Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate WP_011653645.1 RL_RS21900 ABC transporter ATP-binding protein
Query= reanno::Smeli:SM_b21216 (360 letters) >NCBI__GCF_000009265.1:WP_011653645.1 Length = 371 Score = 358 bits (920), Expect = e-103 Identities = 198/366 (54%), Positives = 254/366 (69%), Gaps = 13/366 (3%) Query: 1 MSALEIRNIRKRYGEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDI 60 M+ LEI ++KR+G V+ LKGID+ LE G FLVL+G SGCGKSTLLN IAGL + GDI Sbjct: 1 MAFLEISGLKKRFGAVDILKGIDLELEKGGFLVLVGPSGCGKSTLLNTIAGLETITSGDI 60 Query: 61 LIGERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTARL 120 I R + G+HP RDIAMVFQSYALYPN++VA NI FG+E+R VP+ E +A+ + + Sbjct: 61 KIDGRDISGLHPSKRDIAMVFQSYALYPNMTVAGNIAFGMEIRGVPKEERARAIAQVSDM 120 Query: 121 LQIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRLH 180 LQI +LLDRKPSQLSGGQRQRVA+GRALVRNPQVFLFDEPLSNLDAKLR++MRTE+KRLH Sbjct: 121 LQIGHLLDRKPSQLSGGQRQRVAMGRALVRNPQVFLFDEPLSNLDAKLRVDMRTEIKRLH 180 Query: 181 QMLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPPMN 240 Q + TT VYVTHDQIEAMTLAT+IAV++DG ++Q P E+Y+ P+ ++VA F+GSP MN Sbjct: 181 QRMGTTFVYVTHDQIEAMTLATKIAVLKDGVLQQFGTPAEIYNSPSNIFVADFMGSPAMN 240 Query: 241 ILDA--EMTANGLKI-----EGCEEVLPLPAAFNG-AAWAGRRVKVGIRPEALRLAAGSE 292 +L+A E A GL++ LP+ + +G A+ G++V GIRPEAL G++ Sbjct: 241 LLNATVENGAGGLEVSLERPNAAPLRLPVISGNDGLTAYTGKQVIFGIRPEALTDPDGAD 300 Query: 293 --AQRLTAS---VEVVELTGPELVTTATVGSQRITACLPPRTAVGMGSAHAFTFDGTALH 347 A+ LT +EVVE G + +G + + A L T + G F+ Sbjct: 301 RKARSLTEGDCLIEVVEPAGSDTFAVTKLGGKSVVARLRADTGIAPGQNTRLAFNLDKAV 360 Query: 348 LFDPES 353 FDP S Sbjct: 361 FFDPNS 366 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: 372 Number of extensions: 14 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: 371 Length adjustment: 30 Effective length of query: 330 Effective length of database: 341 Effective search space: 112530 Effective search space used: 112530 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 24 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