Align Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale)
to candidate WP_028488909.1 Q394_RS0108480 spermidine/putrescine ABC transporter ATP-binding protein PotA
Query= uniprot:P40735 (281 letters) >NCBI__GCF_000621325.1:WP_028488909.1 Length = 369 Score = 130 bits (326), Expect = 6e-35 Identities = 82/237 (34%), Positives = 136/237 (57%), Gaps = 7/237 (2%) Query: 1 MNQNQLISVEDIVFRYRKDAERRALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLIL 60 M ++ ++++ +I R+ A + L +L + +GE+ I+G +G GK+T+ R + G Sbjct: 1 MTRSPILTLSNISKRF---ASQEVLSDFNLTIQDGEFFTILGPSGCGKTTVLRLIAGFEQ 57 Query: 61 PESGDIEVAGIQLTEESVWEVRKKIGMVFQNPDNQFVGTTVRDDVAFGLENNGVPREEMI 120 P G I + G + + ++ VFQ+ F TV D+VAFGL+ GV +++ Sbjct: 58 PNEGQILLNGDDIAR--IPAEKRPFNTVFQSYA-LFPHLTVFDNVAFGLKMAGVDVQDIA 114 Query: 121 ERVDWAVKQVNMQDFLDQEPHHLSGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGREE 180 RV A+ V + +F ++PH LSGGQKQRVAIA + RP I++LDE+ S LD R++ Sbjct: 115 VRVADALAIVRLSEFATRKPHQLSGGQKQRVAIARAVVNRPKILLLDESLSALDYKLRQQ 174 Query: 181 VLETVRHLKEQGMATVISITHDLNEA-AKADRIIVMNGGKKYAEGPPEEIFKLNKEL 236 + ++ L+ Q T + +THD EA + +DRI+VM+ G+ G P EI++ + L Sbjct: 175 MQLELKQLQRQLGITFVYVTHDQEEALSMSDRILVMHNGQAQQVGTPREIYESPRNL 231 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: 254 Number of extensions: 10 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: 369 Length adjustment: 28 Effective length of query: 253 Effective length of database: 341 Effective search space: 86273 Effective search space used: 86273 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 Apr 09 2024. 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