Align ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized)
to candidate 351279 BT1751 Glycine betaine transport ATP-binding protein (NCBI ptt file)
Query= reanno::pseudo1_N1B4:Pf1N1B4_774 (244 letters) >FitnessBrowser__Btheta:351279 Length = 408 Score = 144 bits (362), Expect = 4e-39 Identities = 83/229 (36%), Positives = 137/229 (59%), Gaps = 10/229 (4%) Query: 19 DCSTEVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQKGDVIVDGTSIA--DPKTNLPKLR 76 D + + +GE+ V+ G SGSGKSTL++C+N L G+VI++GT IA K L R Sbjct: 45 DANLSINEGEIFVIMGLSGSGKSTLLRCINRLIRPTSGEVIINGTDIAKVSDKELLQIRR 104 Query: 77 SRVGMVFQHFELFPHLSIMDNLTIAQVKVLGRSKEEASKKALQLLERVGLSAHAKKHPGQ 136 + MVFQ+F L PH S++ N+ +++ G K E +KA++ ++ VGL + + + Sbjct: 105 KELAMVFQNFGLLPHRSVLHNIAFG-LELQGVKKGEREQKAMESMQLVGLKGYENQMVSE 163 Query: 137 LSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVNEVLDVMVQLAHE-GMTMMCVTHE 195 LSGG QQRV +ARALA +P V+L DE SALDP + ++ D ++ L + T++ +TH+ Sbjct: 164 LSGGMQQRVGLARALANNPEVLLMDEAFSALDPLIRVQMQDELLTLQSKMKKTIVFITHD 223 Query: 196 MGFARKVADRVIFMDQGKIIEDCKKEEFFGDITARSDRAQHFLEKILQH 244 + A K+ DR+ M G+I++ EE ++ A ++E+ +++ Sbjct: 224 LSEAIKLGDRIAIMKDGEIVQIGTSEEIL------TEPANAYVERFVEN 266 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: 240 Number of extensions: 11 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: 408 Length adjustment: 27 Effective length of query: 217 Effective length of database: 381 Effective search space: 82677 Effective search space used: 82677 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