Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate Ac3H11_2941 Various polyols ABC transporter, ATP-binding component
Query= reanno::Smeli:SM_b21216 (360 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2941 Length = 350 Score = 289 bits (740), Expect = 7e-83 Identities = 156/351 (44%), Positives = 223/351 (63%), Gaps = 13/351 (3%) Query: 1 MSALEIRNIRKRYGEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDI 60 M+ L++R I K +GE +KGID+ ++ GEF+V +G SGCGKSTLL +IAGL GG + Sbjct: 1 MAYLQLRGIEKFFGEHRAIKGIDLTIQQGEFIVFVGPSGCGKSTLLRLIAGLEAIDGGSL 60 Query: 61 LIGERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTARL 120 ++ R + RD+AMVFQSYALYP++SV N+ F L++ +V + D+ V++ AR+ Sbjct: 61 MLDGRDITDQPSSKRDLAMVFQSYALYPHMSVYENMSFALKLAKVDKQVIDEKVQNAARI 120 Query: 121 LQIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRLH 180 L + L R P +LSGGQRQRVAIGRA+VR P+VFLFDEPLSNLDA LR + R E+ +LH Sbjct: 121 LNLTQYLQRTPKELSGGQRQRVAIGRAIVRAPKVFLFDEPLSNLDAALRGQTRVEIAKLH 180 Query: 181 QMLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPPMN 240 + L T +YVTHDQ+EAMTLA R+ V+RDG IEQ+ P E+YD+PA +VA F+G+P MN Sbjct: 181 RDLGATTIYVTHDQVEAMTLADRVVVLRDGIIEQVGTPLELYDKPANQFVAQFIGTPQMN 240 Query: 241 ILDAEMTANGLKIEGCEEVLPLPAAFNGAAWAGRRVKVGIRPEALRLAAGSEAQRLTASV 300 ++ + ++ + PAA GAA +G+RPE + + + A + V Sbjct: 241 VVPVDKLPQPVQQQA-------PAAPAGAAVGA----IGLRPENITVRT-TGATPVGGQV 288 Query: 301 EVVELTGPE-LVTTATVGSQRITACLPPRTAVGMGSAHAFTFDGTALHLFD 350 +++E G E L+ T G + + RT + +G A + D + H FD Sbjct: 289 DLIEALGAETLIYVTTPGGAQFVSRQNDRTDLRVGDAVSLDIDASQAHWFD 339 Lambda K H 0.320 0.136 0.385 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: 324 Number of extensions: 6 Number of successful extensions: 1 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: 360 Length of database: 350 Length adjustment: 29 Effective length of query: 331 Effective length of database: 321 Effective search space: 106251 Effective search space used: 106251 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