Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate GFF3011 HP15_2955 ATP-binding component of ABC transporter
Query= BRENDA::Q70HW1 (384 letters) >FitnessBrowser__Marino:GFF3011 Length = 372 Score = 344 bits (883), Expect = 2e-99 Identities = 178/377 (47%), Positives = 253/377 (67%), Gaps = 16/377 (4%) Query: 1 MARVLLEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEG 60 M+++ L I KTYPG E T+K ++DI EF + VGPSGCGK+T + IAGLE IT+G Sbjct: 1 MSQLELRSIRKTYPGVAEETLKGIDIDIASGEFLILVGPSGCGKSTLMNTIAGLETITDG 60 Query: 61 NLYIGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAA 120 ++ + + ++ + PKDRDIAMVFQ+YALYP M+V +N+AFGLK+R +PK EID+ V+ A Sbjct: 61 SIVLDGKDISTMEPKDRDIAMVFQSYALYPTMSVRENIAFGLKIRGLPKHEIDQEVERVA 120 Query: 121 KILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRK 180 +L I+ L+++KP LSGGQ+QRVA+GRA+ R P+++L DEPLSNLDAKLRV+MR EI+K Sbjct: 121 DLLQISPLMNKKPANLSGGQQQRVAMGRALARRPRIYLFDEPLSNLDAKLRVEMRTEIKK 180 Query: 181 LHQRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPA 240 LHQRL+TT++YVTHDQ EAMT+ DRI V++DG +QQ TP+ VY +P+N+FVAGF+GSPA Sbjct: 181 LHQRLKTTIVYVTHDQIEAMTLADRIAVLKDGELQQLGTPKEVYDRPENLFVAGFMGSPA 240 Query: 241 MNFI-----RGEIVQDGDAFYFRAPSISLRLPEGRYGVLKASGAIGKPVVLGVRPEDL-- 293 M+F+ +GE + S+ L +PE + +GK V+LG+RPE + Sbjct: 241 MSFVPVTVEQGEGGLQAEVRGNDGRSVKLPVPE------FLADRVGKKVILGIRPEHITQ 294 Query: 294 -HDEEVFMTTYPDSVLQMQVEVVEHMGSEVYLHTSIGPNTIVARVNPRHVYHVGSSVKLA 352 D++ T + +EV E G +V + + R++P H G + +L Sbjct: 295 PQDQKNDQTLVAKG--EFTIEVTEPTGPDVIALIQLNDTNVHCRIDPEHPVTWGETAELM 352 Query: 353 IDLNKIHIFDAETEESI 369 D+ K+ FD ETE+ I Sbjct: 353 FDMKKVVFFDPETEKRI 369 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: 420 Number of extensions: 15 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: 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