Align ABC transporter for Lactose, ATPase component (characterized)
to candidate PfGW456L13_2830 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)
Query= reanno::Smeli:SM_b20002 (358 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2830 Length = 361 Score = 247 bits (630), Expect = 4e-70 Identities = 138/356 (38%), Positives = 209/356 (58%), Gaps = 11/356 (3%) Query: 4 LQLSDVRKSY----GGLEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGD 59 +++ +V K Y G + V +DI EF +GPSGCGK+TLLR IAG E +S G+ Sbjct: 7 IEVRNVSKRYSDDPGLAPALDNVSVDIADNEFFTLLGPSGCGKTTLLRTIAGFEHVSDGE 66 Query: 60 LTIDDVRMNDVDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEAAH 119 + + +ND+ P KR + VFQSYAL+PHM+V +N+ F L G+ R I +RV+E Sbjct: 67 IRLAGEPVNDLPPFKRRVNTVFQSYALFPHMSVAQNIAFGLEMQGLDRKLIPQRVDEMLA 126 Query: 120 ILELGALLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIARL 179 ++++ L RKP +LSGGQ+QRVA+ RA+ PK+ L DEPLS LD +LR M++E+ R+ Sbjct: 127 LVQMQHLAKRKPAELSGGQQQRVALARALAPKPKVLLLDEPLSALDLKLRKEMQVELKRV 186 Query: 180 HKQLATTIVYVTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFIGSPKM 239 K+ T ++VTHDQ EA+TL+D+I VM AG + Q+GSP ++Y+ P + FVA FIG + Sbjct: 187 QKEAGITFIFVTHDQEEALTLSDRIAVMSAGKILQIGSPNEIYERPQHQFVAQFIGD--I 244 Query: 240 NFLKGVIEIDEDQAYARLPDYGDAKIPVTLQAAAGTAVTIGIRPEH---FDEAGPAALDL 296 NFL G I+ + +P+ +IP Q G+ V + RPE + P L Sbjct: 245 NFLPGHIKRGQQNEKLFVPNGMPVEIPCPAQGFDGSKVQLAFRPERSQLVEPTQPHHLRG 304 Query: 297 AIDMLEHLGGETFAYARHHGNGELIVVETKNG--RGLKTGDRLTARFDPVSVLVFD 350 I+ + ++G T R + + ++++ E G G GDR+ P + L+ + Sbjct: 305 VIEAVLYVGTATLYQCRLNNDIKVMLRENNEGLNHGRVVGDRVAVNLPPHACLLME 360 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: 335 Number of extensions: 12 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: 358 Length of database: 361 Length adjustment: 29 Effective length of query: 329 Effective length of database: 332 Effective search space: 109228 Effective search space used: 109228 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