Align Regucalcin; RC; Gluconolactonase; GNL; Senescence marker protein 30; SMP-30; xSMP-30; EC 3.1.1.17 (characterized)
to candidate Pf1N1B4_413 L-arabinolactonase (EC 3.1.1.15)
Query= SwissProt::Q9I922 (299 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_413 Length = 314 Score = 113 bits (283), Expect = 5e-30 Identities = 88/300 (29%), Positives = 138/300 (46%), Gaps = 23/300 (7%) Query: 9 VVSETYKIGESPVWEEKEGTLLFVDITGQKVCRWDPSTKKVQSVSVEAPIGSVALRKSGG 68 V ++GE P W+ L +VDI G++ R + ++ + + + +SG Sbjct: 29 VTGHRAQLGEGPFWDAPTQALYWVDIAGKQALRLIGANVEIWQMPEH--VSAFIPCESGD 86 Query: 69 YVLAMGNTFSALNWEDQSVT---TLARVDEDKPNNRFNDGKVDPEGRFLAGTMSQEI--- 122 ++ + + L+ + TL V + +P NR N+ + D +GR GTM I Sbjct: 87 ALVTLSSGVYRLDLASPGLEPRLTLFCVADPQPGNRPNEARCDAQGRLWLGTMQNNIGEQ 146 Query: 123 -RPAVVERNQGSLFTLYPDHSVVKHFDMVDISNGLDWSLDHKTLYYIDSLSFKVDALDYD 181 V R G LF + D V + I N L WS D TLY+ DSL D+ Y Sbjct: 147 GEDLPVVRRSGGLFRIDRDARVTPLLRGLGIPNTLLWSDDGTTLYFADSL----DSTLYR 202 Query: 182 MKTGKSSNRRTLYKL--QQDEGIPDGMCIDAEGKLWVACYNGGRVIRIDPETGKQIQTVK 239 N T Y + G PDG +DAEG +W A ++G ++R++P+ G + ++ Sbjct: 203 HFIHTDGNLDTAYVWFGPHERGGPDGSAMDAEGYVWNARWDGSCLLRLNPD-GYVDRVIE 261 Query: 240 LPIDKTTSCCFGGPDYSEMYVTSACDGMDEDWKKRQPQSGGIYKITGLGVKGIAPTAFAG 299 LP+ + TSC FGG D+ +Y+TSA ++ P G + I + V G A FAG Sbjct: 262 LPVSRPTSCVFGGEDFKTLYITSAASPLN------HPLDGALLSIR-VDVPGKACQRFAG 314 Lambda K H 0.316 0.135 0.409 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: 331 Number of extensions: 23 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: 299 Length of database: 314 Length adjustment: 27 Effective length of query: 272 Effective length of database: 287 Effective search space: 78064 Effective search space used: 78064 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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