Align ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized)
to candidate PP_1018 PP_1018 mannose/glucose ABC transporter - ATP binding subunit
Query= reanno::pseudo13_GW456_L13:PfGW456L13_3039 (367 letters) >FitnessBrowser__Putida:PP_1018 Length = 384 Score = 311 bits (798), Expect = 1e-89 Identities = 168/361 (46%), Positives = 239/361 (66%), Gaps = 9/361 (2%) Query: 1 MANLKIKNLQKGFEGF--SIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSGG 58 MA L+++N+ K + +K I L + D EF++ VGPSGCGKSTL+ IAGLE+++GG Sbjct: 1 MATLELRNVNKTYGSGLPDTLKDIQLSIKDGEFLILVGPSGCGKSTLMNCIAGLEQITGG 60 Query: 59 TIELDGRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVAKAEVEKKVSEAA 118 I +D +D++ +SP RD+AMVFQ+YALYP MSVR+N+ F L + + +A ++++V+ A Sbjct: 61 AILIDEQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKLPQAAIDEEVARVA 120 Query: 119 RILELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELLR 178 ++L++ +L RKP QLSGGQ+QRVA+GRA+ R PKI+LFDEPLSNLDA LRV+MR E+ Sbjct: 121 KLLQIEHLLARKPAQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 Query: 179 LHKELQATMIYVTHDQVEAMTMADKVVVLNGGKIEQVGSPLDLYHQPANLFVAGFLGTPK 238 +H+ L+ T +YVTHDQ+EAMT+ DKV V+ G I+Q G+P +Y+ PAN FVA F+G+P Sbjct: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPQQIYNDPANQFVASFIGSPP 240 Query: 239 MGFLKGKITRVDSQGCEVQLDAG-TRVSLPLG-GRHLSVGSAVTLGIRPEHLELAKP--- 293 M F+ ++ R D + + LD+G R LPLG G + LGIRPE + L Sbjct: 241 MNFIPVRLARQDGRLLAL-LDSGQARCELPLGEAADALEGREIILGIRPEQIALGAADGN 299 Query: 294 GDCALQVTADVSERLGSDTFCHVRTASGEALTMRVRGDLASRYGETLSLHLDAQHCHLFD 353 G A++ V+E G D V T + + R+ D+A R G+TL+L D LFD Sbjct: 300 GLPAIRAEVQVTEPTGPDLLVFV-TLNQTKVCCRLAPDVACRVGDTLNLQFDPARVLLFD 358 Query: 354 A 354 A Sbjct: 359 A 359 Lambda K H 0.320 0.137 0.389 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: 388 Number of extensions: 22 Number of successful extensions: 3 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: 367 Length of database: 384 Length adjustment: 30 Effective length of query: 337 Effective length of database: 354 Effective search space: 119298 Effective search space used: 119298 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