Align ABC transporter for D-Alanine, ATPase component (characterized)
to candidate WP_013645374.1 METBO_RS08905 ABC transporter ATP-binding protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_5405 (254 letters) >NCBI__GCF_000191585.1:WP_013645374.1 Length = 223 Score = 137 bits (344), Expect = 2e-37 Identities = 81/217 (37%), Positives = 133/217 (61%), Gaps = 5/217 (2%) Query: 14 IIQMQGVNKWY--GQFHVLKDINLNVKQGERIVLCGPSGSGKSTTIRCLNRLEEHQQGRI 71 II+++ + K Y G L +++L +++GE + + GPSGSGKST + + L++ +G+I Sbjct: 6 IIKIKNLKKEYEDGSIIALNNVDLEIERGESVSIIGPSGSGKSTLLNMIGGLDKANEGQI 65 Query: 72 VVDGVELTNDLKQIEAIRREVGMVFQHFNLFPHLTILQNCTLAPMWVRKMPKRKAEEIAM 131 V GV L ++ E+G VFQ NL P+LT+L+N + P+ + +K EE A+ Sbjct: 66 SVAGVNLMDNSDLSNFRSNEIGFVFQLHNLIPNLTVLENVQI-PLLGTDIDDKKMEERAL 124 Query: 132 HYLERVRIPEQAHKYPGQLSGGQQQRVAIARALCMKPKIMLFDEPTSALDPEMVKEVLDT 191 L+ V + + + P +LSGG++QRVAIARAL P I+L DEPT ALD E + +L Sbjct: 125 KLLKSVNLENKVDQKPTKLSGGERQRVAIARALVNHPSIILADEPTGALDSETQEVILKL 184 Query: 192 MIGL-AEDGMTMLCVTHEMGFARTVANRVIFMDKGEI 227 ++ + ++ +T++ VTHE A+ A+R I++ G+I Sbjct: 185 LLDIHKKENVTLIMVTHEPYVAKQ-ADRSIYVLDGKI 220 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: 122 Number of extensions: 4 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: 223 Length adjustment: 23 Effective length of query: 231 Effective length of database: 200 Effective search space: 46200 Effective search space used: 46200 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: 46 (22.3 bits)
This GapMind analysis is from Apr 09 2024. 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