Align Protein containing DUF162 (characterized, see rationale)
to candidate GFF2944 HP15_2888 protein containing DUF162
Query= uniprot:E4PLR7 (223 letters) >FitnessBrowser__Marino:GFF2944 Length = 217 Score = 226 bits (577), Expect = 2e-64 Identities = 116/221 (52%), Positives = 153/221 (69%), Gaps = 4/221 (1%) Query: 1 MSARANILGKLRNSLAGTTPRPDEFDERLVTAPWRYAPEDRIERLRSLMEAVHTEVHPCR 60 MS+R IL +LRN G P+ LV W + ++RIER ++E+VH EVH C Sbjct: 1 MSSRETILQRLRNRTGGELTVPECDFSVLVRDDW--STKERIERFEKMIESVHGEVHHCT 58 Query: 61 SDNWPELVAELLNKRNLTNLLCAPSKEHGRALQAYFEATEQKVELLAYDQPVEAWKEELF 120 D W + +AE+LN R NLL E G++L++ ELL YD+P+E+W+ LF Sbjct: 59 EDMWMDRLAEVLNTRGARNLLIPKQHEIGQSLRS--AGRNDLPELLIYDEPIESWQAHLF 116 Query: 121 WSVEASLTGTLGGIAATGTLVLWPDCHEPRLMSLVPPVHIALLKASEIHDNLYDMMVAQD 180 V+AS+T T GGIA TG+L+LWP+ EPRLMSLVPPVHIA+L+ASE++ ++ M AQ+ Sbjct: 117 NEVDASITSTRGGIAETGSLILWPNEDEPRLMSLVPPVHIAVLRASELYTTFHEAMKAQN 176 Query: 181 WAAGLPTNVLLVSGPSKTADIEQVLAYGAHGPRELIVLVLE 221 WAAG+PTN LL+SGPSKTADIEQ LAYG HGP+ELIVL++E Sbjct: 177 WAAGMPTNALLISGPSKTADIEQTLAYGVHGPKELIVLIIE 217 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: 187 Number of extensions: 5 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: 217 Length adjustment: 22 Effective length of query: 201 Effective length of database: 195 Effective search space: 39195 Effective search space used: 39195 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: 45 (21.9 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