Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_089303491.1 CHB84_RS21590 ABC transporter ATP-binding protein
Query= uniprot:A0A165KC78 (242 letters) >NCBI__GCF_900188115.1:WP_089303491.1 Length = 275 Score = 192 bits (489), Expect = 4e-54 Identities = 109/247 (44%), Positives = 153/247 (61%), Gaps = 13/247 (5%) Query: 2 AEKSNKVLLQVKGLKVAYGGIQAVK---GVDFEVREGELVSLIGSNGAGKTTTMKAITGT 58 AE+S + + ++V G + V G E+ EGELV +IG NGAGK+T +KA+ G Sbjct: 29 AERSTGSEVILDAVEVVAGYVPEVNVLTGCSLELGEGELVGVIGPNGAGKSTLIKAMFGL 88 Query: 59 LSMNDGNIEYLGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRKDKAGI 118 + + G++ + G I G LV+ GL VP+ VF +T+ ENL+MG +++ Sbjct: 89 VPVRGGSVRFRGADITGAQTHTLVQHGLGYVPQRDNVFPALTVEENLRMGTFLKP----- 143 Query: 119 LADIEKMFT----IFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLS 174 + E+ F +F RL ER+ Q AG++SGGE+QMLAMGR LM++P+VL LDEPS GLS Sbjct: 144 -REFERRFAWVTELFSRLAERRKQRAGSLSGGERQMLAMGRTLMAEPEVLFLDEPSAGLS 202 Query: 175 PIMVDKIFEVVRDVYALGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDPK 234 P D++F V+ + GV+IV+VEQNA R L I DRGYV++ G +G G LL+DPK Sbjct: 203 PANQDQVFGQVQRINDTGVSIVMVEQNARRCLQICDRGYVLDQGRNAYSGAGHDLLHDPK 262 Query: 235 VRAAYLG 241 V YLG Sbjct: 263 VIEYYLG 269 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: 193 Number of extensions: 14 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: 275 Length adjustment: 24 Effective length of query: 218 Effective length of database: 251 Effective search space: 54718 Effective search space used: 54718 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