Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate GFF4127 HP15_4067 spermidine/putrescine ABC transporter ATPase subunit
Query= uniprot:Q6MNM2 (347 letters) >FitnessBrowser__Marino:GFF4127 Length = 362 Score = 215 bits (548), Expect = 1e-60 Identities = 111/274 (40%), Positives = 162/274 (59%), Gaps = 10/274 (3%) Query: 11 KSFGSADVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGTISIDGKKINDI 70 + FGS + + LD+ G F ++GPSGCGK+TLLR LAG + D G I I G+++ND+ Sbjct: 12 RRFGSNAAVDHVSLDVPAGTFFSILGPSGCGKTTLLRLLAGFDKPDQGDIHIRGERMNDV 71 Query: 71 EPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEISELLQIKHLLDRK 130 P R + MVFQ AL+P MTV +N+ +GLK + + E KR+ + E + + L R Sbjct: 72 PPNRRPVNMVFQHLALFPTMTVGDNIAYGLKRRKMPLVERRKRIARVLEQVGLPDLEHRN 131 Query: 131 PKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRLHHNSKSTMIYV 190 P+ELSGGQRQRVAL R L + ++L DEPL LD LR QM++E+K L +T +Y+ Sbjct: 132 PQELSGGQRQRVALARCLVLEPTLLLLDEPLGALDLKLREQMKVELKHLQKQFGTTFVYI 191 Query: 191 THDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSPEMNFLEGAVLEKI 250 THDQ EA + D++AV++DG +Q+ P E+Y P F+A F+G + N L G ++ Sbjct: 192 THDQSEAMVMSDQVAVMRDGRFDQVAPPEELYREPATPFVAGFVG--DNNRLSGELVS-- 247 Query: 251 PWPEARKADQILGIRPDAFALNQGPLGTQEVALG 284 D + +R D L QG + + + G Sbjct: 248 ------VRDSLAELRLDDGVLVQGRVASDNLQAG 275 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: 321 Number of extensions: 14 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: 362 Length adjustment: 29 Effective length of query: 318 Effective length of database: 333 Effective search space: 105894 Effective search space used: 105894 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