Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate PP_3817 PP_3817 Polyamine ABC transporter, ATP-binding protein
Query= reanno::Smeli:SMc04256 (361 letters) >FitnessBrowser__Putida:PP_3817 Length = 382 Score = 217 bits (553), Expect = 4e-61 Identities = 138/375 (36%), Positives = 202/375 (53%), Gaps = 27/375 (7%) Query: 2 TSVSVRDLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQIF 61 T VS+R L+ ++G T +D L+L+I GEFL LGSSG GKST L+ +AG S G+I Sbjct: 13 TLVSLRGLNKHYGDFTAVDNLDLEIQDGEFLTFLGSSGSGKSTTLSMLAGFETPSSGEIL 72 Query: 62 IKDRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEIL 121 + +++ P R IGMVFQ Y+L+P + V N++F L + K+ AE KRV +++ Sbjct: 73 VDGQSLVNVPPHKRDIGMVFQRYSLFPHLNVRDNIAFPLAIRKLGAAETAKRVDAMLKLV 132 Query: 122 QIQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLHQ 181 Q++ RKPS++SGGQ+QRVAI RALV + + L DEPL LD KLR +L+ E+++LH+ Sbjct: 133 QLEQFAHRKPSQMSGGQQQRVAIARALVYEPRILLMDEPLGALDKKLREDLQDELRQLHR 192 Query: 182 SLKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMNF 241 L T++YVTHDQ EA+ L+ RIA+ G I L +Y P N FVA F+G + NF Sbjct: 193 RLGITIVYVTHDQEEAMRLSQRIAIFSHGKIVGLGTGYDLYQNPPNAFVASFLG--NSNF 250 Query: 242 FRGEVEPKDGRSFVRAGGIAFDVTAYPAHTRLQPG----QKVVLGLRPEHVKVDEARDG- 296 R + SF P RL PG Q ++ +RPE A Sbjct: 251 LRIKASSNGAGSF----------EGQPVAIRLTPGLAASQDALIMVRPEKAVAMSAEQAM 300 Query: 297 -EPTHQAVVDIEEPMGADNLLW-------LTFAGQSMSVRIAGQRRYP--PGSTVRLSFD 346 EP ++ +G L +T G ++V+ P PG +V++ + Sbjct: 301 REPLPAGWNEVTAKVGEVLFLGESQTCHVVTAGGTELTVKALSAAGMPMQPGDSVKVRWA 360 Query: 347 MGVASIFDAESENRL 361 + A I+ +E+ L Sbjct: 361 VADACIYTEWAESDL 375 Lambda K H 0.320 0.137 0.392 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: 333 Number of extensions: 11 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: 361 Length of database: 382 Length adjustment: 30 Effective length of query: 331 Effective length of database: 352 Effective search space: 116512 Effective search space used: 116512 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 (21.8 bits) S2: 49 (23.5 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