Align spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized)
to candidate Synpcc7942_1490 Synpcc7942_1490 nitrate transport ATP-binding subunits C and D
Query= CharProtDB::CH_024626 (378 letters) >FitnessBrowser__SynE:Synpcc7942_1490 Length = 663 Score = 153 bits (387), Expect = 1e-41 Identities = 94/218 (43%), Positives = 133/218 (61%), Gaps = 10/218 (4%) Query: 14 LSPLVQLAGIRKCFD---GKE--VIPQLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLET 68 +S V + I K F G E + +DL I GEF++L+G SGCGK+T+L LIAGLE Sbjct: 1 MSLFVAVENIEKSFPLSGGNEYLALKGIDLEIKQGEFISLIGHSGCGKSTLLNLIAGLEL 60 Query: 69 VDSGRIMLDNEDITHVPAENRYVNTVFQSYALFPHMTVFENVAFGLR--MQKTPAAEITP 126 G + L+ + IT P +R V VFQ+Y+LFP +TV EN+A + ++ P E Sbjct: 61 PTDGAVSLEGQQIT-APGPDRMV--VFQNYSLFPWLTVRENIALAVDEVLRDLPKEERQA 117 Query: 127 RVMEALRMVQLETFAQRKPHQLSGGQQQRVAIARAVVNKPRLLLLDESLSALDYKLRKQM 186 V E +++V L A + P QLSGG +QRVAIAR + +P+LLLLDE ALD R + Sbjct: 118 IVEEHIQLVGLGHAADKPPAQLSGGMKQRVAIARGLATRPKLLLLDEPFGALDALTRGNL 177 Query: 187 QNELKALQRKLGITFVFVTHDQEEALTMSDRIVVMRDG 224 Q +L + + +T V VTHD +EA+ +SDRIV++ +G Sbjct: 178 QEKLMQICEENHVTAVMVTHDVDEAVLLSDRIVMLTNG 215 Lambda K H 0.319 0.136 0.385 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: 504 Number of extensions: 22 Number of successful extensions: 3 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: 378 Length of database: 663 Length adjustment: 34 Effective length of query: 344 Effective length of database: 629 Effective search space: 216376 Effective search space used: 216376 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 (21.7 bits) S2: 52 (24.6 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