Align DUF1852 domain-containing protein (characterized, see rationale)
to candidate PP_2699 PP_2699 conserved protein of unknown function
Query= uniprot:Q6F6Z7 (355 letters) >FitnessBrowser__Putida:PP_2699 Length = 350 Score = 496 bits (1277), Expect = e-145 Identities = 241/327 (73%), Positives = 281/327 (85%), Gaps = 2/327 (0%) Query: 13 ITMSQTFEFSIKSIRFDEDYRPSDNTRITTNFANLARGESRQENLRNTLNMINNRFNALA 72 +TM + F++K I FDE Y P++NTRITTNFANLARG +RQ+NLRNTL MINNRFNALA Sbjct: 22 VTMDKAPTFTVKRIAFDEHYLPAENTRITTNFANLARGANRQQNLRNTLTMINNRFNALA 81 Query: 73 DWDNPNGDRYAVELDIISVDIDVEGN--GETFPTIEILKTNIIDYKNNQRIEGIVGNNFS 130 WDNP DRY VELDIISV++++E G P IEILKT I+D KNN R+EG+VGNNFS Sbjct: 82 HWDNPEHDRYRVELDIISVEMNLESAQYGNALPLIEILKTYIVDRKNNTRLEGMVGNNFS 141 Query: 131 SYVRDYDFSVLLLEHNKNQAKFSTPENYGELHGKIFKSFVNSNTFNDNFSKQPVICLSVS 190 SYVRDYDFSVLLLEHNK+++ FSTP+++GELHG +FK FVNS T+ ++FSK PVICLSVS Sbjct: 142 SYVRDYDFSVLLLEHNKHRSTFSTPDHFGELHGNLFKCFVNSQTYQEHFSKPPVICLSVS 201 Query: 191 TTKTYHRTTNQHPVLGVEYQQDAYSLTDEYFAKMGLKVRYFMPKNSVAPLAFYFRGDLLS 250 +++TY RT NQHPVLGVEYQQD YSLTDEYF KMGL VRYFMP NSVAPLAFYF GDLL+ Sbjct: 202 SSRTYLRTENQHPVLGVEYQQDEYSLTDEYFKKMGLTVRYFMPPNSVAPLAFYFAGDLLA 261 Query: 251 DYTDLELIGTISTMETFQKIYRPEIYNANSVAGQIYQPSLKHQDFSLTRIVYDREERSQL 310 DYTDLELI TISTM+TFQKIYRPEIYNANS AG+ YQPSLK+QD+SLTRIVYDREERS+L Sbjct: 262 DYTDLELISTISTMDTFQKIYRPEIYNANSPAGKAYQPSLKNQDYSLTRIVYDREERSRL 321 Query: 311 AIKQGKWTEEHFMKPYQSILERWAANY 337 AI+QGK+ EE F+KPYQ+ L +W+A Y Sbjct: 322 AIEQGKFAEEQFVKPYQATLAQWSAQY 348 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: 538 Number of extensions: 12 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: 350 Length adjustment: 29 Effective length of query: 326 Effective length of database: 321 Effective search space: 104646 Effective search space used: 104646 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