Align Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale)
to candidate 350819 BT1291 spermidine/putrescine transport ATP-binding protein (NCBI ptt file)
Query= uniprot:P40735 (281 letters) >FitnessBrowser__Btheta:350819 Length = 463 Score = 120 bits (300), Expect = 7e-32 Identities = 75/231 (32%), Positives = 131/231 (56%), Gaps = 4/231 (1%) Query: 1 MNQNQLISVEDIVFRYRKDAERRALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLIL 60 MN + S+ ++ + ++ ALD V+L V +GE++ I+G +G GK+TL R + G Sbjct: 1 MNMQEDKSIIEVSHVSKFFGDKTALDDVTLNVKKGEFVTILGPSGCGKTTLLRLIAGFQT 60 Query: 61 PESGDIEVAGIQLTEESVWEVRKKIGMVFQNPDNQFVGTTVRDDVAFGLENNGVPREEMI 120 G+I ++G ++T+ ++ + VFQ F V D++AFGL+ P++ + Sbjct: 61 ASEGEIRISGKEITQTPPH--KRPVNTVFQKYA-LFPHLNVYDNIAFGLKLKKTPKQTIG 117 Query: 121 ERVDWAVKQVNMQDFLDQEPHHLSGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGREE 180 ++V A+K V M D+ ++ LSGGQ+QRVAIA I P++++LDE + LD R++ Sbjct: 118 KKVKAALKMVGMTDYEYRDVDSLSGGQQQRVAIARAIVNEPEVLLLDEPLAALDLKMRKD 177 Query: 181 VLETVRHLKEQGMATVISITHDLNEA-AKADRIIVMNGGKKYAEGPPEEIF 230 + ++ + + T + +THD EA +D I+VM+ GK G P +I+ Sbjct: 178 MQMELKEMHKSLGITFVYVTHDQEEALTLSDTIVVMSEGKIQQIGTPIDIY 228 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: 294 Number of extensions: 14 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: 463 Length adjustment: 29 Effective length of query: 252 Effective length of database: 434 Effective search space: 109368 Effective search space used: 109368 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 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