Align TreV, component of Trehalose porter (characterized)
to candidate 5207560 Shew_0094 ABC transporter-related protein (RefSeq)
Query= TCDB::Q97ZC0 (324 letters) >FitnessBrowser__PV4:5207560 Length = 369 Score = 129 bits (325), Expect = 8e-35 Identities = 76/215 (35%), Positives = 123/215 (57%), Gaps = 8/215 (3%) Query: 26 ETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKI-IADGADITDKP-----PEKRNVAMV 79 + GE ++GPSG GKSTL++++AG+ K + G+I D + + P++R++ V Sbjct: 27 KAGEVLAVVGPSGGGKSTLMRMIAGLTKPESGEIRYGDSVWFSSESGRYLTPQQRHLGYV 86 Query: 80 FQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLLGISEILDKKVTQISGGQQQ 139 Q++ L+PNM+ N+ L + K E + R + + + + + D+ +SGGQ+Q Sbjct: 87 PQHFGLFPNMTALANVVAALDH--IPKAERVARAKDWLERVNLHGLPDRLPANLSGGQRQ 144 Query: 140 RVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQKELKGTFIYVTHDQKEALSL 199 RVALARA+ R P LLDEP S +D R EL R++++L I VTHD EAL L Sbjct: 145 RVALARALAREPRVLLLDEPFSAVDRETRERLYLELARLKEQLAIPVIMVTHDLNEALLL 204 Query: 200 ADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFVG 234 ADR+ ++ +G Q P+ + P+ + VA+ +G Sbjct: 205 ADRMILISQGTLLQQGSPREVLSRPRNEAVAKQMG 239 Lambda K H 0.318 0.137 0.385 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: 251 Number of extensions: 14 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: 324 Length of database: 369 Length adjustment: 29 Effective length of query: 295 Effective length of database: 340 Effective search space: 100300 Effective search space used: 100300 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 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