Align DUF1624 domain-containing protein (characterized, see rationale)
to candidate CA265_RS21920 CA265_RS21920 DUF5009 domain-containing protein
Query= uniprot:L0FVP4 (369 letters) >FitnessBrowser__Pedo557:CA265_RS21920 Length = 386 Score = 358 bits (919), Expect = e-103 Identities = 185/383 (48%), Positives = 251/383 (65%), Gaps = 15/383 (3%) Query: 2 PKQRILALDVFRGITIFAMILVNNPGSWSHVYAPLLHAKWHGCTPTDLIFPFFLFIVGVA 61 PKQR+L+LD FRG+T+ AMILVNNPGSW H+YAPL HA+W+GCTPTDLIFPFFL+IVGV+ Sbjct: 4 PKQRLLSLDFFRGLTVAAMILVNNPGSWGHIYAPLEHAEWNGCTPTDLIFPFFLWIVGVS 63 Query: 62 IELSLGGQLKKGTPKGFLLRKSLIRALKLIGLGLLLTAIPYFDLA------------HLR 109 I ++ T + K++ R + L LG L A +R Sbjct: 64 IAFAMSSSKTDPTTHQKTIIKAIKRGIILYLLGFFLAIFGKIISAIIDGRSIWEAFQTVR 123 Query: 110 FPGVLQRIGLVYFISTVMYLYWSPKALVFSSGILLIGYWLCMTFIPVPGIGPANLEPGTN 169 GVLQRIG+V+ IS+++++ S K + + ++L YW MTFIPVPG+G NLE TN Sbjct: 124 LLGVLQRIGIVFIISSIIFIKVSNKTIFKTLIVILAVYWALMTFIPVPGVGYPNLEKETN 183 Query: 170 LAAWIDQQVLT-GHMWSQTKTWDPEGLFSTLPAIVTCLLGVACGKILTGNSSHKARLTKW 228 LAAWID+ +LT H W+ +KTWDPEG+ STLPAI TCL G+ G + W Sbjct: 184 LAAWIDRGILTEAHTWASSKTWDPEGILSTLPAIGTCLFGILVGVWMRRKDVDNPTKVAW 243 Query: 229 -GIAGVTLVFGGLAWSLFFPLNKALWTSSFVLYTAGWAFLGLAACYWILDVKGWKKWSLP 287 G+T V GL W L FP+NKALWTSS+VLY G A +GLA CYWI+DV+G+KK++ P Sbjct: 244 LFTTGITSVILGLLWDLQFPINKALWTSSYVLYAGGLASIGLALCYWIIDVQGYKKFTTP 303 Query: 288 FVIYGMNAITVFFLSGVIAKLFGLIKVNW-EGTRVSLKLFLQEALFNGWLAPKDASLCGA 346 FV+YG+NAITVFFL+G++ ++ LI++ +GT+ L + E + + +P +ASL A Sbjct: 304 FVVYGVNAITVFFLAGLMPRVLNLIQITKPDGTKTGLLVRFYETCYTPFFSPINASLVWA 363 Query: 347 ILMMIILFIPAYFMWKRNIIIKV 369 I ++ ++ YFM+K+NIIIKV Sbjct: 364 ITYVLGFYVLLYFMYKKNIIIKV 386 Lambda K H 0.329 0.145 0.486 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: 626 Number of extensions: 42 Number of successful extensions: 6 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: 369 Length of database: 386 Length adjustment: 30 Effective length of query: 339 Effective length of database: 356 Effective search space: 120684 Effective search space used: 120684 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 50 (23.9 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