Align ABC transporter for L-asparagine and L-glutamate, periplasmic substrate-binding component (characterized)
to candidate WP_011386136.1 AMB_RS19155 amino acid ABC transporter substrate-binding protein
Query= reanno::pseudo1_N1B4:Pf1N1B4_771 (304 letters) >NCBI__GCF_000009985.1:WP_011386136.1 Length = 302 Score = 226 bits (576), Expect = 5e-64 Identities = 125/296 (42%), Positives = 178/296 (60%), Gaps = 2/296 (0%) Query: 5 PHILGAAIAAALISTPVFAAELTGTLKKIKESGTITLGHRDASIPFSYIADASGKPVGYS 64 P +L +A A+IST AA TL K+K +G++ LG R+AS P SY+ D KP+GY Sbjct: 3 PFVLPLFLALAVISTGG-AARAEPTLDKVKRTGSVVLGVREASYPLSYL-DGDKKPIGYH 60 Query: 65 HDIQLKIVEAIKKDLDMPNLQVKYNLVTSQTRIPLVQNGTVDVECGSTTNNVERQQQVDF 124 DI ++ EA+K L + L+V+ +VTS+TRIP + +G +D+ECGSTTNN RQ QV F Sbjct: 61 VDICRRVTEAVKAQLGLAALEVRTEVVTSKTRIPRLLDGGIDLECGSTTNNAARQTQVAF 120 Query: 125 SVGIFEIGTKLLSKKDSAYKDFADLKGKNVVTTAGTTSERILKSMNADKQMGMNVISAKD 184 + + ++ KK + + L GK V TTAG+TS ++LK+ + + + + D Sbjct: 121 APTTYVASVRIAVKKAAHIGKLSQLDGKAVATTAGSTSVQLLKARVQGRDIKVTELFGND 180 Query: 185 HGESFQMLETGRAVAFMMDDALLAGEMAKAKKPTDWAVTGTAQSNEIYGCMVRKGDAPFK 244 H ESF+MLE+ +A AF+MDD LLAG +A + P D+ + + E M+RKGD FK Sbjct: 181 HAESFKMLESDQAAAFVMDDNLLAGLIASSAAPKDYQILPQTLNTEPIAIMLRKGDPEFK 240 Query: 245 KAVDDAIIATYKSGEINKIYEKWFMQPIPPKGLNLMFPMSEELKALIANPTDKAAD 300 VD + A +SGE+ ++Y KWF PIPP L FPMS L +LI P D A+ Sbjct: 241 ALVDRTVKAMMESGEVGRLYAKWFQSPIPPMNAALDFPMSPVLLSLIKFPGDDPAE 296 Lambda K H 0.315 0.131 0.365 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: 304 Length of database: 302 Length adjustment: 27 Effective length of query: 277 Effective length of database: 275 Effective search space: 76175 Effective search space used: 76175 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 (21.6 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