Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate GFF3591 Psest_3658 spermidine/putrescine ABC transporter ATP-binding subunit
Query= uniprot:Q6MNM2 (347 letters) >FitnessBrowser__psRCH2:GFF3591 Length = 369 Score = 233 bits (595), Expect = 4e-66 Identities = 126/281 (44%), Positives = 179/281 (63%), Gaps = 15/281 (5%) Query: 4 IQFSNIKKSF-GSADVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGTISI 62 + F I+KS+ G + +++ ++LDI GEFL L+GPSG GK+T L LAG E+ +G I + Sbjct: 11 VSFRGIQKSYDGESLIVRDLNLDIRRGEFLTLLGPSGSGKTTSLMMLAGFETPTAGEILL 70 Query: 63 DGKKINDIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEISELLQ 122 DG+ IN++ P RD+ MVFQ+YAL+PHMTV+EN+ F L ++ +A +I +RV ++Q Sbjct: 71 DGRAINNVPPHKRDMGMVFQNYALFPHMTVSENLAFPLSVRGMAKPDIKERVKRALAMVQ 130 Query: 123 IKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRLHHN 182 ++ +R P +LSGGQ+QRVAL RAL + ++L DEPL LD LR QM++EIK LH Sbjct: 131 LEGFRNRYPAQLSGGQQQRVALARALVFEPQLVLMDEPLGALDKQLREQMQMEIKHLHER 190 Query: 183 SKSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSPEMNFL 242 T++YVTHDQ EA T+ DR+AV G I+QI P +Y +P NTF+A F+G E N L Sbjct: 191 LGVTVVYVTHDQGEALTMSDRVAVFHQGQIQQIEDPRTLYEKPVNTFVANFLG--ENNRL 248 Query: 243 EGAVLEKIPWPEARKADQIL-----GIRPDAFALNQGPLGT 278 +L+ R+ D G +A A+N G GT Sbjct: 249 PAHLLD-------RRGDSCTVKLGRGETVEALAVNVGAAGT 282 Lambda K H 0.318 0.136 0.383 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: 294 Number of extensions: 11 Number of successful extensions: 1 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: 347 Length of database: 369 Length adjustment: 29 Effective length of query: 318 Effective length of database: 340 Effective search space: 108120 Effective search space used: 108120 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: 49 (23.5 bits)
This GapMind analysis is from Sep 17 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