Align MsiK protein, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized)
to candidate 350819 BT1291 spermidine/putrescine transport ATP-binding protein (NCBI ptt file)
Query= TCDB::P96483 (377 letters) >FitnessBrowser__Btheta:350819 Length = 463 Score = 226 bits (577), Expect = 8e-64 Identities = 120/294 (40%), Positives = 181/294 (61%), Gaps = 17/294 (5%) Query: 17 DKPAVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGAIRIGDRDVTHLPPKD 76 DK A+D + + ++ GEF+ ++GPSGCGK+T LR++AG + + G IRI +++T PP Sbjct: 21 DKTALDDVTLNVKKGEFVTILGPSGCGKTTLLRLIAGFQTASEGEIRISGKEITQTPPHK 80 Query: 77 RDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAAKILDLTQYLDRKPKAL 136 R + VFQ YAL+PH+ V DN+ F LK+ PK I +KV+ A K++ +T Y R +L Sbjct: 81 RPVNTVFQKYALFPHLNVYDNIAFGLKLKKTPKQTIGKKVKAALKMVGMTDYEYRDVDSL 140 Query: 137 SGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIASLQRRLGITTVYVTHDQ 196 SGGQ+QRVA+ RAIV EP+V L+DEPL+ LD K+R + ++ + + LGIT VYVTHDQ Sbjct: 141 SGGQQQRVAIARAIVNEPEVLLLDEPLAALDLKMRKDMQMELKEMHKSLGITFVYVTHDQ 200 Query: 197 VEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPAMNLVEVPITDGGVKFG 256 EA+T+ D + V+ +G +QQ+ +P ++Y++P N FVA FIG N++ G Sbjct: 201 EEALTLSDTIVVMSEGKIQQIGTPIDIYNEPINSFVADFIGE--SNIL------NGTMIH 252 Query: 257 NSVVPVNREALSAADKG---DRTVTVGVRPEHF------DVVELGGAVAASLSK 301 + +V D+G + V V +RPE ++ +L G V S+ K Sbjct: 253 DKLVRFCGTEFECVDEGFGENTPVDVVIRPEDLYIFPVSEMAQLTGVVQTSIFK 306 Lambda K H 0.317 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: 418 Number of extensions: 13 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: 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 (21.6 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