Align MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized)
to candidate 350819 BT1291 spermidine/putrescine transport ATP-binding protein (NCBI ptt file)
Query= TCDB::Q8DT25 (377 letters) >FitnessBrowser__Btheta:350819 Length = 463 Score = 227 bits (579), Expect = 4e-64 Identities = 129/321 (40%), Positives = 190/321 (59%), Gaps = 23/321 (7%) Query: 20 SVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEGNLYIDDKLMNDASPKDRDI 79 ++++ L++ EF+ +GPSGCGK+T LR+IAG + +EG + I K + P R + Sbjct: 24 ALDDVTLNVKKGEFVTILGPSGCGKTTLLRLIAGFQTASEGEIRISGKEITQTPPHKRPV 83 Query: 80 AMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAAEILGLTEFLERKPADLSGG 139 VFQ YAL+PH++VY+N+AFGLKL+K K I K+V A +++G+T++ R LSGG Sbjct: 84 NTVFQKYALFPHLNVYDNIAFGLKLKKTPKQTIGKKVKAALKMVGMTDYEYRDVDSLSGG 143 Query: 140 QRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAKIHRRIGATTIYVTHDQTEA 199 Q+QRVA+ RAIV + +V L+DEPL+ LD K+R M+ E+ ++H+ +G T +YVTHDQ EA Sbjct: 144 QQQRVAIARAIVNEPEVLLLDEPLAALDLKMRKDMQMELKEMHKSLGITFVYVTHDQEEA 203 Query: 200 MTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANKFVAGFIGSPAMNFFEVTVE 259 +TL+D IV+MS G+I+QIGTP ++YNEP N FVA FIG N T+ Sbjct: 204 LTLSDTIVVMSE----------GKIQQIGTPIDIYNEPINSFVADFIGE--SNILNGTMI 251 Query: 260 KERLVNQDGLSLALPQGQEKILEEKGYLGKKVTLGIRPEDISSDQIVHETFPNASVTADI 319 ++LV G + ++E V + IRPED+ + A +T + Sbjct: 252 HDKLVRFCGTEF-------ECVDEGFGENTPVDVVIRPEDL----YIFPVSEMAQLTGVV 300 Query: 320 LVSELLGSESMLYVKFGSTEF 340 S G + V G EF Sbjct: 301 QTSIFKGVHYEMTVLCGGYEF 321 Lambda K H 0.318 0.135 0.379 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: 433 Number of extensions: 18 Number of successful extensions: 2 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: 377 Length of database: 463 Length adjustment: 32 Effective length of query: 345 Effective length of database: 431 Effective search space: 148695 Effective search space used: 148695 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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