Align Senescence marker protein-30 family protein (characterized, see rationale)
to candidate BWI76_RS23720 BWI76_RS23720 calcium-binding protein
Query= uniprot:Q888H2 (294 letters) >FitnessBrowser__Koxy:BWI76_RS23720 Length = 292 Score = 162 bits (409), Expect = 1e-44 Identities = 111/300 (37%), Positives = 158/300 (52%), Gaps = 14/300 (4%) Query: 1 MDAELIVDAQNATGESPVWSVREQALYWVDIPNGELHRWDSSQDRTRSWKAPQMLACIAA 60 M E+++D + GESPVW + +Q L+WVD +G L ++ +SW Q + A Sbjct: 1 MRIEVLLDLKTRLGESPVWDIEQQRLWWVDSLDGRLFACNAQGGAIKSWDVRQKIGSFAL 60 Query: 61 DSRG-GWIAGMENGLYHLQPCDDGSLISTLLASVEHAQTGMRFNDGRCDRQGRFWAGTML 119 G G + ++NG+ HL G L TLL E + R NDG+ DRQGRF G+M Sbjct: 61 RQNGEGAVVALQNGV-HLLDFASGGL--TLLHHPEADRPFNRLNDGKVDRQGRFLFGSM- 116 Query: 120 MDMAAGAVVGALYRYSAGQKTLEAQLKDLIVPNGLAFSPDGKTMYLSDSHPAVQKIWAFD 179 DM GALYR A +L K++IV N +SP G+T Y +D+ +I A+D Sbjct: 117 -DMREEEPSGALYRLDA-DLSLHVLKKNIIVSNAPCWSPSGETFYFADTWTG--EICAWD 172 Query: 180 YDTDSGTPHDRRLFVDMNNYLG-RPDGAAIDADGCYWICGNDAGLVHRFTPNGKLDRSLV 238 Y+T +G R+F ++ G DGA +D++G W AG + R+TP G++DR + Sbjct: 173 YNTATGDLSGERVFCHVDRSEGGAADGATVDSEGYLWNALVYAGKLVRYTPEGEVDRIIE 232 Query: 239 VPVKKPAMCAFGGPNLDTLFVTSIRP---GGDLSDQPLAGGVFALRP-GVKGLEEPVFQG 294 +PVKK FGG NLD L+VTS+ D L G +FA+ GV G+ E F G Sbjct: 233 MPVKKVTSVMFGGENLDVLYVTSMAQPPLPRFPEDNQLRGSLFAIYDLGVTGVAERRFAG 292 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: 316 Number of extensions: 27 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: 294 Length of database: 292 Length adjustment: 26 Effective length of query: 268 Effective length of database: 266 Effective search space: 71288 Effective search space used: 71288 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