Align ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized)
to candidate WP_086510784.1 BZY95_RS15425 ABC transporter ATP-binding protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_3039 (367 letters) >NCBI__GCF_002151265.1:WP_086510784.1 Length = 373 Score = 311 bits (797), Expect = 2e-89 Identities = 173/370 (46%), Positives = 238/370 (64%), Gaps = 18/370 (4%) Query: 1 MANLKIKNLQKGFEGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSGGTI 60 MA L+I N+ K F ++K + L ++ EF++ VGPSGCGKSTL+ IAGLE V+ G I Sbjct: 1 MAALEINNVCKDFGSEQVLKDVSLAIDSGEFLILVGPSGCGKSTLMNAIAGLEPVTSGEI 60 Query: 61 ELDGRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVAKAEVEKKVSEAARI 120 + G +T +PA+RD+AMVFQ+YALYP M+VR+N+SF L++ V KAE E V A + Sbjct: 61 RIAGESVTWQTPAERDIAMVFQSYALYPSMTVRQNISFGLEMRKVPKAEREAAVERVADL 120 Query: 121 LELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELLRLH 180 L++G +LERKP QLSGGQRQRVA+GRA+ R PK++LFDEPLSNLDA LRV MR E+ +LH Sbjct: 121 LQIGHLLERKPSQLSGGQRQRVAMGRALAREPKVYLFDEPLSNLDAKLRVDMRTEIKKLH 180 Query: 181 KELQATMIYVTHDQVEAMTMADKVVVLNGGKIEQVGSPLDLYHQPANLFVAGFLGTPKMG 240 + L T++YVTHDQ+EAMT+AD + V+ G+I Q+GSP ++Y+ P +LFVAGF+G+P M Sbjct: 181 QRLGTTIVYVTHDQIEAMTLADCIAVMRDGRILQLGSPDEVYNDPVDLFVAGFMGSPSMN 240 Query: 241 FLKGKIT--------RVDSQGCE-VQLDAGTRVSLPLGGRHLSVGSAVTLGIRPEHL--E 289 F+ + RV++ G E ++L P G VG V LG+RPEH + Sbjct: 241 FISATLVGGSGAYRLRVETPGEETLELPWPQERETPALGE--KVGERVILGLRPEHFTED 298 Query: 290 LAKPGD----CALQVTADVSERLGSDTFCHVRTASGEALTMRVRGDLASRYGETLSLHLD 345 A+ G+ AL V E G+D ++ GEA T RV + GE L+L +D Sbjct: 299 DARLGEYAEGVALTPRITVVEPTGADILLQLKLGDGEA-TARVGPKCRVKAGERLTLRID 357 Query: 346 AQHCHLFDAD 355 +FD + Sbjct: 358 MGRAVMFDRE 367 Lambda K H 0.320 0.137 0.389 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: 17 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: 367 Length of database: 373 Length adjustment: 30 Effective length of query: 337 Effective length of database: 343 Effective search space: 115591 Effective search space used: 115591 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