Align glycolate oxidase subunit glcD (characterized)
to candidate Synpcc7942_0276 Synpcc7942_0276 glycolate oxidase subunit GlcD
Query= CharProtDB::CH_024646 (499 letters) >FitnessBrowser__SynE:Synpcc7942_0276 Length = 490 Score = 469 bits (1207), Expect = e-136 Identities = 242/468 (51%), Positives = 315/468 (67%), Gaps = 1/468 (0%) Query: 19 TSVLMALREHVPGLEILHTDEEIIPYECDGLSAYRTRPLLVVLPKQMEQVTAILAVCHRL 78 T++ A RE + +++ EE++ YECDGL+ +R P LVVLP+ E+V A + +C++ Sbjct: 14 TAIAQAFREVLGREQVVERREELLVYECDGLTNHRQIPPLVVLPRSTEEVAAAVRLCNQF 73 Query: 79 RVPVVTRGAGTGLSGGALPLEKGVLLVMARFKEILDINPVGRRARVQPGVRNLAISQAVA 138 + V RGAGTGLSGGALP+E VL+V AR ++IL+I+ R RVQPGV N ++QA Sbjct: 74 DLSFVARGAGTGLSGGALPVEDSVLIVTARMRQILEIDYDNLRVRVQPGVINSWVTQATT 133 Query: 139 PHNLYYAPDPSSQIACSIGGNVAENAGGVHCLKYGLTVHNLLKIEVQTLDGEALTLGSDA 198 +YAPDPSSQ CSIGGNVAEN+GGVHCLK+G+T +++L + + D + +G Sbjct: 134 GAGFFYAPDPSSQSVCSIGGNVAENSGGVHCLKHGVTNNHVLGLTLVLPDASVIQVGGAI 193 Query: 199 LDSPGFDLLALFTGSEGMLGVTTEVTVKLLPKPPVARVLLASFDSVEKAGLAVGDIIANG 258 D PG+DL +F GSEG LG+ TEVT++L P P +VLLA F S+E AG AV IIA G Sbjct: 194 ADLPGYDLCGIFVGSEGTLGIATEVTLRLQPLPQSVQVLLADFSSIEAAGAAVSGIIAAG 253 Query: 259 IIPGGLEMMDNLSIRAAEDFIHAG-YPVDAEAILLCELDGVESDVQEDCERVNDILLKAG 317 I+P GLE+MDN SI A ED + + YP DA AILL ELDG S+V + V + + G Sbjct: 254 ILPAGLELMDNFSINAVEDVVKSDCYPRDAAAILLAELDGRASEVAQQIRDVEAVCRQHG 313 Query: 318 ATDVRLAQDEAERVRFWAGRKNAFPAVGRISPDYYCMDGTIPRRALPGVLEGIARLSQQY 377 A + +A D +R+R W GRK AF AVGRISP YY DG IPR LP VL I +L Q++ Sbjct: 314 ARSIAIATDAEDRLRLWKGRKAAFAAVGRISPSYYVQDGVIPRSTLPFVLHEIEQLGQKH 373 Query: 378 DLRVANVFHAGDGNMHPLILFDANEPGEFARAEELGGKILELCVEVGGSISGEHGIGREK 437 RVANVFHAGDGN+HPLIL+D N+PG R E LGG+IL+LCV VGGSISGEHGIG +K Sbjct: 374 GYRVANVFHAGDGNLHPLILYDRNDPGALERVEALGGEILKLCVNVGGSISGEHGIGADK 433 Query: 438 INQMCAQFNSDEITTFHAVKAAFDPDGLLNPGKNIPTLHRCAEFGAMH 485 M A F+S+++ T ++ AFDP NP K PT C E G+++ Sbjct: 434 RCYMPAMFSSEDLETMQWLRHAFDPLERANPTKVFPTPRTCGERGSVN 481 Lambda K H 0.320 0.140 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: 728 Number of extensions: 27 Number of successful extensions: 2 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: 499 Length of database: 490 Length adjustment: 34 Effective length of query: 465 Effective length of database: 456 Effective search space: 212040 Effective search space used: 212040 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