Align BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate Echvi_1582 Echvi_1582 ABC-type antimicrobial peptide transport system, ATPase component
Query= TCDB::Q52666 (263 letters) >FitnessBrowser__Cola:Echvi_1582 Length = 225 Score = 135 bits (339), Expect = 1e-36 Identities = 82/208 (39%), Positives = 130/208 (62%), Gaps = 9/208 (4%) Query: 37 VLRDINLTVHRGERIVIAGPSGSGKSTMIRCINRLEEHQSGKIIVDG--IELTSDLKNID 94 VL DINL+V G+ I I GPSGSGK+T++ L+ SG + ++G +E S+ + Sbjct: 22 VLEDINLSVKAGDSIAIVGPSGSGKTTLLGLCAGLDSASSGSVALNGHRLEGLSEDQRAA 81 Query: 95 KVRSEVGMVFQHFNLFPHLTILENLTLAPIWVRKVPKREAEETAMYYLEKVKIPEQAQKY 154 E+G +FQ+F L P LT LEN+ + P+ ++K +++A++ A L++V + ++ Y Sbjct: 82 VRSQEIGFIFQNFQLLPTLTALENV-MVPLELKK--RKDAKQKATELLQQVGLGDRMTHY 138 Query: 155 PGQLSGGQQQRVAIARSLCMKPKIMLFDEPTSALDPEMIKEVLDTMIQLAEE--GMTMLC 212 P QLSGG+QQRV+IAR+ +PKI+ DEPT LD E E+++T+I + G T++ Sbjct: 139 PTQLSGGEQQRVSIARAFANEPKILFADEPTGNLDTE-TGELIETLIFDLNKALGTTLIL 197 Query: 213 VTHEMGFAQAVANRVIFMADGQIVEQNN 240 VTH+ A A NR+I + G+I E+ + Sbjct: 198 VTHDTDLA-AKTNRIIHIKGGKIQEEQH 224 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: 140 Number of extensions: 9 Number of successful extensions: 3 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: 225 Length adjustment: 23 Effective length of query: 240 Effective length of database: 202 Effective search space: 48480 Effective search space used: 48480 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: 46 (22.3 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