSQQVRLGQYLQS---EHPHRPRVHAA 512 LGL + L +L + + R + H A Sbjct: 493 LGLHFPKGSEAVLDAWLAARGGQQSGREQAHEA 525 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: 812 Number of extensions: 32 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: 534 Length adjustment: 35 Effective length of query: 477 Effective length of database: 499 Effective search space: 238023 Effective search space used: 238023 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