Align GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate Pf1N1B4_5115 Maltose/maltodextrin transport ATP-binding protein MalK (EC 3.6.3.19)
Query= TCDB::G3LHY9 (356 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5115 Length = 381 Score = 199 bits (507), Expect = 8e-56 Identities = 115/308 (37%), Positives = 184/308 (59%), Gaps = 16/308 (5%) Query: 25 LKEVDHEWNDGGAYALLGPSGCGKTTLLNIISGLLQPSHGRILFDGKDVTNLSTQSRNIA 84 L++V E G +GPSGCGK+TLL +I+GL G +L DG+ V +L + R + Sbjct: 19 LRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDLLIDGRRVNDLEPRERGVG 78 Query: 85 QVFQFPVIYDTMTVYDNLAFPLRNRGVAEADVDRRVRDILEMIDLASWARRKAQGLTADQ 144 VFQ +Y M+VYDN++F L+ + + RV +++ L +RK + L+ Q Sbjct: 79 MVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQILQLDKLLQRKPKELSGGQ 138 Query: 145 KQKISLGRGLVRNDVNAILFDEPLTVIDPHMKWVLRSQLKRLHKQFGFTMVYVTHDQTEA 204 +Q++++GR + R + + +LFDEPL+ +D ++ +R+++ RLH + G TM+YVTHDQ EA Sbjct: 139 RQRVAMGRAMAR-EPDILLFDEPLSNLDASLRVQMRNEIARLHDRLGSTMIYVTHDQVEA 197 Query: 205 LTFAEKVVVMYDGQIVQIGTPAELFERPSHTFVGYFIGSPGMNFMPARIE--GSTVKV-- 260 +T A+K+VV+ G++ Q+G+P EL+ERP+ FV F+GSP MNF+ AR++ G T V Sbjct: 198 MTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRMNFLSARLQTPGETSLVDT 257 Query: 261 ---GDETLTLEYAPKTSGTAKTELGIRPEFIRL----GREGMPITISKVEDIGRQKIVRA 313 G +L + + +GT LGIRPE + L G G + ++ VE +G + V Sbjct: 258 LVWGITSLPFDSSNLAAGT-PLSLGIRPEHVSLKAADGTAG--VVVTAVEYLGSETYVHL 314 Query: 314 RFA-DQPI 320 D+P+ Sbjct: 315 ETGQDEPL 322 Lambda K H 0.321 0.137 0.405 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: 323 Number of extensions: 14 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: 356 Length of database: 381 Length adjustment: 30 Effective length of query: 326 Effective length of database: 351 Effective search space: 114426 Effective search space used: 114426 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 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