Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate PP_1018 PP_1018 mannose/glucose ABC transporter - ATP binding subunit
Query= reanno::Smeli:SMc02869 (352 letters) >FitnessBrowser__Putida:PP_1018 Length = 384 Score = 293 bits (751), Expect = 4e-84 Identities = 156/322 (48%), Positives = 210/322 (65%), Gaps = 33/322 (10%) Query: 17 VGSLQLKTIRKAFGSH--EVLKGIDLDVKDGEFVIFVGPSGCGKSTLLRTIAGLEDATSG 74 + +L+L+ + K +GS + LK I L +KDGEF+I VGPSGCGKSTL+ IAGLE T G Sbjct: 1 MATLELRNVNKTYGSGLPDTLKDIQLSIKDGEFLILVGPSGCGKSTLMNCIAGLEQITGG 60 Query: 75 SVQIDGVEVGHVAPAKRGIAMVFQSYALYPHLTVKDNMGLGLKQAGVPKAEIEEKVAKAA 134 ++ ID +V ++P R IAMVFQSYALYP ++V++N+ GLK +P+A I+E+VA+ A Sbjct: 61 AILIDEQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKLPQAAIDEEVARVA 120 Query: 135 GMLSLEPYLARRPAELSGGQRQRVAIGRAIVREPKLFLFDEPLSNLDAALRVNTRLEIAR 194 +L +E LAR+PA+LSGGQ+QRVA+GRA+ R PK++LFDEPLSNLDA LRV R E+ Sbjct: 121 KLLQIEHLLARKPAQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 Query: 195 LHRSLKATMIYVTHDQVEAMTLADKIVVLNAGRIEQVGSPMELYNRPANLFVAGFIGSPQ 254 +H+ LK T +YVTHDQ+EAMTL DK+ V+ G I+Q G+P ++YN PAN FVA FIGSP Sbjct: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPQQIYNDPANQFVASFIGSPP 240 Query: 255 MNFI---------------------------EAAKLGDGEAKTIGIRPEHIGLSRESGDW 287 MNFI EAA +G +GIRPE I L G+ Sbjct: 241 MNFIPVRLARQDGRLLALLDSGQARCELPLGEAADALEGREIILGIRPEQIALGAADGNG 300 Query: 288 ----KGKVIHVEHLGADTIIYI 305 + +V E G D ++++ Sbjct: 301 LPAIRAEVQVTEPTGPDLLVFV 322 Lambda K H 0.320 0.137 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: 350 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: 352 Length of database: 384 Length adjustment: 30 Effective length of query: 322 Effective length of database: 354 Effective search space: 113988 Effective search space used: 113988 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