Align Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale)
to candidate GFF4127 HP15_4067 spermidine/putrescine ABC transporter ATPase subunit
Query= uniprot:P40735 (281 letters) >FitnessBrowser__Marino:GFF4127 Length = 362 Score = 134 bits (336), Expect = 4e-36 Identities = 82/223 (36%), Positives = 131/223 (58%), Gaps = 7/223 (3%) Query: 10 EDIVFRYRKDAERRALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPESGDIEVA 69 E +V R+ +A A+D VSL V G + +I+G +G GK+TL R L G P+ GDI + Sbjct: 8 EGLVRRFGSNA---AVDHVSLDVPAGTFFSILGPSGCGKTTLLRLLAGFDKPDQGDIHIR 64 Query: 70 GIQLTEESVWEVRKKIGMVFQNPDNQFVGTTVRDDVAFGLENNGVPREEMIERVDWAVKQ 129 G ++ + V R+ + MVFQ+ F TV D++A+GL+ +P E +R+ ++Q Sbjct: 65 GERMND--VPPNRRPVNMVFQHLA-LFPTMTVGDNIAYGLKRRKMPLVERRKRIARVLEQ 121 Query: 130 VNMQDFLDQEPHHLSGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGREEVLETVRHLK 189 V + D + P LSGGQ+QRVA+A + P +++LDE LD RE++ ++HL+ Sbjct: 122 VGLPDLEHRNPQELSGGQRQRVALARCLVLEPTLLLLDEPLGALDLKLREQMKVELKHLQ 181 Query: 190 EQGMATVISITHDLNEA-AKADRIIVMNGGKKYAEGPPEEIFK 231 +Q T + ITHD +EA +D++ VM G+ PPEE+++ Sbjct: 182 KQFGTTFVYITHDQSEAMVMSDQVAVMRDGRFDQVAPPEELYR 224 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: 224 Number of extensions: 13 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: 281 Length of database: 362 Length adjustment: 27 Effective length of query: 254 Effective length of database: 335 Effective search space: 85090 Effective search space used: 85090 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