Align DUF1852 domain-containing protein (characterized, see rationale)
to candidate BWI76_RS15395 BWI76_RS15395 DUF1852 domain-containing protein
Query= uniprot:Q6F6Z7 (355 letters) >FitnessBrowser__Koxy:BWI76_RS15395 Length = 325 Score = 493 bits (1268), Expect = e-144 Identities = 236/323 (73%), Positives = 275/323 (85%) Query: 15 MSQTFEFSIKSIRFDEDYRPSDNTRITTNFANLARGESRQENLRNTLNMINNRFNALADW 74 M+Q F ++IK FDE+Y PS+NTRITTNFANLARGE+R+ENLRNTL MINNRFN LA W Sbjct: 1 MNQQFTYTIKRTLFDENYNPSENTRITTNFANLARGENRRENLRNTLAMINNRFNNLAHW 60 Query: 75 DNPNGDRYAVELDIISVDIDVEGNGETFPTIEILKTNIIDYKNNQRIEGIVGNNFSSYVR 134 DNP GDRYAVEL+IIS ++ + G+TFP IEIL+T IID ++RI+GIVGNNFSSYVR Sbjct: 61 DNPKGDRYAVELEIISAEMKINATGDTFPVIEILQTGIIDKNTDKRIDGIVGNNFSSYVR 120 Query: 135 DYDFSVLLLEHNKNQAKFSTPENYGELHGKIFKSFVNSNTFNDNFSKQPVICLSVSTTKT 194 DYDFSV+LLEHNK +A FS PE +G+LHG IFK FVNS + NF K PVICLSVS+ T Sbjct: 121 DYDFSVVLLEHNKGRAGFSIPEGFGDLHGNIFKDFVNSAQYKANFKKTPVICLSVSSKDT 180 Query: 195 YHRTTNQHPVLGVEYQQDAYSLTDEYFAKMGLKVRYFMPKNSVAPLAFYFRGDLLSDYTD 254 YH+T NQHPVLG+EY+ A SLT++YF KMGL+VRYFMPKNSVAPLAFYF GDLLSDYT Sbjct: 181 YHQTGNQHPVLGLEYRPTASSLTEQYFGKMGLQVRYFMPKNSVAPLAFYFSGDLLSDYTS 240 Query: 255 LELIGTISTMETFQKIYRPEIYNANSVAGQIYQPSLKHQDFSLTRIVYDREERSQLAIKQ 314 LELI TISTMETFQKIYRPEIYNANS AG YQP L HQD SLT+IVYDREERSQLA++Q Sbjct: 241 LELISTISTMETFQKIYRPEIYNANSAAGLCYQPDLHHQDHSLTKIVYDREERSQLAVEQ 300 Query: 315 GKWTEEHFMKPYQSILERWAANY 337 GK+TEEHF+KPY++IL++W+A+Y Sbjct: 301 GKYTEEHFIKPYKNILQQWSAHY 323 Lambda K H 0.317 0.133 0.388 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: 492 Number of extensions: 8 Number of successful extensions: 1 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: 355 Length of database: 325 Length adjustment: 28 Effective length of query: 327 Effective length of database: 297 Effective search space: 97119 Effective search space used: 97119 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: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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