Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate WP_012048833.1 SWIT_RS13320 amino acid ABC transporter ATP-binding protein
Query= uniprot:D8IPI1 (406 letters) >NCBI__GCF_000016765.1:WP_012048833.1 Length = 241 Score = 141 bits (356), Expect = 2e-38 Identities = 90/230 (39%), Positives = 127/230 (55%), Gaps = 11/230 (4%) Query: 4 IHCQALAKHYAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGTLRI 63 IH + K Y GG L + L + GE +V+ GPSG GKST++R I GLE G +RI Sbjct: 2 IHMAGVGKWY-GGYHALRNVSLDVARGERIVICGPSGSGKSTLIRCINGLETHDEGVIRI 60 Query: 64 GGTVVND----LPARERNVAMVFQNYALYPHMSVYDNIAFG---LRRLKRPAAEIDRRVR 116 G V L V MVFQ++ L+PH+++ +N A +R L R AAE R Sbjct: 61 GEDEVRPDRRVLQRIRARVGMVFQDFNLFPHLTILENCALAPMKVRGLARDAAEA--LAR 118 Query: 117 EVAALLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGD 176 E+ + + ++ P +SGGQQQR AIARA+ P + LFDEP S LDA++ ++ D Sbjct: 119 ELLERVRIADQADKYPAQLSGGQQQRTAIARALAMQPEIILFDEPTSALDAEMVKEVL-D 177 Query: 177 IKRLHQRLRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYP 226 I + T + VTH+ A +ADR+I M G+IV+ GSP + + P Sbjct: 178 IMKALATEGITMLCVTHEMGFAREVADRIIFMDAGQIVETGSPRDFFTAP 227 Lambda K H 0.321 0.137 0.403 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: 218 Number of extensions: 9 Number of successful extensions: 4 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: 406 Length of database: 241 Length adjustment: 27 Effective length of query: 379 Effective length of database: 214 Effective search space: 81106 Effective search space used: 81106 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 (21.8 bits) S2: 48 (23.1 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