Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate HSERO_RS18940 HSERO_RS18940 sn-glycerol-3-phosphate ABC transporter ATP-binding protein
Query= BRENDA::Q8NMV1 (376 letters) >FitnessBrowser__HerbieS:HSERO_RS18940 Length = 364 Score = 304 bits (778), Expect = 3e-87 Identities = 177/386 (45%), Positives = 229/386 (59%), Gaps = 34/386 (8%) Query: 1 MATVTFKDASLSYPGAKEPT--VKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVT 58 MA + K +Y + + + EIADGEF+V+VGPSGCGKST LRM+AGLE ++ Sbjct: 1 MAAIHLKQVRKTYGAGTKAVDVIHGIDAEIADGEFIVMVGPSGCGKSTLLRMVAGLEEIS 60 Query: 59 DGAIFIGDKDVTHVAPRDRDIAMVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDE 118 G I IGD+ V + P++RDIAMVFQNYALYPHMTV +NM + LKI G S+ EI+ RV Sbjct: 61 SGQIVIGDRVVNDLEPKERDIAMVFQNYALYPHMTVYQNMAYGLKIQGLSKSEIDARVQR 120 Query: 119 AAATLGLTEFLERKPKALSGGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQI 178 AAA L L LER P+ LSGGQRQRVAMGRAIVR P VFL DEPLSNLDAKLRVQ R +I Sbjct: 121 AAAILELGALLERTPRQLSGGQRQRVAMGRAIVRKPAVFLFDEPLSNLDAKLRVQMRLEI 180 Query: 179 AALQRKLGVTTVYVTHDQTEALTMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGS 238 L L T++YVTHDQ EA+T+G R+ V+ G +Q+G P E+Y RPA FVA FIGS Sbjct: 181 QKLHASLRTTSLYVTHDQVEAMTLGQRMIVMNRGVAEQIGTPAEVYARPATTFVASFIGS 240 Query: 239 PAMNL---------GTFSVKDGDATSGHARIKLSPETLAAMTPEDNGRITIGFRPEALEI 289 P MNL +F V G+A+ I P+ L ++ +G RPE L Sbjct: 241 PPMNLLQGKLSADGASFEVSKGNASD----ILRLPQPLTGAAGQER---ILGVRPEHLLP 293 Query: 290 IPEGESTDLSIPIKLDFVEELGSDSFLYGKLVGEGDLGSSSEDVPESGQIVVRAAPNAAP 349 I +G + LS+ ++L VE LG++ ++ + G+ +V+R N Sbjct: 294 ILDGSAAQLSLEVEL--VEALGAELLVHARCGGQA--------------LVLRCPANVQV 337 Query: 350 APGSVFHARIVEGGQHNFSASTGKRL 375 G A G H F + +R+ Sbjct: 338 RTGQRIGASFGAGDVHWFDVKSTRRI 363 Lambda K H 0.316 0.135 0.380 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: 350 Number of extensions: 10 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: 376 Length of database: 364 Length adjustment: 30 Effective length of query: 346 Effective length of database: 334 Effective search space: 115564 Effective search space used: 115564 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 (21.6 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