Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_078427103.1 BK574_RS00955 ABC transporter ATP-binding protein
Query= uniprot:A0A165KC86 (260 letters) >NCBI__GCF_002019605.1:WP_078427103.1 Length = 509 Score = 125 bits (314), Expect = 2e-33 Identities = 69/228 (30%), Positives = 122/228 (53%), Gaps = 12/228 (5%) Query: 9 VLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTFEL 68 V+++ I K F G+ A +V + +K+G+++ L+G NGAGK+T NV+ GLY P+ G + Sbjct: 4 VIEMKDIRKEFPGIVANDNVTLQVKQGEIHALLGENGAGKSTLMNVLFGLYQPEKGEILV 63 Query: 69 AGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRTKGFK 128 GKP + T + + GI Q+ L + T EN+++G+ T G K Sbjct: 64 KGKPVKITDPNVANRLGIGMVHQHFMLVEKFTVTENIILGKE------------PTAGGK 111 Query: 129 AEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPAAGM 188 AK + + G+ K + +S G Q+R+EI + L +++ DEP A + Sbjct: 112 INIKKAAKAVETISKQYGLAVDPYAKIQDISVGMQQRVEILKTLYRGAEILIFDEPTAAL 171 Query: 189 NATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQI 236 E +L +++ ++ ++ ++I+LI H +K +M +CDR TV+ G+ I Sbjct: 172 TPQEITELIQIMKKLVSEGKSIILITHKLKEIMEVCDRCTVIRRGRGI 219 Score = 79.3 bits (194), Expect = 1e-19 Identities = 55/231 (23%), Positives = 111/231 (48%), Gaps = 12/231 (5%) Query: 22 LQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTFELAGKPYEPTAVHEV 81 + A++D+ + + G++ G+ G +G G+T ITGL P G +L G+ ++ Sbjct: 270 ITAVNDLHLEVHAGEILGVAGVDGNGQTELIEAITGLRKPTGGNIQLNGQDITGLTPRKI 329 Query: 82 AKAGIARTFQNIR---LFAEMTALENVMVGRHIRTGSGLFGAVFRTKGFKAEEAAIAKRA 138 AG+ Q+ L + T EN+++ + + G + + I K+A Sbjct: 330 TGAGVGHIPQDRHKHGLVLDFTVGENIVLQTYYQKPYSTSGVLNFNE--------IYKKA 381 Query: 139 QELLDYVGIGKFADYK-ARTLSYGDQRRLEIARALATDPQLIALDEPAAGMNATEKVQLR 197 EL++ + +++ AR LS G+Q++ IAR + P L+ +P G++ + Sbjct: 382 NELIEDYDVRTPSEHTLARALSGGNQQKAIIAREVDRSPDLLIAAQPTRGLDVGAIESIH 441 Query: 198 ELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEVQKNE 248 + + R+ + +LLI ++ V+ + DR+ V+ GK +A + + +NE Sbjct: 442 HRLVKERDKGKAVLLISLELDEVLNVSDRIAVIYEGKIVAIVDADKTNENE 492 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: 328 Number of extensions: 14 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 260 Length of database: 509 Length adjustment: 29 Effective length of query: 231 Effective length of database: 480 Effective search space: 110880 Effective search space used: 110880 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: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. 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