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 CCNA_03235 CCNA_03235 spermidine/putrescine transport ATP-binding protein potA
Query= TCDB::Q8DT25 (377 letters) >FitnessBrowser__Caulo:CCNA_03235 Length = 381 Score = 220 bits (561), Expect = 4e-62 Identities = 133/316 (42%), Positives = 185/316 (58%), Gaps = 18/316 (5%) Query: 1 MTTLK----LDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLED 56 MTT K +N+ KR+ K +V+N +L +++ EF +GPSGCGK+T LRM+AG E Sbjct: 8 MTTPKPIITFENVTKRF--GKLAAVDNVSLTVNEGEFFALLGPSGCGKTTLLRMLAGFET 65 Query: 57 ITEGNLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRV 116 TEG + ID + +++ P R + MVFQ+YA++PHM+V +N+A+GLK+ K + RV Sbjct: 66 PTEGRILIDGQDISNVPPNKRPVNMVFQSYAVFPHMTVADNVAYGLKVDNVPKAEREARV 125 Query: 117 HEAAEILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRA 176 EA E++ L RKP LSGGQRQRVA+ RA+V+ +V L+DEPLS LDAKLR MR Sbjct: 126 AEALELVQLGGLGGRKPDQLSGGQRQRVALARALVKRPRVLLLDEPLSALDAKLREQMRT 185 Query: 177 EIAKIHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNE 236 E+ + ++G T I VTHDQ EA+ LA R +MS G ++Q+ TP +LY Sbjct: 186 ELCTLQEKVGITFIMVTHDQDEALALASRCAVMSK----------GLLQQVATPSDLYEF 235 Query: 237 PANKFVAGFIGSPAMNFFEVTVEKERLVNQDGLSLALPQGQEKILEEKGYLGKKVTLGIR 296 P ++FVA FIG +N FE + + + S LP G G V IR Sbjct: 236 PNSRFVADFIGQ--VNLFEGVLAVDEPSHAVIKSPDLPVDIFLDHGVTGPRGGTVWAAIR 293 Query: 297 PEDISSDQIVHETFPN 312 PE I + +T PN Sbjct: 294 PEKIELHKKADDTPPN 309 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: 343 Number of extensions: 14 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: 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 (21.7 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