Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate WP_086510784.1 BZY95_RS15425 ABC transporter ATP-binding protein
Query= uniprot:Q6MNM2 (347 letters) >NCBI__GCF_002151265.1:WP_086510784.1 Length = 373 Score = 306 bits (783), Expect = 7e-88 Identities = 170/369 (46%), Positives = 229/369 (62%), Gaps = 29/369 (7%) Query: 1 MAKIQFSNIKKSFGSADVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGTI 60 MA ++ +N+ K FGS VLK + L I GEFL+LVGPSGCGKSTL+ +AGLE SG I Sbjct: 1 MAALEINNVCKDFGSEQVLKDVSLAIDSGEFLILVGPSGCGKSTLMNAIAGLEPVTSGEI 60 Query: 61 SIDGKKINDIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEISEL 120 I G+ + P RDIAMVFQSYALYP MTV +N+ FGL+++ + AE V +++L Sbjct: 61 RIAGESVTWQTPAERDIAMVFQSYALYPSMTVRQNISFGLEMRKVPKAEREAAVERVADL 120 Query: 121 LQIKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRLH 180 LQI HLL+RKP +LSGGQRQRVA+GRAL+R+ V LFDEPLSNLDA LR MR EIK+LH Sbjct: 121 LQIGHLLERKPSQLSGGQRQRVAMGRALAREPKVYLFDEPLSNLDAKLRVDMRTEIKKLH 180 Query: 181 HNSKSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSPEMN 240 +T++YVTHDQ+EA TL D IAV++DG I Q+G+P E+Y+ P + F+A F+GSP MN Sbjct: 181 QRLGTTIVYVTHDQIEAMTLADCIAVMRDGRILQLGSPDEVYNDPVDLFVAGFMGSPSMN 240 Query: 241 FLEGAVLE-----------------KIPWPEARKADQ---------ILGIRPDAFALNQG 274 F+ ++ ++PWP+ R+ ILG+RP+ F + Sbjct: 241 FISATLVGGSGAYRLRVETPGEETLELPWPQERETPALGEKVGERVILGLRPEHFTEDDA 300 Query: 275 PLG--TQEVALGDFQIDISENLGGQQMLHGTLAGNNVRILVDSMDNFSMKQTLPLKIDLT 332 LG + VAL +I + E G +L L V + L L+ID+ Sbjct: 301 RLGEYAEGVALTP-RITVVEPTGADILLQLKLGDGEATARVGPKCRVKAGERLTLRIDMG 359 Query: 333 KAHLFDKKT 341 +A +FD++T Sbjct: 360 RAVMFDRET 368 Lambda K H 0.318 0.136 0.383 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: 342 Number of extensions: 13 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: 347 Length of database: 373 Length adjustment: 29 Effective length of query: 318 Effective length of database: 344 Effective search space: 109392 Effective search space used: 109392 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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