Align DUF1852 domain-containing protein (characterized, see rationale)
to candidate GFF3668 PS417_18770 hypothetical protein
Query= uniprot:Q6F6Z7 (355 letters) >FitnessBrowser__WCS417:GFF3668 Length = 327 Score = 511 bits (1317), Expect = e-150 Identities = 246/324 (75%), Positives = 287/324 (88%), Gaps = 2/324 (0%) Query: 15 MSQTFEFSIKSIRFDEDYRPSDNTRITTNFANLARGESRQENLRNTLNMINNRFNALADW 74 M++ F F++KSIRFDE Y P++NTRITTNFANLARG SRQENLRNTL MI+NRFNALA W Sbjct: 1 MNKEFAFTVKSIRFDEHYHPAENTRITTNFANLARGASRQENLRNTLRMIDNRFNALAHW 60 Query: 75 DNPNGDRYAVELDIISVDIDVEG--NGETFPTIEILKTNIIDYKNNQRIEGIVGNNFSSY 132 DNP GDRY+VELDIISV++D++ +G P IEILKT+I+D K N+R+ GIVGNNFSSY Sbjct: 61 DNPKGDRYSVELDIISVEMDIDDQRSGHAIPLIEILKTHIVDRKTNERLPGIVGNNFSSY 120 Query: 133 VRDYDFSVLLLEHNKNQAKFSTPENYGELHGKIFKSFVNSNTFNDNFSKQPVICLSVSTT 192 VRDYDFSV LLEHNK+Q FSTP ++GELHGK+FKSFVNS+T+ ++F+K PVICLSVS+ Sbjct: 121 VRDYDFSVRLLEHNKDQPHFSTPADFGELHGKLFKSFVNSSTYKEHFNKPPVICLSVSSA 180 Query: 193 KTYHRTTNQHPVLGVEYQQDAYSLTDEYFAKMGLKVRYFMPKNSVAPLAFYFRGDLLSDY 252 KTYHRT N HPVLGVEY QD YSLTDEYF KMGLKVRYFMP NSVAPLAFYF GD+LSDY Sbjct: 181 KTYHRTENLHPVLGVEYLQDEYSLTDEYFKKMGLKVRYFMPANSVAPLAFYFAGDVLSDY 240 Query: 253 TDLELIGTISTMETFQKIYRPEIYNANSVAGQIYQPSLKHQDFSLTRIVYDREERSQLAI 312 T LELI TISTM+TFQKIYRPEIYNANS AG+ YQPSL+HQD+SLTRIVYDREERS+LAI Sbjct: 241 TTLELISTISTMDTFQKIYRPEIYNANSAAGKSYQPSLQHQDYSLTRIVYDREERSRLAI 300 Query: 313 KQGKWTEEHFMKPYQSILERWAAN 336 +QGK+ EE+F+KPYQS+LE+W+A+ Sbjct: 301 EQGKFVEENFIKPYQSVLEQWSAH 324 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: 513 Number of extensions: 9 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: 355 Length of database: 327 Length adjustment: 28 Effective length of query: 327 Effective length of database: 299 Effective search space: 97773 Effective search space used: 97773 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