Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate GFF2270 PS417_11575 spermidine/putrescine ABC transporter ATPase
Query= reanno::Smeli:SMc03065 (362 letters) >FitnessBrowser__WCS417:GFF2270 Length = 342 Score = 243 bits (619), Expect = 7e-69 Identities = 132/341 (38%), Positives = 198/341 (58%), Gaps = 18/341 (5%) Query: 1 MTGLLLKDIRKSYGAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDM 60 M L L + K YGAVD + DL +++GEFV +GPSGCGK+T L+MIAG +++GG + Sbjct: 1 MAFLQLNALSKRYGAVDAVVATDLAVEKGEFVSLLGPSGCGKTTTLQMIAGFVDVSGGQI 60 Query: 61 FIDGERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAADM 120 +DG + P+ RG+ +VFQSYAL+PHM+V DN+AFG+++ + EI +V+ ++ Sbjct: 61 LLDGRDITHAKPASRGLGVVFQSYALFPHMSVRDNVAFGLKMRKVPAAEIASKVKTVLEL 120 Query: 121 LQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLS 180 ++L P+ DR P+ LSGGQRQRVA+ RA+ P V L DEPLSNLDA LR + EI ++ Sbjct: 121 VRLAPHADRYPRELSGGQRQRVALARALVIEPPVLLLDEPLSNLDANLREEMQFEIRRIQ 180 Query: 181 ERMSDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPAM 240 + TT++ VTHDQ EA++++DR+VV+ AG + Q+ AP +LYE P F++ F+G Sbjct: 181 CAVGITTLM-VTHDQAEALSISDRVVVMQAGRVTQIDAPYKLYEHPRTRFISDFVGK--A 237 Query: 241 NVIPATITATGQQTAVSLAGGKSVTLDVPTNASENGKTASFGVRPEDLRVTEADDFLFEG 300 N++P G +G +TL +RPE +++ +A +G Sbjct: 238 NLLPGDYDLLGSPQVRHESGDGELTL---------------SLRPEKIQLVDAGSGRLQG 282 Query: 301 TVSIVEALGEVTLLYIEGLVENEPIIAKMPGIARVGRGDKV 341 V G L I + ++ G A +G G V Sbjct: 283 KVLDSYFFGSQWLYRIHTSLGEITVVRSNDGSAPLGYGAAV 323 Lambda K H 0.320 0.137 0.387 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: 293 Number of extensions: 10 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: 362 Length of database: 342 Length adjustment: 29 Effective length of query: 333 Effective length of database: 313 Effective search space: 104229 Effective search space used: 104229 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 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