Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate RR42_RS18590 RR42_RS18590 hypothetical protein
Query= BRENDA::Q70HW1 (384 letters) >FitnessBrowser__Cup4G11:RR42_RS18590 Length = 359 Score = 356 bits (914), Expect = e-103 Identities = 198/370 (53%), Positives = 250/370 (67%), Gaps = 12/370 (3%) Query: 1 MARVLLEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEG 60 MA V + I K Y G T+ ++ ++DI D +FTV VGPSGCGK+T LRMIAGLE+IT G Sbjct: 1 MASVQIRGIQK-YFGSTQ-VIRGVDIDIADGQFTVLVGPSGCGKSTLLRMIAGLEEITTG 58 Query: 61 NLYIGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAA 120 + IG+R VN +PPK+RDIAMVFQNYALYPHMTVY NMAF LKL K K EI R+V +A+ Sbjct: 59 EIAIGNRVVNRLPPKERDIAMVFQNYALYPHMTVYDNMAFSLKLAKGDKEEIKRKVAKAS 118 Query: 121 KILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRK 180 IL + LL+R P+ LSGGQRQRVA+GRAIVR+PQVFL DEPLSNLDAKLRVQMRAEI++ Sbjct: 119 AILGLDSLLERYPRQLSGGQRQRVAMGRAIVRDPQVFLFDEPLSNLDAKLRVQMRAEIKE 178 Query: 181 LHQRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPA 240 LHQRL+TT +YVTHDQ EAMTM D+IVVMRDG ++Q P +Y P N+FVAGFIGSPA Sbjct: 179 LHQRLRTTSVYVTHDQIEAMTMADQIVVMRDGRVEQRGKPLALYDHPDNLFVAGFIGSPA 238 Query: 241 MNFIRGEIVQDGDAFYFRAPSISLRLP-EGRYGVLKASGAIGKPVVLGVRPEDLHDEEVF 299 MNF+ G + + G P RLP R+ +G G+ V+ GVRPE L Sbjct: 239 MNFVPGVLRRSGGDAAVEFPD-GTRLPAPARFDA--TAGTDGQRVIYGVRPEHL------ 289 Query: 300 MTTYPDSVLQMQVEVVEHMGSEVYLHTSIGPNTIVARVNPRHVYHVGSSVKLAIDLNKIH 359 P LQ +V VVE G+ +++ ++ RH + G + L D H Sbjct: 290 TLGMPGQGLQTRVSVVEPTGANTEIYSRFCEAEFISIFRERHDFAAGDILNLVPDHQHTH 349 Query: 360 IFDAETEESI 369 +FDA++ +++ Sbjct: 350 LFDADSGQTL 359 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: 441 Number of extensions: 21 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: 384 Length of database: 359 Length adjustment: 30 Effective length of query: 354 Effective length of database: 329 Effective search space: 116466 Effective search space used: 116466 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 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