Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate Pf1N1B4_5115 Maltose/maltodextrin transport ATP-binding protein MalK (EC 3.6.3.19)
Query= BRENDA::Q70HW1 (384 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5115 Length = 381 Score = 316 bits (809), Expect = 8e-91 Identities = 171/365 (46%), Positives = 236/365 (64%), Gaps = 17/365 (4%) Query: 3 RVLLEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNL 62 ++ L+++ K G ++D +L+I EF VFVGPSGCGK+T LR+IAGL+ I G+L Sbjct: 3 KLKLDNVNKQLGGMR--ILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDL 60 Query: 63 YIGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAAKI 122 I RRVND+ P++R + MVFQ+YALYPHM+VY N++FGLKL K K + RV + A+I Sbjct: 61 LIDGRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQI 120 Query: 123 LDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRKLH 182 L + LL RKPK LSGGQRQRVA+GRA+ REP + L DEPLSNLDA LRVQMR EI +LH Sbjct: 121 LQLDKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLH 180 Query: 183 QRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPAMN 242 RL +T+IYVTHDQ EAMT+ D+IVV+ G ++Q +P+ +Y +P + FVAGF+GSP MN Sbjct: 181 DRLGSTMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRMN 240 Query: 243 FIRGEIVQDGDAFYFRAPSISLRLPEGRYGVLKASG--AIGKPVVLGVRPEDLHDEEVFM 300 F+ + G+ S+ L G + S A G P+ LG+RPE + + Sbjct: 241 FLSARLQTPGET------SLVDTLVWGITSLPFDSSNLAAGTPLSLGIRPEHVSLKAA-- 292 Query: 301 TTYPDSVLQMQVEVVEHMGSEVYLHTSIGPN-TIVARVNPRHVYHVGSSVKLAIDLNKIH 359 D + V VE++GSE Y+H G + ++ R + G V+L +DL+ +H Sbjct: 293 ----DGTAGVVVTAVEYLGSETYVHLETGQDEPLICRCEVSAGWQAGDRVELLLDLDNLH 348 Query: 360 IFDAE 364 +FDA+ Sbjct: 349 LFDAD 353 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: 411 Number of extensions: 21 Number of successful extensions: 4 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: 381 Length adjustment: 30 Effective length of query: 354 Effective length of database: 351 Effective search space: 124254 Effective search space used: 124254 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 Apr 09 2024. 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