Align DUF1624 domain-containing protein (characterized, see rationale)
to candidate Echvi_3416 Echvi_3416 Uncharacterized conserved protein
Query= uniprot:L0FVP4 (369 letters) >FitnessBrowser__Cola:Echvi_3416 Length = 363 Score = 322 bits (826), Expect = 8e-93 Identities = 170/366 (46%), Positives = 237/366 (64%), Gaps = 8/366 (2%) Query: 4 QRILALDVFRGITIFAMILVNNPGSWSHVYAPLLHAKWHGCTPTDLIFPFFLFIVGVAIE 63 +R+++LDV RG+TI AMILVN PGSW HV+ PL HA+W+G TPTD IFPFFLFIVGV+I Sbjct: 6 KRLISLDVLRGMTIAAMILVNFPGSWEHVFPPLHHAQWNGITPTDFIFPFFLFIVGVSIV 65 Query: 64 LSLGGQLKKGTPKGFLLRKSLIRALKLIGLGLLLTAIPYFDLAHLRFPGVLQRIGLVYFI 123 ++ G+++ K + +K R K+ LG+LL IP FD + +R GVLQRI LV+ Sbjct: 66 MAYAGKMEMD--KTIVYKKLFFRGAKIFALGVLLGMIPEFDFSAIRVAGVLQRIALVFVA 123 Query: 124 STVMYLYWSPKALVFSSGILLIGYWLCMTFIPVPGIGPANLEPGTNLAAWIDQQVLTGHM 183 T+M+L K + +LL+GYWL MT IP PG LEPG NLAAW+DQ +L G M Sbjct: 124 CTLMFLNLDWKQQAYLGLLLLVGYWLMMTLIPTPGFDRPMLEPGKNLAAWVDQYLLPGKM 183 Query: 184 WSQTKTWDPEGLFSTLPAIVTCLLGVACGKILTGNSSHKARLTKWGIAGVTLVFGGLAWS 243 W T WDPEG+FSTLPAI T +LG+ G++L + + G+ L GL W+ Sbjct: 184 WQDT--WDPEGVFSTLPAIATGILGMLAGQLLKSQLKEVEKANNLMVIGLVLTLWGLFWA 241 Query: 244 LFFPLNKALWTSSFVLYTAGWAFLGLAACYWILDVKGWKKWSLPFVIYGMNAITVFFLSG 303 FFP+NK LWTSSFVL T G AF L A Y+ +DVKG + + P+VI+G NAITV+ L+ Sbjct: 242 WFFPINKNLWTSSFVLVTGGTAFSFLGAFYYWIDVKGNSQGTTPWVIFGSNAITVYVLAD 301 Query: 304 VIAKLFGLIKVNWEGTRVSLKLFLQEALFNGWLAPKDASLCGAILMMIILFIPAYFMWKR 363 +++ F ++ +G +S F+Q A G + P+ AS+ A+ ++I FIPA+ ++++ Sbjct: 302 ILSLFF--YQLPLDGQSISAH-FMQAAKSLG-MMPEIASMVFALCFVLINFIPAWLLYRK 357 Query: 364 NIIIKV 369 + IK+ Sbjct: 358 KVFIKL 363 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: 543 Number of extensions: 31 Number of successful extensions: 3 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: 363 Length adjustment: 30 Effective length of query: 339 Effective length of database: 333 Effective search space: 112887 Effective search space used: 112887 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: 49 (23.5 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