Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate HSERO_RS02210 HSERO_RS02210 sugar ABC transporter ATP-binding protein
Query= BRENDA::Q70HW1 (384 letters) >FitnessBrowser__HerbieS:HSERO_RS02210 Length = 372 Score = 344 bits (882), Expect = 3e-99 Identities = 194/384 (50%), Positives = 249/384 (64%), Gaps = 19/384 (4%) Query: 1 MARVLLEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEG 60 MA V + ++ K Y ++D NL+I+D EF VFVGPSGCGK+T LRMIAGLE+I++G Sbjct: 1 MAAVSIRNLAKRY--DDNEVMRDINLEIEDGEFVVFVGPSGCGKSTLLRMIAGLEEISDG 58 Query: 61 NLYIGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAA 120 +L IG RR+N+VP R +AMVFQ+YALYPHM++Y NMAFGLK+ KAEID VQ AA Sbjct: 59 DLDIGARRMNEVPASKRGVAMVFQSYALYPHMSLYDNMAFGLKIAGKSKAEIDAAVQHAA 118 Query: 121 KILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRK 180 KIL I HLLDRKP+ALSGGQRQRVA+GRAI R+P VFL DEPLSNLDA LRV+MR E K Sbjct: 119 KILHIDHLLDRKPRALSGGQRQRVAIGRAITRQPSVFLFDEPLSNLDAALRVKMRLEFAK 178 Query: 181 LHQRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPA 240 LH L+TT+IYVTHDQ EAMT+ D+IVV+ +G I+Q +PQ +Y P N FVAGFIGSP Sbjct: 179 LHDDLKTTMIYVTHDQIEAMTLADKIVVLSEGRIEQVGSPQQLYHHPANRFVAGFIGSPK 238 Query: 241 MNFIRGEIVQDGDAFYFRAPSISLRLPEGRYGVLKASGA---IGKPVVLGVRPEDLHDEE 297 MNFI DG +A + ++LP G G+ +G+ V LGVRPE L+ Sbjct: 239 MNFI------DGTVAAIQADGVQVQLPGGGLQWAAVDGSTLQVGQKVTLGVRPEHLN--- 289 Query: 298 VFMTTYPDSVLQMQVEVVEHMGSEVYLHTSI--GPNTIVARVNPRHVYHVGSSVKLAIDL 355 + LQ + +E +G YL+ + + ++ RV GS + LA D Sbjct: 290 ---IAQGQAALQARCTALELLGDFSYLYAAYEGSEDALILRVPDSLDAPHGSVLPLAADP 346 Query: 356 NKIHIFDAETEESIGFAAGPAGER 379 + H+F A+ + A+ A R Sbjct: 347 ARCHLFGADGQALPRLASSVAAPR 370 Lambda K H 0.321 0.138 0.395 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: 402 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: 384 Length of database: 372 Length adjustment: 30 Effective length of query: 354 Effective length of database: 342 Effective search space: 121068 Effective search space used: 121068 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: 50 (23.9 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