Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_018371968.1 BN415_RS05940 ABC transporter ATP-binding protein
Query= uniprot:A0A165KC78 (242 letters) >NCBI__GCF_000341525.1:WP_018371968.1 Length = 296 Score = 96.7 bits (239), Expect = 5e-25 Identities = 67/221 (30%), Positives = 118/221 (53%), Gaps = 15/221 (6%) Query: 9 LLQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDGNIEY 68 L+ VK L + G + +K + F++ +G+ V+LIG NGAGKTT M + G + G + Sbjct: 3 LITVKNLAKSIRGKEILKKISFDIEDGDCVALIGPNGAGKTTLMDCLLGDKFVTSGEV-- 60 Query: 69 LGKSIKG-KGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRKDKAGILAD--IEKM 125 +IKG + D +K + ++P+ V A++ + E ++ + ++ L+D ++K+ Sbjct: 61 ---AIKGLQPTDDKLKVSVAVLPQENAVPAKLKVKELIR---FFQEVYPNSLSDQEVDKL 114 Query: 126 FTIFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDKIFEVV 185 + +KDQLA +SGG++++L+ L+ +PK+L LDEP+ + + +E+V Sbjct: 115 LRFSDK---QKDQLAEKLSGGQKRLLSFVLTLIGRPKILFLDEPTASMDTSTRQRFWEIV 171 Query: 186 RDVYALGVTIVLVEQNASRALAIADRGYVMESG-LITMTGP 225 ++ A VTIV ADR V+ G LI T P Sbjct: 172 AELKAQDVTIVYSSHYIEEVEHTADRILVLHKGELIRDTTP 212 Lambda K H 0.317 0.136 0.373 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: 153 Number of extensions: 10 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: 242 Length of database: 296 Length adjustment: 25 Effective length of query: 217 Effective length of database: 271 Effective search space: 58807 Effective search space used: 58807 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: 47 (22.7 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