Align ABC transporter related (characterized, see rationale)
to candidate GFF3101 Psest_3160 ABC-type polar amino acid transport system, ATPase component
Query= uniprot:B2TBJ9 (263 letters) >FitnessBrowser__psRCH2:GFF3101 Length = 255 Score = 234 bits (597), Expect = 1e-66 Identities = 127/253 (50%), Positives = 168/253 (66%), Gaps = 12/253 (4%) Query: 3 ATAPVALSVKNIHKSFGDHHVLKGISLDAHQGDVISILGASGSGKSTFLRCLNLLETPDD 62 A+ PV + ++ +HK FG HVLK I+L QG+ I + G SGSGKST +RCLN LE Sbjct: 11 ASGPV-IQMQGVHKWFGQFHVLKDINLSVRQGERIVLCGPSGSGKSTTIRCLNRLEEHQQ 69 Query: 63 GSVSLAGEELKMKRRGDGKLQPSDRRQVDRVRSQLGMVFQNFNLWSHMTVLENLIEGPMR 122 G + + G EL SD +Q++ +RS++GMVFQ+FNL+ H+TVL+N PM Sbjct: 70 GRIVINGVELT-----------SDLKQIEAIRSEVGMVFQHFNLFPHLTVLQNCTLAPMW 118 Query: 123 VQKRSRAESVEEAEALLAKVGLAEKRGHYPAHLSGGQQQRVAIARALAMHPKVMLFDEPT 182 V+K R ++ E A L +V + E+ +P LSGGQQQRVAIARAL M PK+MLFDEPT Sbjct: 119 VRKLPRRQAEEIAMHYLERVRIPEQANKFPGQLSGGQQQRVAIARALCMKPKIMLFDEPT 178 Query: 183 SALDPELVGEVLRVMRSLAEEGRTMLVVTHEMGFARHVSNRVMFLHQGQVEADGTPDEVF 242 SALDPE+V EVL M SLAE G TML VTHEMGFAR V++RV+F+ +G++ P+ F Sbjct: 179 SALDPEMVKEVLDTMVSLAESGMTMLCVTHEMGFARTVADRVIFMDKGEIVEQAEPEMFF 238 Query: 243 VECKSDRFRQFVS 255 +DR + F+S Sbjct: 239 TNPVNDRTKLFLS 251 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: 177 Number of extensions: 4 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: 263 Length of database: 255 Length adjustment: 24 Effective length of query: 239 Effective length of database: 231 Effective search space: 55209 Effective search space used: 55209 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