Align ABC transporter related (characterized, see rationale)
to candidate Echvi_1582 Echvi_1582 ABC-type antimicrobial peptide transport system, ATPase component
Query= uniprot:B2TBJ9 (263 letters) >FitnessBrowser__Cola:Echvi_1582 Length = 225 Score = 132 bits (332), Expect = 6e-36 Identities = 88/234 (37%), Positives = 136/234 (58%), Gaps = 22/234 (9%) Query: 9 LSVKNIHKSFGDHH----VLKGISLDAHQGDVISILGASGSGKSTFLRCLNLLETPDDGS 64 LS++N+ K + VL+ I+L GD I+I+G SGSGK+T L L++ GS Sbjct: 4 LSIENVSKIYQSGSRTLTVLEDINLSVKAGDSIAIVGPSGSGKTTLLGLCAGLDSASSGS 63 Query: 65 VSLAGEELKMKRRGDGKLQPSDRRQVDRVRSQ-LGMVFQNFNLWSHMTVLENLIEGPMRV 123 V+L G +L+ Q VRSQ +G +FQNF L +T LEN++ P+ + Sbjct: 64 VALNGH----------RLEGLSEDQRAAVRSQEIGFIFQNFQLLPTLTALENVMV-PLEL 112 Query: 124 QKRSRAESVEEAEALLAKVGLAEKRGHYPAHLSGGQQQRVAIARALAMHPKVMLFDEPTS 183 +KR A+ ++A LL +VGL ++ HYP LSGG+QQRV+IARA A PK++ DEPT Sbjct: 113 KKRKDAK--QKATELLQQVGLGDRMTHYPTQLSGGEQQRVSIARAFANEPKILFADEPTG 170 Query: 184 ALDPELVGEVLRVMRSLAEE--GRTMLVVTHEMGFARHVSNRVMFLHQGQVEAD 235 LD E GE++ + + G T+++VTH+ A +NR++ + G+++ + Sbjct: 171 NLDTE-TGELIETLIFDLNKALGTTLILVTHDTDLAAK-TNRIIHIKGGKIQEE 222 Lambda K H 0.318 0.133 0.377 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: 128 Number of extensions: 8 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 (21.7 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