Align Amino acid ABC transporter, permease protein PEB1 (characterized, see rationale)
to candidate Synpcc7942_0248 Synpcc7942_0248 Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine
Query= uniprot:A0A0H3PA28 (219 letters) >FitnessBrowser__SynE:Synpcc7942_0248 Length = 396 Score = 111 bits (277), Expect = 2e-29 Identities = 65/200 (32%), Positives = 112/200 (56%), Gaps = 9/200 (4%) Query: 16 GLFLTLKIALATCIISIVFGTFLAITKNYGDRLSKFLAACYIDIFRNTPLLLWMLAACFV 75 GL LTL AL + + S+ G LA+ + ++L+ YI++FR PL+ + + Sbjct: 190 GLLLTLATALISMVCSLPLGILLALGRQSSLPAIRWLSVTYIELFRGLPLVTILFFGQVM 249 Query: 76 LPVFFG---QFPQAFWGTIGFSLYTSSVMAEIIRGGLNSIPKGQFEAAYSQGFGKFFTLF 132 +P+ + + +G +++ S+ +AE +RGGL +IP+GQFEAA + G F T Sbjct: 250 VPLMLDSEWRIDRILRAIVGLTIFLSAYLAETVRGGLQAIPQGQFEAAAALGLNLFQTYR 309 Query: 133 YIILPQTFRKIIPALLSQIVTTVKDTAYLAGLGIAELTYNSKTILAK---LTSFEEILAM 189 +I+LPQ R IPA++ + ++DT L+ +G+ EL S++ILA L + E+ Sbjct: 310 FIVLPQALRISIPAIVGLFLNLLQDTTLLSIVGLLELLGISRSILANPAYLGRYAEVYLF 369 Query: 190 IGVVAGIYFIICFSLSMLVR 209 +GV +Y++ C+ L+ L R Sbjct: 370 LGV---LYWLCCYGLAQLSR 386 Lambda K H 0.331 0.144 0.428 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: 16 Number of successful extensions: 2 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: 219 Length of database: 396 Length adjustment: 26 Effective length of query: 193 Effective length of database: 370 Effective search space: 71410 Effective search space used: 71410 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 48 (23.1 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