Align TreV, component of Trehalose porter (characterized)
to candidate WP_011382978.1 AMB_RS02755 nitrate/sulfonate/bicarbonate ABC transporter ATP-binding protein
Query= TCDB::Q97ZC0 (324 letters) >NCBI__GCF_000009985.1:WP_011382978.1 Length = 553 Score = 146 bits (369), Expect = 1e-39 Identities = 88/209 (42%), Positives = 128/209 (61%), Gaps = 5/209 (2%) Query: 3 VELIDIVKKYGKNIVINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIAD 62 +EL + K YG + V+ I +IE GEF ILG SG GK+TL+ ++AG+ K D G+++ Sbjct: 4 LELKGVAKSYGASSVLRDIDLEIEDGEFIAILGFSGSGKTTLVSLMAGLIKPDAGEVLLR 63 Query: 63 GADITDKPPEKRNVAMVFQNYALYPNMSVRDNIAFPLK--MRGMKKEEIIERVEKAAKLL 120 G + D P R V VFQ+Y+L P ++V NIA + M K E RV K ++ Sbjct: 64 GKPV-DGPGADRGV--VFQSYSLMPWLTVEGNIALAVDAVMPDASKAERKARVAKYIGMV 120 Query: 121 GISEILDKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQK 180 G+S +++ +++SGG +QRVA+ARA+ +P LLDEPLS LDA R + E++ I + Sbjct: 121 GLSHAAERRPSELSGGMRQRVAVARALAMSPDILLLDEPLSALDALTRAKLQDEIEAIWE 180 Query: 181 ELKGTFIYVTHDQKEALSLADRIAILHKG 209 + K T I +T+D EAL LADRI L+ G Sbjct: 181 QEKKTVILITNDVDEALLLADRIIPLNPG 209 Score = 115 bits (288), Expect = 3e-30 Identities = 66/199 (33%), Positives = 111/199 (55%), Gaps = 5/199 (2%) Query: 13 GKNIVINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIADGADITDKPPE 72 G V++G K+ GEF ++G SG GKST+L + AG+ + +G +I DG ++++ P+ Sbjct: 307 GPLTVVDGFDLKMHQGEFISLIGHSGCGKSTVLTMTAGLTDVSEGGVILDGREVSEAGPD 366 Query: 73 KRNVAMVFQNYALYPNMSVRDNIAFPLKM--RGMKKEEIIERVEKAAKLLGISEILDKKV 130 + A+VFQ +L+P ++ N+A + E ++ V + +G+ + +DKK Sbjct: 367 R---AVVFQAPSLFPWLTALQNVALGVDRVYPHASPAERLDIVSYYLERVGLGDSMDKKA 423 Query: 131 TQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQKELKGTFIYVT 190 + +S G +QRV +ARA +P LLDEP LD+ R + L + + T I VT Sbjct: 424 SDMSNGMRQRVGIARAFALSPKLLLLDEPFGMLDSLTRWELQEVLMEVWTRTRVTAICVT 483 Query: 191 HDQKEALSLADRIAILHKG 209 HD EA+ LAD++ ++ G Sbjct: 484 HDVDEAILLADKVVMMTNG 502 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: 437 Number of extensions: 25 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 324 Length of database: 553 Length adjustment: 32 Effective length of query: 292 Effective length of database: 521 Effective search space: 152132 Effective search space used: 152132 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: 50 (23.9 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