Align Senescence marker protein-30 family protein (characterized, see rationale)
to candidate WP_053939460.1 WG78_RS19225 SMP-30/gluconolactonase/LRE family protein
Query= uniprot:Q888H2 (294 letters) >NCBI__GCF_001294205.1:WP_053939460.1 Length = 301 Score = 144 bits (362), Expect = 3e-39 Identities = 97/273 (35%), Positives = 133/273 (48%), Gaps = 10/273 (3%) Query: 26 LYWVDIPNGELHRWDSSQDRTRSWKAPQMLACIAADSRGGWIAGMENGLYHLQPCDDGSL 85 L+W +I EL + D + R W PQ + C A + + L G++ Sbjct: 33 LWWTNIHAKELWQLDLRTGQHRYWSTPQRVCCFAFTQDDDVLLVAFDAGLALFNTASGAI 92 Query: 86 ISTLLASVEHAQTGMRFNDGRCDRQGRFWAGTMLMDMAAGAVVGALYRYSAGQKTLEAQL 145 L VE G R NDGR DR G GTM A G YR+ + + L Sbjct: 93 --KRLTPVEPETPGTRCNDGRVDRAGNLVFGTMHERSAEAK--GHFYRFDTESRLQQLAL 148 Query: 146 KDLIVPNGLAFSPDGKTMYLSDSHPAVQKIWAFDYDTDSGTPHDRRLFVDMNNYLGRPDG 205 + + N LAFSPDG T+Y DS KI YD+ +G + +F D+ + + PDG Sbjct: 149 PAIAISNSLAFSPDGGTLYWCDS--LQHKIMQCAYDSVTGAIAEISVFHDLGDTVIEPDG 206 Query: 206 AAIDADGCYWICGNDAGLVHRFTPNGKLDRSLVVPVKKPAMCAFGGPNLDTLFVTSIRPG 265 + +DA G W V R+ P+G +DR + +PV +P FGGP +TLF+TS R G Sbjct: 207 STVDAAGYLWNAEWAGHCVTRYAPDGSIDRKIHLPVAQPTCVTFGGPEQNTLFITSARAG 266 Query: 266 GD---LSDQPLAGGVFALR-PGVKGLEEPVFQG 294 D L+ QP AG VFAL PGV+GL E ++ G Sbjct: 267 LDDAALAQQPEAGSVFALEIPGVRGLPENIWLG 299 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: 330 Number of extensions: 26 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: 301 Length adjustment: 26 Effective length of query: 268 Effective length of database: 275 Effective search space: 73700 Effective search space used: 73700 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