Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate Echvi_2204 Echvi_2204 ABC-type antimicrobial peptide transport system, ATPase component
Query= TCDB::P73721 (252 letters) >FitnessBrowser__Cola:Echvi_2204 Length = 240 Score = 126 bits (317), Expect = 4e-34 Identities = 76/218 (34%), Positives = 125/218 (57%), Gaps = 6/218 (2%) Query: 21 LQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPISGGRLEVAGVDLSGAKIDQK 80 +Q L+ VT +I + ++ +GPSG GKST + + L+ + G + D+S + + Sbjct: 21 VQALKSVTIDIIKGEYVAFMGPSGSGKSTLMNIIGCLDTPTAGNYILNNKDVS--HMTEN 78 Query: 81 HLRQLRVR-VGMVFQHFNLFPHLTVLQNLLLAPRKVLRIPMAEAKDRALTYLDKVGLGTK 139 L ++R + +G VFQ FNL P T L+N+ L P ++ +D+A L VGL + Sbjct: 79 ELAEIRNKEIGFVFQTFNLLPRATCLENVAL-PLIYAGYSKSDREDKAFLALKSVGLEDR 137 Query: 140 ADNYPDQLSGGQKQRVAIARGLCMKPEILLFDEPTSALDPELVGEVLNVMKQLAEEGMTM 199 + P++LSGGQ+QRVAIAR L P I+L DEPT LD + +++N+ +L ++G T+ Sbjct: 138 IHHKPNELSGGQRQRVAIARALVNDPSIILADEPTGNLDTKTSYDIMNLFDELHQKGNTI 197 Query: 200 AVVTHEMQFAREVSNRVFFFNQGIIE-EEGDPNEVFRN 236 +VTHE A ++R+ G++E ++ +PN N Sbjct: 198 IMVTHEDDIA-HYAHRIVRLRDGLVETDQNNPNPTRNN 234 Lambda K H 0.321 0.139 0.397 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: 135 Number of extensions: 6 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: 252 Length of database: 240 Length adjustment: 24 Effective length of query: 228 Effective length of database: 216 Effective search space: 49248 Effective search space used: 49248 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: 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