Align 2-dehydro-3-deoxygalactonokinase (characterized, see rationale)
to candidate SMa0705 SMa0705 DgoK2 2-dehydro-3-deoxygalactonokinase
Query= uniprot:A0A1I2AR49 (306 letters) >FitnessBrowser__Smeli:SMa0705 Length = 313 Score = 188 bits (477), Expect = 2e-52 Identities = 115/297 (38%), Positives = 157/297 (52%), Gaps = 17/297 (5%) Query: 8 LDWGSTHLRAYLYGADGHALESRALPHGIRQLPAGGFPEAFSSAVRDWPA----LPVLAC 63 LDWG+T RA+L +DG ++ + GI+ + G S A+ W A L ++A Sbjct: 13 LDWGTTGFRAFLVRSDGSLVDQKEGERGIQSIAKGEHGRVVSEALASWRAGYGPLDIVAA 72 Query: 64 GMVGSRNGWQEVPYLDTPTGVERLAQHLTRIAAPDGHALYLVPGLHDTHR---PDVMRGE 120 GM+GSRNGW E+PY+ TP +A P+G+ + +PGL D PDVMRGE Sbjct: 73 GMIGSRNGWIEMPYVPTPASAADVAAAARTEGLPEGNRITFLPGLTDPTGFPFPDVMRGE 132 Query: 121 ETQIAGV-LAREPATTRLLLPGTHSKWVRLRDGIVTDFATVMTGELYGLLRQHSILGAAL 179 E Q+ G L R+ ++LPGTH+KW +R G + F T +TGE+Y L HS L Sbjct: 133 EAQLVGFGLDRDII---VVLPGTHAKWAEIRGGHIERFRTFVTGEIYATLADHSFLSKVA 189 Query: 180 PEARDDA-DAFRRGVAAAR--GSGPAGALSLLFSARALMLDGVLDPAAVPDYLSGLLIGE 236 RD A DAF GVA A+ + G L+ LF+ R L G + P + LSGL+IG Sbjct: 190 TAERDHAADAFAEGVALAQEESTRAGGLLTRLFAVRTGWLAGAIAPDEMKSRLSGLIIGW 249 Query: 237 ELRMALAAGWADADDAIPMVGEGPLCDRYRRAADTFGLRLARAPDGTTADG---LWR 290 E A GW D I +VG+ L + Y R A+ FG++LA AP G +WR Sbjct: 250 EFVEARTGGWFKEGDTIAVVGDDDLVEVYGRVAENFGVKLAPAPADAAIRGALTIWR 306 Lambda K H 0.321 0.138 0.427 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: 318 Number of extensions: 18 Number of successful extensions: 5 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: 306 Length of database: 313 Length adjustment: 27 Effective length of query: 279 Effective length of database: 286 Effective search space: 79794 Effective search space used: 79794 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: 48 (23.1 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