Align ABC transporter for D-Alanine, ATPase component (characterized)
to candidate GFF3101 Psest_3160 ABC-type polar amino acid transport system, ATPase component
Query= reanno::pseudo6_N2E2:Pf6N2E2_5405 (254 letters) >FitnessBrowser__psRCH2:GFF3101 Length = 255 Score = 448 bits (1153), Expect = e-131 Identities = 221/255 (86%), Positives = 239/255 (93%), Gaps = 1/255 (0%) Query: 1 MSEAIKQPVSPEG-IIQMQGVNKWYGQFHVLKDINLNVKQGERIVLCGPSGSGKSTTIRC 59 MS++ Q G +IQMQGV+KW+GQFHVLKDINL+V+QGERIVLCGPSGSGKSTTIRC Sbjct: 1 MSDSNAQVEQASGPVIQMQGVHKWFGQFHVLKDINLSVRQGERIVLCGPSGSGKSTTIRC 60 Query: 60 LNRLEEHQQGRIVVDGVELTNDLKQIEAIRREVGMVFQHFNLFPHLTILQNCTLAPMWVR 119 LNRLEEHQQGRIV++GVELT+DLKQIEAIR EVGMVFQHFNLFPHLT+LQNCTLAPMWVR Sbjct: 61 LNRLEEHQQGRIVINGVELTSDLKQIEAIRSEVGMVFQHFNLFPHLTVLQNCTLAPMWVR 120 Query: 120 KMPKRKAEEIAMHYLERVRIPEQAHKYPGQLSGGQQQRVAIARALCMKPKIMLFDEPTSA 179 K+P+R+AEEIAMHYLERVRIPEQA+K+PGQLSGGQQQRVAIARALCMKPKIMLFDEPTSA Sbjct: 121 KLPRRQAEEIAMHYLERVRIPEQANKFPGQLSGGQQQRVAIARALCMKPKIMLFDEPTSA 180 Query: 180 LDPEMVKEVLDTMIGLAEDGMTMLCVTHEMGFARTVANRVIFMDKGEIVEQAAPNDFFDN 239 LDPEMVKEVLDTM+ LAE GMTMLCVTHEMGFARTVA+RVIFMDKGEIVEQA P FF N Sbjct: 181 LDPEMVKEVLDTMVSLAESGMTMLCVTHEMGFARTVADRVIFMDKGEIVEQAEPEMFFTN 240 Query: 240 PQNDRTKLFLSQILH 254 P NDRTKLFLSQILH Sbjct: 241 PVNDRTKLFLSQILH 255 Lambda K H 0.322 0.137 0.407 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: 310 Number of extensions: 7 Number of successful extensions: 1 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: 255 Length adjustment: 24 Effective length of query: 230 Effective length of database: 231 Effective search space: 53130 Effective search space used: 53130 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 (21.9 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