Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate WP_078429421.1 BK574_RS17060 ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF1302 (334 letters) >NCBI__GCF_002019605.1:WP_078429421.1 Length = 351 Score = 214 bits (546), Expect = 2e-60 Identities = 130/354 (36%), Positives = 195/354 (55%), Gaps = 36/354 (10%) Query: 1 MGQIKLESVTK--NFGPVEVIPPLDLTIEDGEFTVFVGPSGCGKSTLLRLIAGLEDITSG 58 M I+ ++VTK N + L+L I +GE +GPSGCGK+T LR++AG E T+G Sbjct: 1 MSFIQFDNVTKYYNRAATPAVDQLNLEILEGEIITLLGPSGCGKTTTLRMLAGFEQPTTG 60 Query: 59 TIRIDGE----DATNIPPAKRGLAMVFQSYALYPHMSVRKNIAFPMKMAGIPADEQKRRI 114 IRI E D +PP KRG+ MVFQ YAL+PH+++ KN+ F + ++K+R Sbjct: 61 KIRIGDEVVYDDRRALPPEKRGIGMVFQDYALFPHLTIEKNVTFGLNRW--KNRDKKKRA 118 Query: 115 DNAAAALNLTDYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVGMRL 174 + L ++ R P +LSGGQ+QRVA+ RA+ P L DEP SNLDA LR MR Sbjct: 119 QEVLELVGLGEFGHRLPSELSGGQQQRVALARALAPRPKVILMDEPFSNLDAGLREKMRY 178 Query: 175 EISELHKRLATTMIYVTHDQVEAMTMADKIVVLQAGVIEQVGSPMELYRAPRNVFVAGFI 234 +++ + ++ T I VTHDQ +A ++D++VV+ G+I+Q+ +P E+YR P N FVA F+ Sbjct: 179 DVTNILRKANATAIIVTHDQKDAFAVSDRVVVMNEGIIQQIAAPKEMYRCPANCFVAQFV 238 Query: 235 GSPKMNLLTG------------------PQAAQH--NAATIGIRPEHLSISETEGMWAGT 274 G K NL++G PQ + IRPE ++E +G +AG Sbjct: 239 G--KTNLISGTLCPDLKHVETHIGRVCLPQETDKVIENVMVSIRPEGCRLAE-KGRYAGL 295 Query: 275 IGVSEHLGSDTFFHVQCDA---FDDPLTVRASGELDLGYGERVF--LTPDMTHL 323 + + G HV+ + +DP+ + A E D+ G V +TP++ L Sbjct: 296 VERVTYSGEYQEVHVRLQSDQVSNDPMIIYAPIEQDIEIGSVVSFDITPELVAL 349 Lambda K H 0.320 0.138 0.400 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: 292 Number of extensions: 9 Number of successful extensions: 3 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: 334 Length of database: 351 Length adjustment: 29 Effective length of query: 305 Effective length of database: 322 Effective search space: 98210 Effective search space used: 98210 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: 49 (23.5 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