Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_012112663.1 XAUT_RS03225 ABC transporter ATP-binding protein
Query= uniprot:A0A165KC86 (260 letters) >NCBI__GCF_000017645.1:WP_012112663.1 Length = 278 Score = 217 bits (552), Expect = 2e-61 Identities = 110/256 (42%), Positives = 163/256 (63%) Query: 1 MTEKSNEVVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYT 60 M+ + +L V + RFGGL A++D+ + G++ LIGPNGAGKTT FN++TG Sbjct: 9 MSHPAGTAILNVEHVGMRFGGLTAIADLHFDVHAGEIVSLIGPNGAGKTTAFNIMTGFLK 68 Query: 61 PDAGTFELAGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGA 120 P G G+ T +E+A+ G+ARTFQ +FA+ T +NV++G + L Sbjct: 69 PTQGRVLFRGQDLSQTRPNEIARLGLARTFQRTSVFADDTVRDNVLIGLNRHGDVALLDR 128 Query: 121 VFRTKGFKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIA 180 +F T + EAA+ +RA+ +LD VG+ AD KA +LSYG+QR + A ALA +P+++ Sbjct: 129 LFPTPRGRRAEAAVRERAEAILDLVGLAARADEKAGSLSYGEQRLVGFALALAVEPKMLL 188 Query: 181 LDEPAAGMNATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGN 240 LDEP +GMNA+E LI ++R++ TILL+EHD+ +VM + DR+ L+YG+ IAEG Sbjct: 189 LDEPVSGMNASETQGFVRLIRKVRDEGVTILLVEHDMPMVMEVSDRIVCLNYGRLIAEGP 248 Query: 241 PAEVQKNEKVIEAYLG 256 PA ++ + VIEAYLG Sbjct: 249 PAAIRADPNVIEAYLG 264 Lambda K H 0.319 0.137 0.384 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: 219 Number of extensions: 15 Number of successful extensions: 1 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: 260 Length of database: 278 Length adjustment: 25 Effective length of query: 235 Effective length of database: 253 Effective search space: 59455 Effective search space used: 59455 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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