Align ABC transporter for D-Alanine, ATPase component (characterized)
to candidate Ga0059261_3653 Ga0059261_3653 phosphate ABC transporter ATP-binding protein, PhoT family (TC 3.A.1.7.1)
Query= reanno::pseudo6_N2E2:Pf6N2E2_5405 (254 letters) >FitnessBrowser__Korea:Ga0059261_3653 Length = 276 Score = 125 bits (315), Expect = 7e-34 Identities = 79/244 (32%), Positives = 129/244 (52%), Gaps = 14/244 (5%) Query: 18 QGVNKWYGQFHVLKDINLNVKQGERIVLCGPSGSGKSTTIRCLNRLEE-----HQQGRIV 72 +GVN +YG+ ++D++++V GPSG GKST +R LNR+ + +G I Sbjct: 32 RGVNVFYGEKQAIRDVSIDVDMENVTAFIGPSGCGKSTFLRTLNRMNDTVASARVEGEIT 91 Query: 73 VDGVELTNDLKQIEAIRREVGMVFQHFNLFPHLTILQNCTLAPMWVRKMPKRKAE--EIA 130 +DG + + + +R VGMVFQ N FP +I +N P + + + K + +I Sbjct: 92 LDGENIYDKSMDVVQLRARVGMVFQKPNPFPK-SIYENVAYGPR-IHGLARAKGDMDQIV 149 Query: 131 MHYLERV----RIPEQAHKYPGQLSGGQQQRVAIARALCMKPKIMLFDEPTSALDPEMVK 186 L+R + ++ + LSGGQQQR+ IARA+ + P+++L DEP SALDP + Sbjct: 150 ERSLKRAGLWEEVKDRLNDSGTALSGGQQQRLCIARAIAVDPEVILMDEPCSALDP-IAT 208 Query: 187 EVLDTMIGLAEDGMTMLCVTHEMGFARTVANRVIFMDKGEIVEQAAPNDFFDNPQNDRTK 246 ++ +I ++ VTH M A V+ R F G +VE + F P+ +RTK Sbjct: 209 AKIEELIHELRGRYAIVIVTHNMQQAARVSQRTAFFHLGTLVEYGETDQIFTAPRQERTK 268 Query: 247 LFLS 250 +++ Sbjct: 269 DYIT 272 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: 152 Number of extensions: 9 Number of successful extensions: 4 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: 276 Length adjustment: 25 Effective length of query: 229 Effective length of database: 251 Effective search space: 57479 Effective search space used: 57479 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