Align Senescence marker protein-30 family protein (characterized, see rationale)
to candidate WP_090439687.1 BLS63_RS03215 SMP-30/gluconolactonase/LRE family protein
Query= uniprot:Q888H2 (294 letters) >NCBI__GCF_900100495.1:WP_090439687.1 Length = 296 Score = 466 bits (1200), Expect = e-136 Identities = 223/294 (75%), Positives = 253/294 (86%), Gaps = 2/294 (0%) Query: 1 MDAELIVDAQNATGESPVWSVREQALYWVDIPNGELHRWDSSQDRTRSWKAPQMLACIAA 60 M AELIVDA+NATGESPVW V+EQALYWVDIP L RW + RT+SW +MLACIA Sbjct: 1 MPAELIVDARNATGESPVWHVQEQALYWVDIPARRLQRWSPADGRTQSWSGAEMLACIAR 60 Query: 61 DSRGGWIAGMENGLYHLQPCDDGSLISTLLASVEHAQTGMRFNDGRCDRQGRFWAGTMLM 120 + GGWIAGM++GL+ LQP DGSL ++ L V+HAQ GMRFNDGRCDRQGRFWAG+ML Sbjct: 61 HADGGWIAGMQSGLFRLQPNADGSLQASALIGVQHAQPGMRFNDGRCDRQGRFWAGSMLQ 120 Query: 121 DMAAGAVVGALYRYSAGQ-KTLEAQLKDLIVPNGLAFSPDGKTMYLSDSHPAVQKIWAFD 179 DMAAGA +GALYRYSAGQ + L AQL++LIVPNGLAFSPDGKTMYLSDSHPAVQ IWAFD Sbjct: 121 DMAAGAPLGALYRYSAGQSEPLGAQLRELIVPNGLAFSPDGKTMYLSDSHPAVQAIWAFD 180 Query: 180 YDTDSGTPHDRRLFVDMNNYLGRPDGAAIDADGCYWICGNDAGLVHRFTPNGKLDRSLVV 239 YDTD+GTPH+RRLFVDM + GRPDGAA+DA+GCYWIC NDAGL+HRF+P+G+LDRSL V Sbjct: 181 YDTDTGTPHNRRLFVDMREHPGRPDGAAVDAEGCYWICANDAGLIHRFSPDGRLDRSLAV 240 Query: 240 PVKKPAMCAFGGPNLDTLFVTSIRPGG-DLSDQPLAGGVFALRPGVKGLEEPVF 292 PV+KP+MCAFGG LDTLFVTSIRP G DL++QPLAGGVFALRPGV GLEEP F Sbjct: 241 PVQKPSMCAFGGRQLDTLFVTSIRPAGVDLAEQPLAGGVFALRPGVTGLEEPPF 294 Lambda K H 0.320 0.138 0.441 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: 509 Number of extensions: 22 Number of successful extensions: 3 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: 294 Length of database: 296 Length adjustment: 26 Effective length of query: 268 Effective length of database: 270 Effective search space: 72360 Effective search space used: 72360 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