Align galactaro-1,5-lactonase (characterized)
to candidate WP_012975445.1 AZL_RS15505 SMP-30/gluconolactonase/LRE family protein
Query= reanno::WCS417:GFF3393 (291 letters) >NCBI__GCF_000010725.1:WP_012975445.1 Length = 305 Score = 187 bits (474), Expect = 3e-52 Identities = 120/293 (40%), Positives = 159/293 (54%), Gaps = 18/293 (6%) Query: 6 IVDARNAVGECPVWVPGENALYWVDIPKGGLQRWSAATGHVAAWTAPQMLACIARTDAGN 65 ++DAR +GE PVW E ALYWVDI L R+ A+G A P+ + C+A G Sbjct: 18 VLDARAKLGEGPVWSVDEQALYWVDIKGRALNRFDPASGANRAMALPEEIGCVAPRKGGG 77 Query: 66 WVAGMETGFFQLTPHNDGSLDTTLLAAVEHPRQDMRLNDGRCDRQGRFWAGSMVLNMGLN 125 ++AG+ +G +QL +G L LAA + R NDGR D GR+ AG+ L+ Sbjct: 78 FIAGLRSGLWQLD--GEGGL-VARLAANPEDQGASRFNDGRTDPVGRYLAGT--LDEPKA 132 Query: 126 AAEGTLYRYTS-GAAPHAQLDGFITLNGLAFSPDGRTMYASDSHPLVQQIWAFDYDIDTG 184 + LYRY G A A G +T NGLAFSPDGRT+Y +D+ + + YD TG Sbjct: 133 GGKAHLYRYDRRGLAVLA--GGLLTSNGLAFSPDGRTLYHADTPTFT--VRRYRYDPATG 188 Query: 185 TPSNRRVFVDMHKH---LGRPDGAAVDADGCYWICANDAGLIHRFSPDGRLDRSLTVPVK 241 S+ F+ + GRPDGAAVDA+GCYW + G + RFSP G L +P + Sbjct: 189 AISDGEPFIRLEPKEGDRGRPDGAAVDAEGCYWTALYEGGRVARFSPAGALLSEHPLPAR 248 Query: 242 KPTMCAFGGSRLDTLFVTSIRDDQSEQSL-----SGGVFALNPGVVGLPEPTF 289 PTM AFGG L TL+VT+ + + L SGG+FA+ V GLP P F Sbjct: 249 CPTMVAFGGPDLRTLYVTTASAGRPAEELERFPQSGGLFAMTVEVPGLPVPPF 301 Lambda K H 0.321 0.137 0.443 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: 386 Number of extensions: 28 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: 291 Length of database: 305 Length adjustment: 26 Effective length of query: 265 Effective length of database: 279 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