Align TreV, component of Trehalose porter (characterized)
to candidate Echvi_2123 Echvi_2123 ABC-type spermidine/putrescine transport systems, ATPase components
Query= TCDB::Q97ZC0 (324 letters) >FitnessBrowser__Cola:Echvi_2123 Length = 318 Score = 140 bits (354), Expect = 3e-38 Identities = 88/265 (33%), Positives = 146/265 (55%), Gaps = 15/265 (5%) Query: 3 VELIDIVKKYGK-NIVINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIA 61 +++ ++ K+Y ++ + + +++ G ++G SG GKS+LL+I+AG+E G + Sbjct: 4 LKVSEVSKRYDAGSLALEDFSLQVKRGGVVSMVGESGSGKSSLLRIIAGLEVQSAGVVHL 63 Query: 62 DGADITDKP----PEKRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAA 117 I + P + ++ Q Y LYPN +V +NIA PL + ++ ER + Sbjct: 64 GDQKILNPAQKLVPGYDEIQLIHQEYKLYPNSTVEENIARPLLLYDKAYQK--ERTAEIL 121 Query: 118 KLLGISEILDKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKR 177 +LL + DKK Q+SGGQQQ+VA+ RA+ P LLDEP S+LDA + ELK Sbjct: 122 ELLSLRAFKDKKPRQLSGGQQQKVAIGRALSIEPEVLLLDEPFSSLDAIQKRDLIEELKE 181 Query: 178 IQKELKGTFIYVTHDQKEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFVGEFP 237 I L+ T I+VTHD +AL +++ + I+ KGK Q + + ++ P + +VA+ G Sbjct: 182 IFDALEVTVIFVTHDVDDALLMSEELLIIQKGKLLQQGNVREVFRKPASAYVARLFGY-- 239 Query: 238 MNFLPGELMKEKAQEIGFRPEWVEV 262 +N +PG A+E RP V++ Sbjct: 240 LNLIPG------AEEAYVRPSEVKI 258 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: 240 Number of extensions: 13 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: 324 Length of database: 318 Length adjustment: 28 Effective length of query: 296 Effective length of database: 290 Effective search space: 85840 Effective search space used: 85840 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: 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