Align BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate SMc03135 SMc03135 amino-acid transport system ATP-binding ABC transporter protein
Query= TCDB::Q52666 (263 letters) >FitnessBrowser__Smeli:SMc03135 Length = 251 Score = 343 bits (880), Expect = 2e-99 Identities = 163/250 (65%), Positives = 205/250 (82%), Gaps = 3/250 (1%) Query: 15 MQVSDEIA---IQISQMNKWYGQFHVLRDINLTVHRGERIVIAGPSGSGKSTMIRCINRL 71 M S +IA I +S ++KWYGQ+H L DINL++ E++VI GPSGSGKST+IRC+NRL Sbjct: 1 MPTSIDIASPEITLSGVHKWYGQYHALDDINLSIASREKVVICGPSGSGKSTLIRCVNRL 60 Query: 72 EEHQSGKIIVDGIELTSDLKNIDKVRSEVGMVFQHFNLFPHLTILENLTLAPIWVRKVPK 131 E HQ G+I+V G+E+ D + +D +R EVGMVFQ FNLFPHLTILEN LAP+WV+++P+ Sbjct: 61 EAHQQGRIVVGGVEVGEDERKVDAIRREVGMVFQQFNLFPHLTILENCILAPMWVKRMPR 120 Query: 132 REAEETAMYYLEKVKIPEQAQKYPGQLSGGQQQRVAIARSLCMKPKIMLFDEPTSALDPE 191 +A E AM YL +V+IPEQA KYPGQLSGGQQQRVAIAR+LCM PK+MLFDEPTSALDPE Sbjct: 121 AQATEIAMDYLNRVRIPEQANKYPGQLSGGQQQRVAIARALCMNPKVMLFDEPTSALDPE 180 Query: 192 MIKEVLDTMIQLAEEGMTMLCVTHEMGFAQAVANRVIFMADGQIVEQNNPHDFFHNPQSE 251 M+KEVLDTM+ LA +GMTM+CVTHEMGFA+ VA+RVIFM G+IVE+ P +FF +P+++ Sbjct: 181 MVKEVLDTMVALANDGMTMVCVTHEMGFARQVADRVIFMDQGRIVEEGEPDEFFAHPKTD 240 Query: 252 RTKQFLSQIL 261 R FLSQ+L Sbjct: 241 RASLFLSQLL 250 Lambda K H 0.320 0.134 0.391 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: 259 Number of extensions: 6 Number of successful extensions: 1 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: 263 Length of database: 251 Length adjustment: 24 Effective length of query: 239 Effective length of database: 227 Effective search space: 54253 Effective search space used: 54253 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 (21.8 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