Align Protein containing DUF162 (characterized, see rationale)
to candidate AZOBR_RS25105 AZOBR_RS25105 hypothetical protein
Query= uniprot:E4PLR7 (223 letters) >FitnessBrowser__azobra:AZOBR_RS25105 Length = 223 Score = 180 bits (457), Expect = 2e-50 Identities = 98/220 (44%), Positives = 134/220 (60%), Gaps = 3/220 (1%) Query: 3 ARANILGKLRNSLAGTTPRPDEFDERLVTAPWRYAPEDRIERLRSLMEAVHTEVHPCRSD 62 +R ILGKLR P E D ++ R+ +R+ER++ +MEAVHTE Sbjct: 4 SRNAILGKLRAGRDAHPLTPPESDFAVLRNK-RWDGAERLERIKRMMEAVHTEFLETTEA 62 Query: 63 NWPELVAELLNKRNLTNLLCAPSKEHGRALQAYFEATEQK--VELLAYDQPVEAWKEELF 120 +WP V L + NLL P+ E G L + + A+ EL+ Y VE +KE LF Sbjct: 63 DWPADVQAFLTAQGTRNLLFGPATEAGGRLSSEWAASGMAGGPELIPYADRVETFKERLF 122 Query: 121 WSVEASLTGTLGGIAATGTLVLWPDCHEPRLMSLVPPVHIALLKASEIHDNLYDMMVAQD 180 ++A +T TLG IA TG+L++WP EPRLMSLVP +H+ALL+A ++D + M Sbjct: 123 DGIDAGITTTLGAIADTGSLIVWPTPEEPRLMSLVPHMHLALLRADALYDTFWQAMTENR 182 Query: 181 WAAGLPTNVLLVSGPSKTADIEQVLAYGAHGPRELIVLVL 220 WA G+PTN LL+SGPSKTADIEQ LAYG HGP+ L+V+++ Sbjct: 183 WADGMPTNALLISGPSKTADIEQTLAYGVHGPKRLVVVIV 222 Lambda K H 0.317 0.133 0.406 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: 178 Number of extensions: 7 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: 223 Length of database: 223 Length adjustment: 22 Effective length of query: 201 Effective length of database: 201 Effective search space: 40401 Effective search space used: 40401 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 (21.7 bits) S2: 46 (22.3 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