Align glycerol-3-phosphate dehydrogenase; EC 1.1.5.3 (characterized)
to candidate HSERO_RS04840 HSERO_RS04840 glycerol-3-phosphate dehydrogenase
Query= CharProtDB::CH_091834 (512 letters) >FitnessBrowser__HerbieS:HSERO_RS04840 Length = 510 Score = 541 bits (1395), Expect = e-158 Identities = 282/505 (55%), Positives = 350/505 (69%), Gaps = 16/505 (3%) Query: 15 YDVAVVGGGINGVGIAADAAGRGLSVFLCEQHDLAQHTSSASSKLIHGGLRYLEHYEFRL 74 YD+ VVGGGING GIA DAAGRGL V LCEQHDLAQHTSSAS+KLIHGGLRYLE+YEF+L Sbjct: 5 YDLLVVGGGINGAGIARDAAGRGLRVLLCEQHDLAQHTSSASTKLIHGGLRYLEYYEFKL 64 Query: 75 VREALAEREVLLAKAPHIVKPLRFVLPHRPHLRPAWMIRAGLFLYDHLGKREKLPASRG- 133 VR+AL EREVLL APHI+ PLRFV+PH + RPAWMIRAGLF+YDHL KRE LP S G Sbjct: 65 VRKALQEREVLLRSAPHIIWPLRFVMPHDANQRPAWMIRAGLFMYDHLAKREILPPSEGA 124 Query: 134 --LRFTGSSPLKAEIRRGFEYSDCAVDDARLVVLNAISAREHGAHVHTRTRCVSARRSKG 191 R PLK + R+GF YSD VDDARLVVLNA+ A+E GA + TRT+C+SARR Sbjct: 125 NLARHDAGQPLKGDYRKGFVYSDGWVDDARLVVLNAMDAQERGARILTRTKCISARREGD 184 Query: 192 LWHLHLE-RSDGSLY--SIRARALVNAAGPWVARFIQDDLKQKSPYGIRLIQGSHIIVPK 248 +WH LE + +G + +RARA+VNAAGPW ARF Q + KS +RLI+GSHI+V + Sbjct: 185 IWHAVLEHQREGGVQQEEVRARAIVNAAGPWAARFAQAVPQAKSGRSLRLIKGSHIVVKR 244 Query: 249 LYEGEHAYILQNEDRRIVFAIPYLDRFTMIGTTDREYQGDPAKVAISEEETAYLLQVVNA 308 +++ +AYI QN D+RI+FAIPY + FT+IGTTD EY GD KV I E YL + N Sbjct: 245 MFDHPYAYIFQNPDKRIIFAIPYQEEFTLIGTTDLEYHGDAGKVEIDAAEIDYLCDMANR 304 Query: 309 HFKQQLAAADILHSFAGVRPLCDDESDEPSAITRDYTLSLSAGNGEPPLLSVFGGKLTTY 368 +FK+Q+ D++ +++GVRPL DD ++ SAITRDY L + P+L+V+GGK+TTY Sbjct: 305 YFKRQIGKEDVVWTYSGVRPLLDDSAENASAITRDYL--LECDDAGAPMLNVWGGKITTY 362 Query: 369 RKLAESALTQLQPFFANLGPAWTAKAPLPGGEQMQ--------SVEALTEQLANRYAWLD 420 RKLAE AL L P +WTA APLPGG+ Q +A + R+ WL Sbjct: 363 RKLAEEALAMLAPHLGASSQSWTAGAPLPGGDLEQPGKMVARYDFDAYLRKFQARHPWLP 422 Query: 421 RELALRWARTYGTRVWRLLDGVNGEADLGEHLGGGLYAREVDYLCKHEWAQDAEDILWRR 480 ELA R+AR+YG+RV +++ + A LGE L GLY E YL +HEWA+ A+DILWRR Sbjct: 423 AELAHRYARSYGSRVEQIIGQADSLAALGEELSPGLYEAEARYLVQHEWARSADDILWRR 482 Query: 481 SKLGLFLSPSQQVRLGQYLQSEHPH 505 SKLGL P + RL +L S H Sbjct: 483 SKLGLHCGPQHRGRLEAWLASLPDH 507 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: 817 Number of extensions: 36 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: 512 Length of database: 510 Length adjustment: 35 Effective length of query: 477 Effective length of database: 475 Effective search space: 226575 Effective search space used: 226575 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