Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate AO353_25130 AO353_25130 ABC transporter
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25130 Length = 381 Score = 301 bits (771), Expect = 2e-86 Identities = 165/360 (45%), Positives = 228/360 (63%), Gaps = 9/360 (2%) Query: 1 MATLELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGG 60 M L+L NVNK G L+++ L+I GEF++ VGPSGCGKSTL+ IAGL++I G Sbjct: 1 MIKLKLDNVNKQLGG--VRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICAG 58 Query: 61 AILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVS 120 +L+D+ ++ + P++R + MVFQSYALYP MSV DNI+FGLK+ K + + E V R + Sbjct: 59 DLLIDERRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTEKSSLRERVLRTA 118 Query: 121 KLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 ++LQ++ LL RKP +LSGGQ+QRVAMGRA+AR P I LFDEPLSNLDA LRV+MR E+ Sbjct: 119 QILQLDKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIAR 178 Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPP 240 +H RL +T +YVTHDQ+EAMTL DK+ V+ G ++Q G+P+++Y PA+ FVA F+GSP Sbjct: 179 LHARLGSTMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPR 238 Query: 241 MNFIPLRLQRKDGRLLALLDSGQARCELPLGMQDAGLEDREVILGIRPEQIILANGEANG 300 MNF+ RL G + LP + D + LG+RPE + L + Sbjct: 239 MNFLAARL-HAPGETSLVDTPVLGMTSLPFDSSNLA-ADTPLSLGVRPEHVSLKAADG-- 294 Query: 301 LPTIRAEVQVTEPTGPDTLVFVNL-NDTKVCCRLAPDVAPAVGETLTLQFDPAKVLLFDA 359 T+ V E G +T V ++ D + CR + VG+ + LQ D + LFDA Sbjct: 295 --TVGVIVTGVEYLGSETYVHLDTGQDDPLICRCEVNAGWQVGDRVELQLDIGNLHLFDA 352 Lambda K H 0.319 0.138 0.393 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: 420 Number of extensions: 19 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: 386 Length of database: 381 Length adjustment: 30 Effective length of query: 356 Effective length of database: 351 Effective search space: 124956 Effective search space used: 124956 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 (21.7 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