Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_058929664.1 AU252_RS04340 ABC transporter ATP-binding protein
Query= uniprot:A0A165KC78 (242 letters) >NCBI__GCF_001484605.1:WP_058929664.1 Length = 257 Score = 197 bits (501), Expect = 2e-55 Identities = 107/235 (45%), Positives = 153/235 (65%), Gaps = 5/235 (2%) Query: 9 LLQVKGLKVAY-GGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDGNIE 67 +++V L Y G+ + G + E R+GEL+ +IG NGAGK+T +KA+ G + ++ G + Sbjct: 19 VVKVTNLVAGYLPGVNILNGCNIEARKGELIGIIGPNGAGKSTLLKAMFGLVKVHSGTVV 78 Query: 68 YLGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIR-KDKAGILADIEKMF 126 G+ I G A LV G+ VP+ VFA +TI EN+QMG + R KD A + + Sbjct: 79 VRGQDITGLKANKLVTMGVGFVPQNNNVFATLTIEENMQMGMFQRPKDFA---ERFDFVT 135 Query: 127 TIFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDKIFEVVR 186 ++FP L +R+ Q AG++SGGE+QM+AMGRALM +P VLLLDEPS GLSP+ D+ F V Sbjct: 136 SLFPELGKRRAQRAGSLSGGERQMVAMGRALMMEPAVLLLDEPSAGLSPVKQDETFLRVH 195 Query: 187 DVYALGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDPKVRAAYLG 241 ++ GV++++VEQNA R L I DR YV++ G TG G++L+ DPKV YLG Sbjct: 196 EINRAGVSVIMVEQNARRCLQICDRAYVLDQGRDAYTGTGRELMKDPKVIQLYLG 250 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: 182 Number of extensions: 8 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: 257 Length adjustment: 24 Effective length of query: 218 Effective length of database: 233 Effective search space: 50794 Effective search space used: 50794 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: 46 (22.3 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