Align Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale)
to candidate H281DRAFT_05181 H281DRAFT_05181 putrescine transport system ATP-binding protein
Query= uniprot:P40735 (281 letters) >FitnessBrowser__Burk376:H281DRAFT_05181 Length = 388 Score = 132 bits (333), Expect = 9e-36 Identities = 89/227 (39%), Positives = 132/227 (58%), Gaps = 9/227 (3%) Query: 7 ISVEDIVFRYRKDAERRALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPESGDI 66 + + D+V +K E A+ V+L V +GE A++G +G GKSTL R L GL SG I Sbjct: 31 VQIVDVV---KKFGETVAVKQVNLSVKKGELFALLGSSGCGKSTLLRMLAGLETVTSGKI 87 Query: 67 EVAGIQLTEESVWEVRKKIGMVFQNPDNQFVGTTVRDDVAFGLENNGVPREEMIERVDWA 126 + G L + + R+ + M+FQ+ F TV +VAFGL+ GVP+ E+ +RV A Sbjct: 88 LIDGEDLAQLPPY--RRPVNMMFQSYA-LFPHMTVESNVAFGLKQEGVPKAELKDRVQTA 144 Query: 127 VKQVNMQDFLDQEPHHLSGGQKQRVAIAGVIAARPDIIILDEATSMLD-PIGREEVLETV 185 ++ V M F +++PH LSGGQ+QRVA+A + RP +++LDE S LD I + +E V Sbjct: 145 LELVQMGRFANRKPHQLSGGQQQRVALARSLVKRPKLLLLDEPMSALDKQIRQRTQIELV 204 Query: 186 RHLKEQGMATVISITHDLNEA-AKADRIIVMNGGKKYAEGPPEEIFK 231 L G+ T I +THD EA A R+ VM+ G+ G P E+++ Sbjct: 205 NILDTVGV-TCIMVTHDQEEAMTMAGRLAVMSEGEIVQLGTPHEVYE 250 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: 251 Number of extensions: 18 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: 388 Length adjustment: 28 Effective length of query: 253 Effective length of database: 360 Effective search space: 91080 Effective search space used: 91080 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: 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