Align TreV, component of Trehalose porter (characterized)
to candidate Pf1N1B4_3974 ABC transporter, ATP-binding protein
Query= TCDB::Q97ZC0 (324 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3974 Length = 341 Score = 227 bits (579), Expect = 3e-64 Identities = 111/242 (45%), Positives = 172/242 (71%), Gaps = 2/242 (0%) Query: 3 VELIDIVKKYGKNIVINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIAD 62 V+L ++ K+YG+ + +E GEF +LGPSG GK+T L+++AG ++ G+I+ D Sbjct: 4 VQLENLGKRYGEIDAVVATNLSVEKGEFVSLLGPSGCGKTTTLQMIAGFVEVSSGRIVLD 63 Query: 63 GADITDKPPEKRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLLGI 122 G DIT P R + +VFQ+YAL+P+M+VRDN+AF L+MR + +E+ +RV++ KL+ + Sbjct: 64 GRDITHAKPASRGLGVVFQSYALFPHMTVRDNVAFGLRMRKVPNDELQQRVDRVLKLVRL 123 Query: 123 SEILDKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQKEL 182 ++ ++ ++SGGQ+QRVALARA+V P LLDEPLSNLDA +R + E++RIQ+E+ Sbjct: 124 NQHAERYPRELSGGQRQRVALARALVIEPPVLLLDEPLSNLDANLREEMQFEIRRIQREV 183 Query: 183 KGTFIYVTHDQKEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFVGEFPMNFLP 242 T + VTHDQ EALS++DR+ ++ G+ Q+ P TLYE+P+T++++ FVG+ N LP Sbjct: 184 GITTLMVTHDQSEALSISDRVVVMQAGRITQIDAPYTLYEHPRTEFISGFVGK--ANLLP 241 Query: 243 GE 244 GE Sbjct: 242 GE 243 Lambda K H 0.318 0.137 0.385 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: 282 Number of extensions: 8 Number of successful extensions: 1 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: 324 Length of database: 341 Length adjustment: 28 Effective length of query: 296 Effective length of database: 313 Effective search space: 92648 Effective search space used: 92648 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 (21.7 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