Align spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized)
to candidate Pf1N1B4_3744 ABC transporter, ATP-binding protein
Query= CharProtDB::CH_024626 (378 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3744 Length = 329 Score = 265 bits (678), Expect = 1e-75 Identities = 136/279 (48%), Positives = 192/279 (68%), Gaps = 2/279 (0%) Query: 18 VQLAGIRKCFDGKEVIPQLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSGRIMLD 77 V + ++K + G V ++ I GEF+TLLGPSGCGK+T+LR IAGL +VD G+I+L+ Sbjct: 4 VSVQHLQKNYSGTTVFSDINCEIKKGEFVTLLGPSGCGKSTLLRCIAGLTSVDGGKILLE 63 Query: 78 NEDITHVPAENRYVNTVFQSYALFPHMTVFENVAFGLRMQKTPAAEITPRVMEALRMVQL 137 +D+ + + R + VFQSYALFP+MTV +NVAFGLRMQK A + RV E L++V+L Sbjct: 64 GQDLVPLSPQKRGIGMVFQSYALFPNMTVEQNVAFGLRMQKVNADDSQKRVAEVLQLVEL 123 Query: 138 ETFAQRKPHQLSGGQQQRVAIARAVVNKPRLLLLDESLSALDYKLRKQMQNELKALQRKL 197 FA R PHQLSGGQ QRVA+AR++V +PRLLLLDE LSALD ++RK ++ +++ +QR+L Sbjct: 124 NDFAARYPHQLSGGQCQRVALARSLVTRPRLLLLDEPLSALDARIRKHLREQIRQIQREL 183 Query: 198 GITFVFVTHDQEEALTMSDRIVVMRDGRIEQDGTPREIYEEPKNLFVAGFIGEINMFNAT 257 G+T +FVTHDQEEALTMSDRI +M G+I Q G +Y P ++F AGFIG N+ +A Sbjct: 184 GLTTIFVTHDQEEALTMSDRIFLMNQGKIVQSGDAETLYTAPVDVFAAGFIGNYNLLDAD 243 Query: 258 VIERLDEQRV--RANVEGRECNIYVNFAVEPGQKLHVLL 294 +L ++ + R + + +N ++ + H LL Sbjct: 244 SASKLLQRPITHRLAIRPEAIELSLNGELDAQIRSHSLL 282 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: 281 Number of extensions: 10 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: 378 Length of database: 329 Length adjustment: 29 Effective length of query: 349 Effective length of database: 300 Effective search space: 104700 Effective search space used: 104700 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: 49 (23.5 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