Align purine-nucleoside phosphorylase (EC 2.4.2.1) (characterized)
to candidate GFF2311 HP15_2259 methylthioadenosine phosphorylase
Query= BRENDA::Q8U2I1 (265 letters) >FitnessBrowser__Marino:GFF2311 Length = 262 Score = 175 bits (444), Expect = 8e-49 Identities = 99/244 (40%), Positives = 139/244 (56%), Gaps = 8/244 (3%) Query: 1 MPRIAIVGGSGVYDFPA-ENKREETVKTPYG--EVKITVGVVGDEEVAFLARHGKGHSIP 57 M + I+GG+G+ E E TP+G + G +GD+ V FL+RHG H IP Sbjct: 7 MHPVGIIGGTGLTTLSGLEITGENKAGTPWGMPSAPLVEGRLGDQPVMFLSRHGNPHRIP 66 Query: 58 PHKINYRANIWALYELGVERIIATSAVGSMNPEMKPGDFVILDQIIDFTVSRPRTFYDGE 117 PH++NYRAN+ ALY+ GV ++ +AVG ++ +M P VI DQIID+T R TF++G Sbjct: 67 PHQVNYRANLKALYDAGVRTVVGVNAVGGIHADMGPAHVVIPDQIIDYTWGRASTFFEGS 126 Query: 118 ESPHERKFVAHVDFTEPYCPEIRKALITAARNLGLPYHPRGTYVCTEGPRFETAAEIRAY 177 V H+DFT PY R+ LI AA +P+ G Y T+GPR ETAAEI Sbjct: 127 LDS-----VTHIDFTWPYDESARQILIDAAGAENVPFSGFGVYGATQGPRLETAAEIIRM 181 Query: 178 RILGGDVVGMTQCPEAILARELEMCYATVAIVTNYAAGMSGKKLTHSEVVELMQKKSEDI 237 G D+VGMT PEA LA EL M Y + +V N+AAG S +T E+ +++ + Sbjct: 182 ERDGCDLVGMTGMPEAALAAELGMRYVCLGLVVNWAAGKSDHIITMEEIEAAIEQGMSGV 241 Query: 238 VKLI 241 +++ Sbjct: 242 KRIL 245 Lambda K H 0.320 0.138 0.412 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: 233 Number of extensions: 15 Number of successful extensions: 2 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: 265 Length of database: 262 Length adjustment: 25 Effective length of query: 240 Effective length of database: 237 Effective search space: 56880 Effective search space used: 56880 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: 47 (22.7 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