Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate AO356_28585 AO356_28585 ABC transporter
Query= BRENDA::Q70HW1 (384 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_28585 Length = 379 Score = 308 bits (790), Expect = 1e-88 Identities = 164/344 (47%), Positives = 224/344 (65%), Gaps = 13/344 (3%) Query: 21 VKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNLYIGDRRVNDVPPKDRDIA 80 ++D +L+I EF VFVGPSGCGK+T LR+IAGL+ I G+L I RRVND+ P++R + Sbjct: 19 LRDVSLEISAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDLLIDGRRVNDLEPRERGVG 78 Query: 81 MVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAAKILDIAHLLDRKPKALSGGQ 140 MVFQ+YALYPHM+VY N++FGLKL K K + RV + A+IL + LL RKP+ LSGGQ Sbjct: 79 MVFQSYALYPHMSVYDNISFGLKLAKTEKTSLRERVLKTAQILQLDKLLQRKPRELSGGQ 138 Query: 141 RQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRKLHQRLQTTVIYVTHDQTEAM 200 RQRVA+GRA+ REP + L DEPLSNLDA LRVQMR EI +LH RL +T+IYVTHDQ EAM Sbjct: 139 RQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLHGRLGSTMIYVTHDQVEAM 198 Query: 201 TMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPAMNFIRGEIVQDGDAFYFRAP 260 T+ D+IVV+ G I+Q +P+ +Y +P + FVAGF+GSP MNF+ + G+ + Sbjct: 199 TLADKIVVLNGGRIEQVGSPRELYERPASRFVAGFLGSPRMNFLAAFLHTPGETSQVESL 258 Query: 261 SISL-RLPEGRYGVLKASGAIGKPVVLGVRPEDLHDEEVFMTTYPDSVLQMQVEVVEHMG 319 + + LP G+ A + LG+RPE + + V VE++G Sbjct: 259 VLGMTSLPFDSSGL-----AANTQLSLGIRPEHI------ALKAAQGTAGIAVSGVEYLG 307 Query: 320 SEVYLHTSIG-PNTIVARVNPRHVYHVGSSVKLAIDLNKIHIFD 362 SE Y+H G + +V R + VG V+L +D++ +H+FD Sbjct: 308 SETYVHLDTGQDDPMVCRCEVNAGWRVGDRVELQLDIDNLHVFD 351 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: 391 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: 379 Length adjustment: 30 Effective length of query: 354 Effective length of database: 349 Effective search space: 123546 Effective search space used: 123546 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