Align DUF1624 domain-containing protein (characterized, see rationale)
to candidate WP_057509306.1 ABB28_RS14520 DUF1624 domain-containing protein
Query= uniprot:L0FVP4 (369 letters) >NCBI__GCF_001431535.1:WP_057509306.1 Length = 355 Score = 197 bits (501), Expect = 4e-55 Identities = 122/313 (38%), Positives = 172/313 (54%), Gaps = 23/313 (7%) Query: 5 RILALDVFRGITIFAMILVNNPGSWSHVYAPLLHAKWHGCTPTDLIFPFFLFIVGVAIEL 64 R+ ++D RGIT+ AM+LVNNPG W HV+APLLHA WHGCTPTDL+FPFFLF+VGV++ Sbjct: 8 RLASIDALRGITVAAMLLVNNPGDWGHVHAPLLHAAWHGCTPTDLVFPFFLFLVGVSMAF 67 Query: 65 SLGGQLKKGTPKGFLLRKSLIRALKLIGLGLLLTAIPYFDLA--HLRFPGVLQRIGLVYF 122 S+ + + L R L RAL+++ GLLL A+ ++ LA H R GVLQRI + Sbjct: 68 SVVPRAADAVARPALTRGVLTRALRILVAGLLLHALAWWLLALPHYRLWGVLQRIAVCSA 127 Query: 123 ISTVMYLYWSPKALVFSSGILLIGY--WLCMTFIPVPGIGPANLEPGTNLAAWI---DQQ 177 + ++ ++ + + +LL GY L P P + A WI D Sbjct: 128 LVGLLAVHARARLQWTALVVLLAGYAGLLLAADTLAPLHNPVSRLDTALFAPWIYQYDPA 187 Query: 178 VLTGHMWSQTKTWDPEGLFSTLPAIVTCLLGVACGKILTGNSSHKARLTKWGIAGVTLVF 237 GH DPEGL STL A+ + LLG+ G++L + + G L+ Sbjct: 188 TGLGH--------DPEGLASTLGALASTLLGLLAGQMLRAGQT-----LRLAFGGALLLA 234 Query: 238 GGLAWSLFFPLNKALWTSSFVLYTAGWAFLGLAACYWILDVKGWKKWSLPFVIYGMNAIT 297 GL + + PLNK LWT +VL+T G A + L A +W++D GW F G+NAIT Sbjct: 235 IGLVAAAWLPLNKHLWTPPYVLWTGGLAIIALLAAHWLVDQHGWPALGRRF---GVNAIT 291 Query: 298 VFFLSGVIAKLFG 310 V+ + V++ L G Sbjct: 292 VYLGASVMSVLLG 304 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: 522 Number of extensions: 38 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 369 Length of database: 355 Length adjustment: 29 Effective length of query: 340 Effective length of database: 326 Effective search space: 110840 Effective search space used: 110840 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 24 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