Align Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale)
to candidate SMc00771 SMc00771 putrescine ABC transporter ATP-binding protein
Query= uniprot:P40735 (281 letters) >FitnessBrowser__Smeli:SMc00771 Length = 381 Score = 143 bits (360), Expect = 7e-39 Identities = 88/226 (38%), Positives = 135/226 (59%), Gaps = 7/226 (3%) Query: 7 ISVEDIVFRYRKDAERRALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPESGDI 66 ISV+++ +K + A+D +SL +Y E+ A++G +G GKSTL R L G P SG+I Sbjct: 24 ISVKNVT---KKFGDFTAVDDLSLNIYTREFFALLGASGCGKSTLLRMLAGFEQPTSGEI 80 Query: 67 EVAGIQLTEESVWEVRKKIGMVFQNPDNQFVGTTVRDDVAFGLENNGVPREEMIERVDWA 126 + G L + R+ + M+FQ+ F TV ++VAFGL+ +G+P+ ++ ERV Sbjct: 81 ILDGQSLA--GIPPYRRPVNMMFQSYA-LFPHMTVENNVAFGLKQDGMPKADIAERVAQM 137 Query: 127 VKQVNMQDFLDQEPHHLSGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGREEVLETVR 186 +K V ++ F ++PH LSGGQ+QRVA+A +A RP +++LDE LD REE + Sbjct: 138 LKLVKLEKFAKRKPHQLSGGQRQRVALARSLAKRPKVLLLDEPLGALDKKLREETQFELM 197 Query: 187 HLKEQGMATVISITHDLNEA-AKADRIIVMNGGKKYAEGPPEEIFK 231 L+++ T + +THD EA ADRI VM+ GK P EI++ Sbjct: 198 DLQQELGLTFVVVTHDQEEAMTMADRIAVMSHGKVVQVATPAEIYE 243 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: 244 Number of extensions: 17 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: 381 Length adjustment: 28 Effective length of query: 253 Effective length of database: 353 Effective search space: 89309 Effective search space used: 89309 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