Align ABC transporter for D-Alanine, ATPase component (characterized)
to candidate PfGW456L13_376 Histidine ABC transporter, ATP-binding protein HisP (TC 3.A.1.3.1)
Query= reanno::pseudo6_N2E2:Pf6N2E2_5405 (254 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_376 Length = 257 Score = 238 bits (606), Expect = 1e-67 Identities = 124/247 (50%), Positives = 167/247 (67%), Gaps = 11/247 (4%) Query: 15 IQMQGVNKWYGQFHVLKDINLNVKQGERIVLCGPSGSGKSTTIRCLNRLEEHQQGRIVVD 74 ++++ ++K YG VLK I+L + G+ I + G SGSGKST +RC+N LE QG+I+V Sbjct: 8 LEIRNLHKRYGSLEVLKGISLTARDGDVISILGSSGSGKSTFLRCINLLENPHQGQILVA 67 Query: 75 GVEL-----------TNDLKQIEAIRREVGMVFQHFNLFPHLTILQNCTLAPMWVRKMPK 123 G EL D KQI +R E+G VFQ+FNL+PH+++L N AP V K Sbjct: 68 GEELKLKAAKNGELVAADGKQINRLRSEIGFVFQNFNLWPHMSVLDNIIEAPRRVLGQSK 127 Query: 124 RKAEEIAMHYLERVRIPEQAHKYPGQLSGGQQQRVAIARALCMKPKIMLFDEPTSALDPE 183 +A E+A L +V I ++ H YP QLSGGQQQR AIAR L M+PK++LFDEPTSALDPE Sbjct: 128 AEAIEVAEALLAKVGIADKRHAYPAQLSGGQQQRAAIARTLAMQPKVILFDEPTSALDPE 187 Query: 184 MVKEVLDTMIGLAEDGMTMLCVTHEMGFARTVANRVIFMDKGEIVEQAAPNDFFDNPQND 243 MV+EVL+ + LAE+G TML VTHEMGFAR V++ V+F+ +G + EQ +P F+NP + Sbjct: 188 MVQEVLNVIRALAEEGRTMLLVTHEMGFARQVSSEVVFLHQGLVEEQGSPQQVFENPLSA 247 Query: 244 RTKLFLS 250 R K F+S Sbjct: 248 RCKQFMS 254 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: 202 Number of extensions: 7 Number of successful extensions: 2 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: 257 Length adjustment: 24 Effective length of query: 230 Effective length of database: 233 Effective search space: 53590 Effective search space used: 53590 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: 47 (22.7 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