Align Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale)
to candidate 200449 SO1271 polyamine ABC transporter, ATP-binding protein (NCBI ptt file)
Query= uniprot:P40735 (281 letters) >FitnessBrowser__MR1:200449 Length = 378 Score = 132 bits (332), Expect = 1e-35 Identities = 85/211 (40%), Positives = 129/211 (61%), Gaps = 6/211 (2%) Query: 23 RALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPESGDIEVAGIQLTEESVWEVR 82 RA+D VSL + +GE A++G +GSGKSTL R L G P SG I + G +T+ +E Sbjct: 34 RAVDDVSLTINKGEIFALLGGSGSGKSTLLRMLAGFERPTSGRIYLDGEDITDLPPYE-- 91 Query: 83 KKIGMVFQNPDNQFVGTTVRDDVAFGLENNGVPREEMIERVDWAVKQVNMQDFLDQEPHH 142 + I M+FQ+ F TV ++AFGL+ + +P+ E+ +RV +K V+M+ + ++PH Sbjct: 92 RPINMMFQSYA-LFPHMTVAQNIAFGLKQDKLPKAEIEQRVQEMLKLVHMEQYGKRKPHQ 150 Query: 143 LSGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGREEV-LETVRHLKEQGMATVISITH 201 LSGGQ+QRVA+A +A RP +++LDE LD R ++ LE V L+ G+ T + +TH Sbjct: 151 LSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRTQMQLEVVEILERVGV-TCVMVTH 209 Query: 202 DLNEA-AKADRIIVMNGGKKYAEGPPEEIFK 231 D EA A RI +M+ G G P +I++ Sbjct: 210 DQEEAMTMAGRISIMSDGWIAQTGSPMDIYE 240 Lambda K H 0.316 0.135 0.383 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: 246 Number of extensions: 10 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: 281 Length of database: 378 Length adjustment: 28 Effective length of query: 253 Effective length of database: 350 Effective search space: 88550 Effective search space used: 88550 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: 48 (23.1 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