Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate SMc04393 SMc04393 ABC transporter ATP-binding protein
Query= reanno::Smeli:SM_b21216 (360 letters) >FitnessBrowser__Smeli:SMc04393 Length = 370 Score = 369 bits (948), Expect = e-107 Identities = 199/369 (53%), Positives = 254/369 (68%), Gaps = 12/369 (3%) Query: 1 MSALEIRNIRKRYGEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDI 60 MS L+I N+RK YG +E LK I++ +E G FLVL+G SGCGKSTLLN IAGL + GDI Sbjct: 1 MSFLKITNLRKSYGALEILKDINLEIEEGGFLVLVGPSGCGKSTLLNTIAGLEPITSGDI 60 Query: 61 LIGERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTARL 120 I RSV G+HP RDIAMVFQSYALYPN++VA NI FG+E+R VP+ E +KA++ A + Sbjct: 61 AINGRSVSGLHPSKRDIAMVFQSYALYPNMTVAGNIAFGMEIRGVPKEEREKAIKQVADM 120 Query: 121 LQIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRLH 180 LQI +LLDRKPSQLSGGQRQRVA+GRALVRNPQVFLFDEPLSNLDAKLR++MRTE+KRLH Sbjct: 121 LQIGHLLDRKPSQLSGGQRQRVAMGRALVRNPQVFLFDEPLSNLDAKLRVDMRTEIKRLH 180 Query: 181 QMLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPPMN 240 ++TT+VYVTHDQIEAMTLAT+IAV++DG ++Q P E+Y+ PA ++VA F+GSP MN Sbjct: 181 HRMKTTIVYVTHDQIEAMTLATKIAVLKDGVLQQFGTPAEIYNNPANMFVADFMGSPAMN 240 Query: 241 ILDAEMTANGLKIEGC-----EEVLPLPAAFNGA--AWAGRRVKVGIRPEALRLAAGSEA 293 +L A++ G ++ E L L NGA A+AG+ V GIRPEAL G++ Sbjct: 241 LLKAQIETAGSQVSVTLARPNAEPLRLAVPHNGALSAYAGKEVVFGIRPEALTDPDGADR 300 Query: 294 QRLTAS-----VEVVELTGPELVTTATVGSQRITACLPPRTAVGMGSAHAFTFDGTALHL 348 + +EVVE G + +G + I A L + G F+ Sbjct: 301 NAQFVAEGECLIEVVEPAGSDTFAVTRLGGKEIVARLRADARIAPGQTSRLAFNLDKAVF 360 Query: 349 FDPESGRSL 357 FDP+S + + Sbjct: 361 FDPQSEKRI 369 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: 386 Number of extensions: 9 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: 360 Length of database: 370 Length adjustment: 30 Effective length of query: 330 Effective length of database: 340 Effective search space: 112200 Effective search space used: 112200 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