Align Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale)
to candidate WP_057507407.1 ABB28_RS04055 cell division ATP-binding protein FtsE
Query= uniprot:Q88GX0 (260 letters) >NCBI__GCF_001431535.1:WP_057507407.1 Length = 228 Score = 143 bits (360), Expect = 4e-39 Identities = 77/223 (34%), Positives = 131/223 (58%), Gaps = 3/223 (1%) Query: 20 LIRIEGLNKHYGAFH-VLRDIDLQVREGERIVLCGPSGSGKSTLIRCINRLEVAQQGSIQ 78 ++R + ++K Y H L D+ V GE + + G SG+GKSTL++ I+ E +G++ Sbjct: 3 VLRFDNVSKQYAGGHEALTDVSFDVAPGEMVFVTGHSGAGKSTLLKLIHLDERPSRGAVV 62 Query: 79 VDGIDLAATTR-EAAQVRSDIGMVFQHFNLFPHMSVLDNCLLAPTSVRGLSRKDAEERAR 137 + +L + + R ++G V+Q L S+ +N L P +RG R D +R R Sbjct: 63 FNERNLLKVRGGDVPRHRREVGAVYQDHRLLMDRSIAENVAL-PLILRGTRRADIGKRVR 121 Query: 138 MYLSKVGIESQAHKYPSQLSGGQQQRVAIARALCMKPRIMLFDEPTSALDPEMVAEVLDV 197 L ++G+ + PSQLS G+QQRV IARA+ +PR+++ DEPT LDP + AE++ + Sbjct: 122 SVLERMGLGHREKALPSQLSAGEQQRVGIARAIVGEPRLLVADEPTGNLDPTLAAEIMAL 181 Query: 198 LVQLAGTGMTMLCVTHEMGFARQVAERVLFLEGGQIIEDSPPQ 240 +L G ++L V+H++ R++ +RVL L+ G++++D PQ Sbjct: 182 FAELPARGTSVLVVSHDLALLRRMRKRVLILDHGRLVDDISPQ 224 Lambda K H 0.322 0.137 0.395 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: 134 Number of extensions: 5 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: 260 Length of database: 228 Length adjustment: 23 Effective length of query: 237 Effective length of database: 205 Effective search space: 48585 Effective search space used: 48585 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 (21.9 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