Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_041937000.1 RL_RS34955 ABC transporter ATP-binding protein
Query= uniprot:A0A165KC78 (242 letters) >NCBI__GCF_000009265.1:WP_041937000.1 Length = 247 Score = 183 bits (464), Expect = 3e-51 Identities = 90/223 (40%), Positives = 148/223 (66%), Gaps = 1/223 (0%) Query: 10 LQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDGNIEYL 69 L ++ L+ YG + + GVD +V G+ V+L+G NGAGK+T +K + G ++ G+I++ Sbjct: 7 LLIRDLRAGYGNLDILNGVDLDVPAGQFVALMGPNGAGKSTLLKTLYGMTTIKQGSIDWR 66 Query: 70 GKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRKDKAGILADIEKMFTIF 129 GK+I G + ++ EG+ VP+GR F M++ ENLQM AY +D A + AD + ++ +F Sbjct: 67 GKNIAGSKSRSILGEGISFVPQGRCNFPVMSVDENLQMAAYTLRD-AKVKADRDYVYDLF 125 Query: 130 PRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDKIFEVVRDVY 189 P L+ R+ LAG MSGGEQQ+L + A++ +PKVLL+DEPS+GLSP + +F+ + ++ Sbjct: 126 PILKNRRATLAGNMSGGEQQLLEVAMAVLQRPKVLLVDEPSVGLSPAAIGIVFDELLRLH 185 Query: 190 ALGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLND 232 A G+TI+LVEQN +A+ +A+R ++ G + G + + +D Sbjct: 186 ADGMTILLVEQNTKKAMEVAERAVILRLGKVIWDGLPKDITHD 228 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: 156 Number of extensions: 4 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: 247 Length adjustment: 24 Effective length of query: 218 Effective length of database: 223 Effective search space: 48614 Effective search space used: 48614 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 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