Align glycerol-3-phosphate dehydrogenase; EC 1.1.5.3 (characterized)
to candidate PfGW456L13_5129 Aerobic glycerol-3-phosphate dehydrogenase (EC 1.1.5.3)
Query= CharProtDB::CH_091834 (512 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5129 Length = 531 Score = 209 bits (531), Expect = 3e-58 Identities = 170/496 (34%), Positives = 259/496 (52%), Gaps = 53/496 (10%) Query: 13 EVYDVAVVGGGINGVGIAADAAGRGLSVFLCEQHDLAQHTSSASSKLIHGGLRYLEHYEF 72 E +D+ V+GGGI+G GI +AA RG L EQ D A TSS SSK++HGGLRY+ ++ Sbjct: 20 ETWDLIVIGGGISGAGILREAARRGWRCLLLEQRDFAWGTSSRSSKMVHGGLRYIAKGQW 79 Query: 73 RLVREALAEREVLLAKAPHIVKPLRFVLPHRPHLRPAWMIRAGLF-LYDHLGKREK--LP 129 RL R+++ ER+ LL +AP +V+P+ F++PH P + GL +YD L R Sbjct: 80 RLTRDSVRERQRLLDEAPGLVEPMSFMMPHYRGGFPGPRVLGGLLSIYDALAGRRSHHFH 139 Query: 130 ASRGLRFTGSSPLKAEIRRGFEYSDCAVDDARLVVLNAISAREHGAHVHTRTRCVSARRS 189 ++ LR+ + ++ G + D DDARLV+ AR GA V R R Sbjct: 140 DAQQLRYLAPGVKEDDLLGGTCFVDALTDDARLVMRVLGEARADGAVVLNGVRVQQLLRE 199 Query: 190 KG-LWHLHLERSD-GSLYSIRARALVNAAGPWVARFIQDDLKQKSPYGIRLIQGSHIIVP 247 +G + + +E + G L ++R AL A G W R D +P +R ++GSH+++P Sbjct: 200 EGRVCGVQVEDCEGGGLLTLRCGALAVATGAWAERLRLPD----APRQLRPLRGSHLLLP 255 Query: 248 --KLYEGEHAYILQNEDRRIVFAIPYLDRFTMIGTTDREYQGD-PAKVAISEEETAYLLQ 304 +L + L DRR VF P+ + T++GTTD ++ GD +IS +E YLL Sbjct: 256 GWRLPVAQAFTFLHERDRRPVFVFPW-EGATVVGTTDLDHHGDLDQSASISFDELDYLLA 314 Query: 305 VVNAHFKQ-QLAAADILHSFAGVRPL----CDDESDEPSAITRDYTLSLSAGNGEPPLLS 359 + F Q ++ AAD+L +++GVRP+ + D+PS TR++ L EP ++ Sbjct: 315 ACSQQFPQAEVVAADVLSTWSGVRPVVGSAAGEHQDKPSNETREHVLW-----QEPGCVT 369 Query: 360 VFGGKLTTYR----KLAESALTQL-QPFFANLGPAWTAKAPLPGGEQMQSVEALTEQLAN 414 + GGKLTT+R ++ ++ T L +PF + P + A PL A+ AN Sbjct: 370 LAGGKLTTFRPQAIEVLKACATMLDRPFVDDATPVFAAVPPL----------AIPGLSAN 419 Query: 415 RYAWLDRELALRWARTYGTRVWRLLDGVNGEADLGEHLGGG---LYAREVDYLCKHEWAQ 471 R+ R LA R R R+ +L+ A+LG GG L+A E+ C E Sbjct: 420 RW----RRLAGRHGRDL-PRLAQLI------AELGHDTVGGTDTLWA-ELAVACDGEMVL 467 Query: 472 DAEDILWRRSKLGLFL 487 +D+L RR++LGL L Sbjct: 468 HLDDLLLRRTRLGLLL 483 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: 705 Number of extensions: 41 Number of successful extensions: 7 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: 531 Length adjustment: 35 Effective length of query: 477 Effective length of database: 496 Effective search space: 236592 Effective search space used: 236592 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