Align glycerol-3-phosphate dehydrogenase (EC 1.1.5.3) (characterized)
to candidate WP_012383389.1 BIND_RS01920 FAD-dependent oxidoreductase
Query= BRENDA::Q06B39 (650 letters) >NCBI__GCF_000019845.1:WP_012383389.1 Length = 539 Score = 412 bits (1058), Expect = e-119 Identities = 225/546 (41%), Positives = 321/546 (58%), Gaps = 29/546 (5%) Query: 67 FDVLVIGGGATGAGCAFDAQTRGLQTALIEREDFASGTSSRSTKLVHGGVRYLEKAVFNL 126 FD+LV+GGGATG G A DA +RGL+ AL+ER DFA GTSS+STKLVHGG RYLE A+ L Sbjct: 16 FDLLVVGGGATGCGVALDAASRGLKVALVERNDFAEGTSSKSTKLVHGGARYLELAIRRL 75 Query: 127 DYDQLKLVYEALHERDRLLSNASHLAHPLPILTPCYNWWEVPYYWAGMKMYDLVAGTSTL 186 D Q LV + L ER L NA HLAH L +L+P Y W++VPY +AG+ +YD +AG L Sbjct: 76 DRVQFNLVRDGLRERAIFLKNAPHLAHRLALLSPLYRWFDVPYVFAGLYLYDRLAGKLGL 135 Query: 187 VPSKFLTSLETLTYLPTMSKNIGGKSLKGSIMYYDGQFNDSRMNVALACSSAAAGATVMN 246 S+ L+ E L P + + LK +++YYDGQFND+RM V LA ++ GA + Sbjct: 136 GGSRLLSRAEALRRFPMLK----AEGLKAAVLYYDGQFNDARMAVTLALTAVEQGAVIAT 191 Query: 247 YTECKQLIKDDQGKVIGARCRDRATGAETDVYARVLINATGAFADDVRRYSEPDAQQTVM 306 + L + +GK+ GA DR + ++ AR +INA G FAD +R ++P+ + Sbjct: 192 RLDVVGLTHE-KGKLRGATVHDRESRKSFEIKARAIINAGGPFADSLRLMADPETAPILT 250 Query: 307 ASSGAHVTLPDFYGSARTGMIIPKTKDGRVIFMLPFQGHVIAGTTDTPIKATSRPRSSEE 366 ASSG H+ L + TG++IP+T+DGR++F+LP+QGH + GTTD P + P++ +E Sbjct: 251 ASSGIHIVLDRRFAPTETGLMIPETEDGRLLFVLPWQGHALIGTTDEPARIEENPQARQE 310 Query: 367 DIDFILATLSDFLDVRVSRGDVLSTWCGIRPLPAPKKNTTSENVVRDHVIFEDKDGLLNV 426 ID++L + + ++ V+ D+LS WCG+RPL + K + + RDH+I K GL+ + Sbjct: 311 AIDYLLRHVRKYFNMNVTEADLLSVWCGLRPLVSDPKAADTARLARDHIIEVSKSGLVTI 370 Query: 427 TGGKWTTYRAMAEQAIDLAMASGKLPKSAKPCQTANYKLLGATNYTYTLMAELAQQHGMP 486 GGKWTTYR MAEQ +D A+A LP +K C+T + L+GA ++ + A Sbjct: 371 CGGKWTTYRKMAEQTVDHAIACFSLPTHSK-CRTLDLPLVGARHF------DAAGGAAAL 423 Query: 487 QRYFGKNSSKERNSNGSPRVAMDTEIAHHLSTAYGDNAMRVIAMAEEEGLGKRLIAGHPI 546 FG + E A HL AYGD A +V+ + + L HP Sbjct: 424 TSTFG----------------LSPETAAHLHQAYGDRAKQVLGCVDTSAMKTLLHPLHPY 467 Query: 547 LEAEVMYTAKHEYCLTIEDFIDRRSRLAFLDVKATEAALPRIAEIMGNTLGWNDKQRTSA 606 LEAEV+Y+A+ E L+ D + RR LA LD +A A PR+ ++ L W D+QR + Sbjct: 468 LEAEVLYSARFEAALSAMDVLARRLPLALLDRQAAREAAPRVIAMLATELAW-DEQRCAN 526 Query: 607 ITAAVK 612 A V+ Sbjct: 527 EAAEVE 532 Lambda K H 0.317 0.132 0.390 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: 806 Number of extensions: 32 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 650 Length of database: 539 Length adjustment: 37 Effective length of query: 613 Effective length of database: 502 Effective search space: 307726 Effective search space used: 307726 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 53 (25.0 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