Align ABC transporter (characterized, see rationale)
to candidate GFF1860 Psest_1899 ABC-type sugar transport systems, ATPase components
Query= uniprot:A0A166QFW2 (381 letters) >FitnessBrowser__psRCH2:GFF1860 Length = 390 Score = 317 bits (811), Expect = 5e-91 Identities = 175/360 (48%), Positives = 231/360 (64%), Gaps = 9/360 (2%) Query: 1 MIKLKLDNVNKQLGGMRI--LRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGG 58 M L+L NV K G +I L+D++L+I AGEF++ VGPSGCGKSTL+ IAGL++I GG Sbjct: 1 MASLELRNVQKSYGNSQIATLKDIALKIDAGEFLILVGPSGCGKSTLMNCIAGLENITGG 60 Query: 59 DLLIDGRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTA 118 ++L+DG ++ P++R + MVFQSYALYP MSV DNI+FGLK+ K + E V + A Sbjct: 61 EILVDGEDISQASPKDRDIAMVFQSYALYPTMSVRDNIAFGLKMRKVPAAKIEEEVARVA 120 Query: 119 QILQLDKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIAR 178 ++LQ++ LL+RKP +LSGGQ+QRVAMGRA+AR P I LFDEPLSNLDA LRV+MR EI Sbjct: 121 KLLQIEPLLERKPSQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEIKL 180 Query: 179 LHDRLGSTMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPR 238 +H RL +T +YVTHDQ+EAMTL DK+ V+ G ++Q G+P E+Y PA+ FVA F+GSP Sbjct: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGVIQQFGTPHEIYNNPANLFVASFIGSPP 240 Query: 239 MNFLSARL-QTPGETSLVDTLVWGITS--LPFDSSNLAAGTPLSLGIRPEHVSLK---AA 292 MNF+ R+ Q G V G LP S + L LGIRPE + L +A Sbjct: 241 MNFVPLRIRQRDGRWVGVLNSEQGSCELPLPITSDDGLRDRELILGIRPEQIGLAPAGSA 300 Query: 293 DGTAGVVVTAVEYLGSETYVHLETGQDEPLICRCEVSAGWQAGDRVELLLDLDNLHLFDA 352 D + V + VE G +T V Q + CR + G+ + L D LFDA Sbjct: 301 DFSLAVDIEVVEPTGPDTLVVFTLNQVK-ACCRLAPDQAPRVGETLNLQFDPRRALLFDA 359 Lambda K H 0.320 0.137 0.394 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: 374 Number of extensions: 11 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: 381 Length of database: 390 Length adjustment: 30 Effective length of query: 351 Effective length of database: 360 Effective search space: 126360 Effective search space used: 126360 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: 50 (23.9 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