Align Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale)
to candidate 8500289 DvMF_1045 glycine betaine/L-proline ABC transporter, ATPase subunit (RefSeq)
Query= uniprot:P40735 (281 letters) >FitnessBrowser__Miya:8500289 Length = 397 Score = 131 bits (330), Expect = 2e-35 Identities = 79/219 (36%), Positives = 124/219 (56%), Gaps = 6/219 (2%) Query: 16 YRKDAERRALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPESGDIEVAGIQLTE 75 Y++ ++ + V EGE + ++G +GSGKSTL R LN LI P G + + G +T Sbjct: 34 YKRTKHAVGVNRATFDVDEGEIVVVMGLSGSGKSTLVRCLNRLIEPTDGTVRIDGTDVTT 93 Query: 76 ESVWEVR----KKIGMVFQNPDNQFVGTTVRDDVAFGLENNGVPREEMIERVDWAVKQVN 131 SV ++R + GMVFQN F TV ++ +GLE G + ++ A+ +V Sbjct: 94 LSVKDLRALRQRTFGMVFQN-FALFPHRTVLENAEYGLEVMGAAKATRRDKAAEALARVG 152 Query: 132 MQDFLDQEPHHLSGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGREEVLETVRHLKEQ 191 + + P LSGG +QRV +A +A PDI+++DEA S LDP+ R ++ + + L++ Sbjct: 153 LAGWEAARPGQLSGGMQQRVGLARALALDPDILLMDEAFSALDPLIRRDMQDELLRLQDD 212 Query: 192 GMATVISITHDLNEAAK-ADRIIVMNGGKKYAEGPPEEI 229 T++ I+HDL+EA K DRI++M G G PE+I Sbjct: 213 VRKTIVFISHDLDEALKIGDRIVLMRDGAVVQVGTPEDI 251 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: 291 Number of extensions: 16 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: 397 Length adjustment: 28 Effective length of query: 253 Effective length of database: 369 Effective search space: 93357 Effective search space used: 93357 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