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 CCNA_03235 CCNA_03235 spermidine/putrescine transport ATP-binding protein potA
Query= TCDB::P96483 (377 letters) >FitnessBrowser__Caulo:CCNA_03235 Length = 381 Score = 244 bits (623), Expect = 3e-69 Identities = 148/357 (41%), Positives = 210/357 (58%), Gaps = 23/357 (6%) Query: 4 VTFDKATRIYPGSDKPAVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGAIR 63 +TF+ T+ + AVD + + + +GEF L+GPSGCGK+T LRMLAG E G I Sbjct: 15 ITFENVTKRF--GKLAAVDNVSLTVNEGEFFALLGPSGCGKTTLLRMLAGFETPTEGRIL 72 Query: 64 IGDRDVTHLPPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAAKIL 123 I +D++++PP R + MVFQ+YA++PHMTVADN+ + LK+ VPKAE +V EA +++ Sbjct: 73 IDGQDISNVPPNKRPVNMVFQSYAVFPHMTVADNVAYGLKVDNVPKAEREARVAEALELV 132 Query: 124 DLTQYLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIASLQR 183 L RKP LSGGQRQRVA+ RA+V+ P+V L+DEPLS LDAKLR RT++ +LQ Sbjct: 133 QLGGLGGRKPDQLSGGQRQRVALARALVKRPRVLLLDEPLSALDAKLREQMRTELCTLQE 192 Query: 184 RLGITTVYVTHDQVEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPAMNL 243 ++GIT + VTHDQ EA+ + R AV+ GLLQQV +P ++Y+ P + FVA FIG +NL Sbjct: 193 KVGITFIMVTHDQDEALALASRCAVMSKGLLQQVATPSDLYEFPNSRFVADFIGQ--VNL 250 Query: 244 VEVPI-----TDGGVKFGNSVVPVNREALSAADKGDRTVTVGVRPEHFDVVELGGAVAAS 298 E + + +K + V + + +G TV +RPE ++ + + Sbjct: 251 FEGVLAVDEPSHAVIKSPDLPVDIFLDHGVTGPRGG-TVWAAIRPEKIELHKKADDTPPN 309 Query: 299 LSKDSADAPAGLAVSVNVVEELGADGYVYGTAEVGGEVKDLVVRVNGRQVPEKGSTL 355 L DAP G N VE G + A +GG V GR+V + S L Sbjct: 310 L----GDAPKG----TNAVE-----GVIKHEAYLGGSSTYEVEIAGGRRVKVQRSNL 353 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: 387 Number of extensions: 17 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: 381 Length adjustment: 30 Effective length of query: 347 Effective length of database: 351 Effective search space: 121797 Effective search space used: 121797 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 Sep 17 2021. 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