Align glycerol-3-phosphate dehydrogenase (EC 1.1.5.3) (characterized)
to candidate WP_022949984.1 H035_RS20290 glycerol-3-phosphate dehydrogenase/oxidase
Query= BRENDA::P43304 (727 letters) >NCBI__GCF_000421465.1:WP_022949984.1 Length = 527 Score = 379 bits (972), Expect = e-109 Identities = 226/562 (40%), Positives = 321/562 (57%), Gaps = 39/562 (6%) Query: 56 SREAQLLTLQN-TSEFDILVIGGGATGSGCALDAVTRGLKTALVERDDFSSGTSSRSTKL 114 +R A L L++ T+ +D++VIGGGATG G A+DA +RG +TAL+E+ DF+ GTSSRSTKL Sbjct: 2 NRSATLERLRSETAPWDVVVIGGGATGLGVAVDAASRGYRTALLEQHDFAKGTSSRSTKL 61 Query: 115 IHGGVRYLQKAIMKLDIEQYRMVKEALHERANLLEIAPHLSAPLPIMLPVYKWWQLPYYW 174 IHGGVRYL++ ++L V+E+LHERA LL APHL PL ++P Y+WWQ YY Sbjct: 62 IHGGVRYLRQGDLQL-------VRESLHERAVLLANAPHLVTPLGFVMPAYRWWQQAYYA 114 Query: 175 VGIKLYDLVAGSNCLKSSYVLSKSRALEHFPMLQKDKLVGAIVYYDGQHNDARMNLAIAL 234 G+KLYDL+AG + S LS+S L++ P LQ L G ++Y+D Q +DAR+ + +A Sbjct: 115 AGLKLYDLLAGRRNIAPSGRLSRSETLDYLPTLQSSHLRGGVLYFDAQFDDARLAVTLAR 174 Query: 235 TAARYGAATANYMEVVSLLKKTDPQTGKVRVSGARCKDVLTGQEFDVRAKCVINATGPFT 294 TAA GAA ANY V L K R+ G D TG+ F + AK V+NATG F+ Sbjct: 175 TAADRGAAVANYTRVTGLRKANG------RIKGVDAVDEETGETFAIPAKTVVNATGVFS 228 Query: 295 DSVRKMDDKDAAAICQPSAGVHIVMPGYYSPESMGLLDPATSDGRVIFFLPWQKMTIAGT 354 D+VR++DD A + PS GVH+V+P + P LL P T DGRV+F +PWQ + GT Sbjct: 229 DTVRRLDDPRARPMIAPSRGVHLVLPKRFLPGENALLIPRTDDGRVLFAIPWQDRVVVGT 288 Query: 355 TDTPTD-VTHHPIPSEEDINFILNEVRNYLSCDVEVRRGDVLAAWSGIRPLVTDPKSADT 413 TD P + P S ++ ++L R YL+ DVL+ ++G+RPLV + T Sbjct: 289 TDVPVKRPSLEPPSSRQEWEYLLTHARRYLT--NPPTESDVLSTFAGLRPLVKADGNTST 346 Query: 414 QSISRNHVVDISESGLITIAGGKWTTYRSMAEDTINAAVKTHNLKAGPSRTVGLFLQGGK 473 ++SR+H + S SGL+TIAGGKWTTYR MA DT++ ++ L T L L G Sbjct: 347 AALSRDHTLLASPSGLVTIAGGKWTTYRKMARDTVDRLIELGPLPPAHCVTEKLRLHGWT 406 Query: 474 DWSPTLYIRLVQDYGLESEVAQHLAATYGDKAFEVAKMASVTGKRWPIVGVRLVSEFPYI 533 D R ++YG +++ + L T P L PY Sbjct: 407 DRPLPEGHR--REYGADADAIRQLIET-------------------PDKETLLHPHLPYR 445 Query: 534 EAEVKYGIK-EYACTAVDMISRRTRLAFLNVQAAEEALPRIVELMGRELNWDDYKKQEQL 592 AEV++ ++ E A T D+++RRTR L+ +A+ EA P + +M EL+ D Q Q+ Sbjct: 446 LAEVRWAVRLEMARTVEDVLARRTRALLLDARASAEAAPMVARVMAEELSRDAAWIQAQI 505 Query: 593 ETARKFLYYEMGYKSRSEQLTD 614 + ++ + +RS TD Sbjct: 506 QVFQRLAKSYLIVPNRSRPKTD 527 Lambda K H 0.318 0.134 0.391 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: 772 Number of extensions: 19 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: 727 Length of database: 527 Length adjustment: 37 Effective length of query: 690 Effective length of database: 490 Effective search space: 338100 Effective search space used: 338100 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