Align glycerol-3-phosphate dehydrogenase, mitochondrial (characterized)
to candidate Echvi_1771 Echvi_1771 Glycerol-3-phosphate dehydrogenase
Query= CharProtDB::CH_122883 (650 letters) >FitnessBrowser__Cola:Echvi_1771 Length = 521 Score = 339 bits (870), Expect = 2e-97 Identities = 211/559 (37%), Positives = 304/559 (54%), Gaps = 70/559 (12%) Query: 62 LKKVPQFDVLVIGGGAVGTGTAVDAATRGLNVCLLEKTDFGAGTSSKSTKMAHGGVRYLE 121 L K +D+++IGGGA G G A+DA +RGL+V L E+ DF GTSS+STK+ HGGVRYL Sbjct: 10 LAKNQLWDIVIIGGGASGLGVALDALSRGLSVALFERADFAKGTSSRSTKLVHGGVRYL- 68 Query: 122 KAIFQLSRAQLDLVIEALNERGNMLRTAPHLCTVLPIMIPVYNWWQVPYFFAGCKMYDWF 181 ++ + LV EAL ERG +L+ APHL P +IP+Y+ Y+ G K YDW Sbjct: 69 ------AQGDILLVWEALRERGRILKNAPHLAHAQPFIIPIYSHATKYYYTVGLKFYDWM 122 Query: 182 AGKQNLRSSTIFSTEQAAAIAPMMDTSNLKATCVYHDGSFNDTRYNVTLALTAIENGATV 241 +G +L S+ S ++ P + T L VYHDG+F+D R + +A T + G + Sbjct: 123 SGWLSLGDSSFISKKETIKRLPEIKTEGLLGGVVYHDGAFDDARLAIAVAQTCDDMGGCI 182 Query: 242 LNYFEVEQLLKDSNGKLYGVKAKDLETNESYEIKAKSVVNATGPFADKILEMDEDPQGLP 301 LNY +V L KD G + GVK +D +SY++KAK VVNATG FADKIL+MD+ Sbjct: 183 LNYMKVTSLTKDGAGIITGVKVRDAIHKKSYDVKAKMVVNATGVFADKILQMDQ------ 236 Query: 302 PKVEQSPRMVVPSSGVHVVLPEYYCPTTYGLLDPSTSDGRVMFFLPWQGKVLAGTTDTPL 361 + +PRM+ PS GVH+VLP+++ L+ P TSDGRV+F +PWQGK++ GTTDT Sbjct: 237 ---KGAPRMIQPSQGVHLVLPQHFLGGQDALMIPKTSDGRVLFAVPWQGKLVVGTTDTIR 293 Query: 362 KKVPENPVPTEEEIQDILNEMQKYLVFPIDRNDVLSAWSGIRPLVRDPSTIPKGQEASGK 421 K P EI IL +YL R DVL+ ++G+RPL PKG+ S K Sbjct: 294 AKTKMEPEALSREINFILANAGQYLSKKPTRKDVLTVYAGLRPL-----AAPKGE--SVK 346 Query: 422 TEGLVRSHLLVQSPTGLVTISGGKWTTYREMAQETIDYVVKHFDFGDKKILPCQTNKLIL 481 T+ + R+H ++ S +GL T++GGKWTT+R+M ++T+D+ + Sbjct: 347 TKEISRNHKVIISDSGLTTLTGGKWTTFRKMGEDTVDHFPR------------------- 387 Query: 482 VGGTDYSKNYSARL-IHEYHIPLKLAKHLSHNYGSRAPLILDLYAES-DYNKLPVTLAAT 539 V G + +++S + +H + P KH YG+ A IL L E+ Y KL Sbjct: 388 VTGEEIKESHSWEIKLHGHGDPTLDDKHWK-IYGTDAVKILQLIKENPPYAKL------- 439 Query: 540 EEFEPSEKKANEDNQLSYQRFDEPFSIAELKYSLKYEYPRTPLDFLARRTRLAFLNAREA 599 P P+ E+ ++++ E DFLARR R+ L+A A Sbjct: 440 --LHP----------------QYPYVAGEVIWAIREEMAMHIEDFLARRIRILLLDAAAA 481 Query: 600 LSAVDGVVEIMSKEYGWDK 618 ++ V +M+ E DK Sbjct: 482 IAMAPLVASLMAAELKKDK 500 Lambda K H 0.316 0.134 0.394 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: 734 Number of extensions: 33 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 650 Length of database: 521 Length adjustment: 36 Effective length of query: 614 Effective length of database: 485 Effective search space: 297790 Effective search space used: 297790 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 (21.6 bits) S2: 53 (25.0 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