Align ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized)
to candidate WP_109939172.1 DLD82_RS00420 glycine betaine/L-proline ABC transporter ATP-binding protein
Query= reanno::pseudo1_N1B4:Pf1N1B4_774 (244 letters) >NCBI__GCF_003173335.1:WP_109939172.1 Length = 376 Score = 152 bits (385), Expect = 7e-42 Identities = 93/243 (38%), Positives = 141/243 (58%), Gaps = 12/243 (4%) Query: 5 KNVNKWYGDFQVLTDCSTEVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQKGDVIVDGTS 64 K + + G L + S VKKGE+ V+ G SG GKSTL++C+N L G +++DG Sbjct: 12 KEIRERTGHVVALKNISFSVKKGEIFVLMGLSGCGKSTLLRCLNRLISPTAGSILLDGED 71 Query: 65 IADPKTNLPKL--RSRVGMVFQHFELFPHLSIMDNLTIAQVKVLGRSKEEASKKALQLLE 122 IA T + RSR+GMVFQ F L PH +I DN+ +++ G S EE + A + L+ Sbjct: 72 IASVSTERMRTIRRSRMGMVFQSFALLPHKNIQDNVAFG-LEIQGISAEERAGIAKETLD 130 Query: 123 RVGLSAHAKKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDP----EMVNEVLDV 178 VGLS + +P QLSGG +QRV +ARA+A P ++L DE SALDP +M NE+LD+ Sbjct: 131 LVGLSGYENSYPDQLSGGMKQRVGLARAIASSPDILLMDEAFSALDPMIRRDMQNELLDI 190 Query: 179 MVQLAHEGMTMMCVTHEMGFARKVADRVIFMDQGKIIEDCKKEEFFGDITARSDRAQHFL 238 +L T++ V+H++ A K+ R+ M G+I++ EE +++ + F+ Sbjct: 191 QDRLE---KTIIFVSHDLDEALKLGTRIGLMKAGEIVQIGTPEEIL--TQPKNEFVERFV 245 Query: 239 EKI 241 E + Sbjct: 246 EDV 248 Lambda K H 0.321 0.135 0.390 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: 217 Number of extensions: 12 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: 244 Length of database: 376 Length adjustment: 27 Effective length of query: 217 Effective length of database: 349 Effective search space: 75733 Effective search space used: 75733 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 24 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