Align Protein containing DUF162 (characterized, see rationale)
to candidate AZOBR_RS01625 AZOBR_RS01625 hypothetical protein
Query= uniprot:E4PLR7 (223 letters) >FitnessBrowser__azobra:AZOBR_RS01625 Length = 228 Score = 81.3 bits (199), Expect = 1e-20 Identities = 74/240 (30%), Positives = 106/240 (44%), Gaps = 36/240 (15%) Query: 2 SARANILGKLRNSLAGTTPRPDEFDERLVTAPWRYAPEDRIERLRSLMEAVHTEVHPCRS 61 SARA ILG +R +L + +E RL T P R+L+ A H Sbjct: 6 SARAQILGGIRKAL-NSAEGSEEARRRLATHP------------RNLIPARAQRPH---- 48 Query: 62 DNWPELVAELLNKRNLTNLLCAPSKEHGRALQAYFEATEQKVEL-LAYDQPVEA--WKEE 118 D EL A + + + T L E A+ Y E+ +A D ++ W + Sbjct: 49 DEQVELFAAMATEVSATVELLGGMAEVPGAVADYLAGLNLPAEVRVAPDAALDPIPWDQR 108 Query: 119 LFWSVE---------ASLTGTLGGIAATGTLVLWPDCHEPRLMSLVPPVHIALLKASEIH 169 +V ASLTG G+A TGTL+L P ++ +P HI +L+ +I Sbjct: 109 ATLTVTKGRARDSDGASLTGAFAGVAETGTLMLLSGAERPTTLNFLPDTHIVVLRRGQIV 168 Query: 170 DNLYDMMV------AQDWAAG-LPTNVLLVSGPSKTADIEQVLAYGAHGPRELIVLVLED 222 + D A D G LP V ++GPS+T DIE + GAHGPR L +L++ED Sbjct: 169 GTMEDAWDRLRAAGATDGGKGALPRTVNFITGPSRTGDIEMRIELGAHGPRRLHILLVED 228 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: 123 Number of extensions: 4 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: 228 Length adjustment: 22 Effective length of query: 201 Effective length of database: 206 Effective search space: 41406 Effective search space used: 41406 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