Align Senescence marker protein-30 family protein (characterized, see rationale)
to candidate HSERO_RS19370 HSERO_RS19370 gluconolactonase
Query= uniprot:Q888H2 (294 letters) >FitnessBrowser__HerbieS:HSERO_RS19370 Length = 302 Score = 174 bits (442), Expect = 2e-48 Identities = 103/282 (36%), Positives = 154/282 (54%), Gaps = 18/282 (6%) Query: 14 GESPVWSVREQALYWVDIPNGELHRWDSSQDRTRSWKAPQMLACIAADSRGGWIAGMENG 73 GESP+W +E ALYW+DIP +HR + + W P+ I ++GG + + G Sbjct: 22 GESPLWHAQEAALYWIDIPGKAVHRLHPESGQHKRWDLPEEPGSIVRHAQGGLVVAIRTG 81 Query: 74 LYHLQPCDDGSLISTLLASVEHAQTGMRFNDGRCDRQGRFWAGTMLMDMAAGAVVGALYR 133 ++HL D G+L TLL + + + +RFNDGRCD GRFW GT+ G LY Sbjct: 82 MFHLNT-DTGAL--TLLLAAPYDSSRIRFNDGRCDASGRFWCGTIYEPRDRDG--GTLYC 136 Query: 134 YSAGQKTLEAQLKDLIVPNGLAFSPDGKTMYLSDSHPAVQKIWAFDYDTDSGTPHDRRLF 193 + + L ++ NGLAFS D + MY +++ PA +I +DYD +G + RL Sbjct: 137 FE--RNALRDAHHAVVTSNGLAFSSDQRLMYHANT-PA-HRINLYDYDLATGATSNCRLL 192 Query: 194 VDMNN------YLGRPDGAAIDADGCYWICGNDAGLVHRFTPNGKLDRSLVVPVKKPAMC 247 ++ Y GRPDGAA+D+ G YW + G V R +P G++ + + +P + P M Sbjct: 193 RQFDSDKSAPDYGGRPDGAAVDSQGAYWCAMFEGGRVLRLSPQGEILQEIRLPARCPTMV 252 Query: 248 AFGGPNLDTLFVTSIRPG---GDLSDQPLAGGVFALRPGVKG 286 AFGG +L TL++T+ R G +L+ P +G V A+R V G Sbjct: 253 AFGGDDLRTLYITTGRNGRSPAELAQYPESGCVLAVRVDVPG 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: 342 Number of extensions: 19 Number of successful extensions: 4 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: 302 Length adjustment: 26 Effective length of query: 268 Effective length of database: 276 Effective search space: 73968 Effective search space used: 73968 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