Align ABC transporter for L-Lysine, ATPase component (characterized)
to candidate GFF3831 PGA1_262p02350 histidine transport ATP-binding protein HisP
Query= reanno::pseudo5_N2C3_1:AO356_05515 (254 letters) >FitnessBrowser__Phaeo:GFF3831 Length = 281 Score = 300 bits (767), Expect = 3e-86 Identities = 156/242 (64%), Positives = 188/242 (77%), Gaps = 4/242 (1%) Query: 9 LHKSYGEHEVLKGVSLKAKTGDVISLIGASGSGKSTFLRCINFLEQPNDGAMTLDGQPVQ 68 LHKS+G EVLKGVSL AK GDV+++IG SGSGKST LRCINFLE PN G + + G+ V Sbjct: 41 LHKSFGSLEVLKGVSLTAKQGDVVAIIGGSGSGKSTMLRCINFLETPNSGEIVIAGETVA 100 Query: 69 MIKDRHGMHVADADELQRIRTRLAMVFQHFNLWSHMTVLENITMAPRRVLGVSKQEADDR 128 M +D AD +++RIRTRLAMVFQ FNLW+H T+LEN+ P VL V + EA R Sbjct: 101 MRQDGSP---ADRRQIERIRTRLAMVFQQFNLWTHRTLLENVIEVPVHVLKVPRSEAIHR 157 Query: 129 ARRYLDKVGLPARVAEQYPAFLSGGQQQRVAIARALAMEPEVMLFDEPTSALDPELVGEV 188 A L +VGL + A+ +PAFLSGGQQQR AIARALA++P VMLFDEPTSALDPELVGEV Sbjct: 158 AHELLARVGLGDK-ADAFPAFLSGGQQQRAAIARALAVDPNVMLFDEPTSALDPELVGEV 216 Query: 189 LKVIQGLAEEGRTMIMVTHEMSFARKVSNQVLFLHQGLVEEEGAPEDVLGNPKSERLKQF 248 L VI+ LA EGRTM++VTHEM FAR+V+N V++L +G +EE+G P +V GNPKSERLKQF Sbjct: 217 LTVIRDLAAEGRTMLLVTHEMKFAREVANHVVYLFEGRIEEQGPPSEVFGNPKSERLKQF 276 Query: 249 LS 250 LS Sbjct: 277 LS 278 Lambda K H 0.319 0.135 0.380 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: 233 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: 254 Length of database: 281 Length adjustment: 25 Effective length of query: 229 Effective length of database: 256 Effective search space: 58624 Effective search space used: 58624 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: 47 (22.7 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