Align 2-dehydro-3-deoxygalactonokinase (characterized, see rationale)
to candidate WP_057509053.1 ABB28_RS13165 hypothetical protein
Query= uniprot:A0A1I2AR49 (306 letters) >NCBI__GCF_001431535.1:WP_057509053.1 Length = 292 Score = 192 bits (488), Expect = 8e-54 Identities = 126/299 (42%), Positives = 162/299 (54%), Gaps = 15/299 (5%) Query: 5 LIGLDWGSTHLRAYLYGADGHALESRALPHGIRQLPAGGFPEAFSSAVRDWPALPVLACG 64 +I +DWGS+ LRA+ DGH ++SR G+ G F E + + W V+ G Sbjct: 1 MIAIDWGSSSLRAFRLDRDGHRVDSRRSDQGLLNAD-GRFAEVLETLIDGWDDALVVMAG 59 Query: 65 MVGSRNGWQEVPYLDTPTGVERLAQHLTRI-AAPDGHALYLVPGLH--DTH-RPDVMRGE 120 MVGSR GW EVPY+ P GV+ +A + R+ +A L+LVPGL D H PDVMRGE Sbjct: 60 MVGSRQGWMEVPYVQAPAGVQEIAAGMCRLQSAAVQRELWLVPGLSCVDVHGTPDVMRGE 119 Query: 121 ETQIAGVL-AREPATTRLLLPGTHSKWVRLRDGIVTDFATVMTGELYGLLRQHSILGAAL 179 ETQ+ +L P +LLPGTHSK R+ DG + F+T MTGEL+ +LRQHS+LG + Sbjct: 120 ETQLCALLPVLGPGRHAVLLPGTHSKHARVVDGRIERFSTFMTGELFAVLRQHSLLGRMM 179 Query: 180 PEARDDADAFRRGVAAARGSGPAGALSLLFSARALMLDGVLDPAAVPDYLSGLLIGEELR 239 +A DA AF GVA A G L LF R L L PA + YLSGLLIG EL+ Sbjct: 180 VDAPLDAAAFAEGVAMAERDG--SLLHQLFGVRTRALFDQLLPAQLASYLSGLLIGNELQ 237 Query: 240 MALAAGWADADDA-IPMVGEGPLCDRYRRAADTFGLRLARAPDGTTADGLWRIAAAAGL 297 DA A + ++ L D Y A G R + T A GL+ +A A L Sbjct: 238 D------LDAHSAPVHVIAADGLADAYLSALARVGRTATRHAEDTVARGLYLLARAREL 290 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: 321 Number of extensions: 13 Number of successful extensions: 6 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: 292 Length adjustment: 27 Effective length of query: 279 Effective length of database: 265 Effective search space: 73935 Effective search space used: 73935 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 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