Align ABC transporter for Lactose, ATPase component (characterized)
to candidate GFF2270 PS417_11575 spermidine/putrescine ABC transporter ATPase
Query= reanno::Smeli:SM_b20002 (358 letters) >FitnessBrowser__WCS417:GFF2270 Length = 342 Score = 244 bits (622), Expect = 3e-69 Identities = 132/330 (40%), Positives = 193/330 (58%), Gaps = 19/330 (5%) Query: 1 MSELQLSDVRKSYGGLEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGDL 60 M+ LQL+ + K YG ++ + DL ++ GEFV +GPSGCGK+T L+MIAG ++S G + Sbjct: 1 MAFLQLNALSKRYGAVDAVVATDLAVEKGEFVSLLGPSGCGKTTTLQMIAGFVDVSGGQI 60 Query: 61 TIDDVRMNDVDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEAAHI 120 +D + P+ RG+ +VFQSYAL+PHM+VR+N+ F L+ VP AEI +V + Sbjct: 61 LLDGRDITHAKPASRGLGVVFQSYALFPHMSVRDNVAFGLKMRKVPAAEIASKVKTVLEL 120 Query: 121 LELGALLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIARLH 180 + L DR P++LSGGQRQRVA+ RA+V P + L DEPLSNLDA LR M+ EI R+ Sbjct: 121 VRLAPHADRYPRELSGGQRQRVALARALVIEPPVLLLDEPLSNLDANLREEMQFEIRRIQ 180 Query: 181 KQLATTIVYVTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFIGSPKMN 240 + T + VTHDQ EA++++D++VVM+AG V Q+ +P LY+ P F++ F+G K N Sbjct: 181 CAVGITTLMVTHDQAEALSISDRVVVMQAGRVTQIDAPYKLYEHPRTRFISDFVG--KAN 238 Query: 241 FLKGVIEIDEDQAYARLPDYGDAKIPVTLQAAAGTAVTIGIRPEHFD--EAGPAALDLAI 298 L G DY P + +T+ +RPE +AG L + Sbjct: 239 LLPG--------------DYDLLGSPQVRHESGDGELTLSLRPEKIQLVDAGSGRLQGKV 284 Query: 299 DMLEHLGGETFAYARHHGNGELIVVETKNG 328 + + G + Y H GE+ VV + +G Sbjct: 285 -LDSYFFGSQWLYRIHTSLGEITVVRSNDG 313 Lambda K H 0.321 0.139 0.396 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: 322 Number of extensions: 10 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: 358 Length of database: 342 Length adjustment: 29 Effective length of query: 329 Effective length of database: 313 Effective search space: 102977 Effective search space used: 102977 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