Align ABC transporter for D-Alanine, ATPase component (characterized)
to candidate N515DRAFT_1085 N515DRAFT_1085 D-methionine transport system ATP-binding protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_5405 (254 letters) >FitnessBrowser__Dyella79:N515DRAFT_1085 Length = 336 Score = 159 bits (401), Expect = 9e-44 Identities = 92/226 (40%), Positives = 129/226 (57%), Gaps = 2/226 (0%) Query: 30 LKDINLNVKQGERIVLCGPSGSGKSTTIRCLNRLEEHQQGRIVVDGVELTN-DLKQIEAI 88 L+ +L++ GE + G SG+GKST IR +N LE G I++DG E+T + A Sbjct: 21 LQPFSLDIADGEVFGIIGHSGAGKSTLIRLINLLERPSGGSILIDGTEMTALGDAALRAQ 80 Query: 89 RREVGMVFQHFNLFPHLTILQNCTLAPMWVRKMPKRKAEEIAMHYLERVRIPEQAHKYPG 148 RR +GM+FQHFNL T+ N + K + L RV + A KYP Sbjct: 81 RRRIGMIFQHFNLLSSQTVADNIAFPLRLAGETDAGKIKARVDELLRRVGLEAHASKYPA 140 Query: 149 QLSGGQQQRVAIARALCMKPKIMLFDEPTSALDPEMVKEVLDTMIGL-AEDGMTMLCVTH 207 QLSGGQ+QRV IARAL +P I+L DE TSALDP+ VL+ + + E +T++ +TH Sbjct: 141 QLSGGQKQRVGIARALANRPSILLCDEATSALDPQTTASVLELLAEINRELKLTIVLITH 200 Query: 208 EMGFARTVANRVIFMDKGEIVEQAAPNDFFDNPQNDRTKLFLSQIL 253 EM R V +RV +D G IVE A D F +P++ T+ F+++ L Sbjct: 201 EMDVVRRVCDRVAVLDAGRIVEHGAVADVFLHPRHPTTRRFVNEAL 246 Lambda K H 0.322 0.137 0.407 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: 198 Number of extensions: 8 Number of successful extensions: 4 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: 254 Length of database: 336 Length adjustment: 26 Effective length of query: 228 Effective length of database: 310 Effective search space: 70680 Effective search space used: 70680 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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