Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate 350819 BT1291 spermidine/putrescine transport ATP-binding protein (NCBI ptt file)
Query= BRENDA::Q70HW1 (384 letters) >FitnessBrowser__Btheta:350819 Length = 463 Score = 236 bits (603), Expect = 7e-67 Identities = 137/360 (38%), Positives = 202/360 (56%), Gaps = 22/360 (6%) Query: 6 LEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNLYIG 65 + H+ K + +T + D L+++ EF +GPSGCGKTT LR+IAG + +EG + I Sbjct: 12 VSHVSKFFGDKT--ALDDVTLNVKKGEFVTILGPSGCGKTTLLRLIAGFQTASEGEIRIS 69 Query: 66 DRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAAKILDI 125 + + PP R + VFQ YAL+PH+ VY N+AFGLKL+K PK I ++V+ A K++ + Sbjct: 70 GKEITQTPPHKRPVNTVFQKYALFPHLNVYDNIAFGLKLKKTPKQTIGKKVKAALKMVGM 129 Query: 126 AHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRKLHQRL 185 R +LSGGQ+QRVA+ RAIV EP+V L+DEPL+ LD K+R M+ E++++H+ L Sbjct: 130 TDYEYRDVDSLSGGQQQRVAIARAIVNEPEVLLLDEPLAALDLKMRKDMQMELKEMHKSL 189 Query: 186 QTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPAMNFIR 245 T +YVTHDQ EA+T+ D IVVM +G IQQ TP +Y++P N FVA FIG N + Sbjct: 190 GITFVYVTHDQEEALTLSDTIVVMSEGKIQQIGTPIDIYNEPINSFVADFIGE--SNILN 247 Query: 246 GEIVQDGDAFYFRAPSISLRLPEGRYGVLKASGAIGKPVVLGVRPEDLHDEEVFMTTYPD 305 G ++ D +R + + PV + +RPEDL+ +P Sbjct: 248 GTMIHDK----------LVRFCGTEFECVDEGFGENTPVDVVIRPEDLY-------IFPV 290 Query: 306 SVLQMQVEVVE-HMGSEVYLHTSIGPNTIVARVNPRHVYHVGSSVKLAIDLNKIHIFDAE 364 S + VV+ + V+ ++ V H + VG+ V L + IHI E Sbjct: 291 SEMAQLTGVVQTSIFKGVHYEMTVLCGGYEFLVQDYHHFEVGAEVGLLVKPFDIHIMKKE 350 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: 433 Number of extensions: 21 Number of successful extensions: 1 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: 463 Length adjustment: 32 Effective length of query: 352 Effective length of database: 431 Effective search space: 151712 Effective search space used: 151712 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