Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_078717009.1 B5D49_RS06865 spermidine/putrescine ABC transporter ATP-binding protein PotA
Query= uniprot:D8IZC7 (521 letters) >NCBI__GCF_900167125.1:WP_078717009.1 Length = 370 Score = 125 bits (315), Expect = 2e-33 Identities = 79/242 (32%), Positives = 133/242 (54%), Gaps = 9/242 (3%) Query: 6 LLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILL 65 ++++ + K F L D+ L IR GE ++G +G GK+TL+++L+G +P GEI+L Sbjct: 7 VIRLEHVAKEFDGETVLHDVCLDIRHGEFLTILGPSGCGKTTLLRLLAGFESPSSGEIIL 66 Query: 66 DGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRTD 125 DGR + P R +N ++Q A+ P++SV NV G R+ I + R Sbjct: 67 DGRSMRDVPPDGRR---VNTVFQSYALFPHMSVFDNVAFG----LRMSGIPKVEIGERVA 119 Query: 126 AVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNV 185 LR +G A LS +QQ+V IARA+V+R ++++DEP +AL + Q+ Sbjct: 120 KALRMVGLAGQAGRRPTSLSGGQQQRVAIARAVVNRPLVLLLDEPLSALDYKLRVQMRTE 179 Query: 186 VRRLRDE-GLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRSL 244 +++LR E G+ I+++H E ++++DRV V+ +G V ++ E+ V M V R + Sbjct: 180 LKQLRREMGITFIFVTHDQEEAFSMSDRVVVMNEGC-VAQVGTPVEVYEQPVNMFVARFV 238 Query: 245 SE 246 E Sbjct: 239 GE 240 Score = 82.0 bits (201), Expect = 3e-20 Identities = 61/203 (30%), Positives = 97/203 (47%), Gaps = 19/203 (9%) Query: 281 DVRAGEVLGFAGLVGAGRTELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVP 340 D+R GE L G G G+T L RLL G + S G+I+L+GR + D P R + Sbjct: 29 DIRHGEFLTILGPSGCGKTTLLRLLAGFESPSSGEIILDGRSMR-DVPPDGRRVNTVF-- 85 Query: 341 EDRKGQGLFLQMAVAANATMNVASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVG 400 + LF M+V N + R+ + +G A++ + + P Sbjct: 86 ---QSYALFPHMSVFDNVAFGL-----RMSGIPKVEIGERVAKALRMVGLAGQAGRRPT- 136 Query: 401 KLSGGNQQKVLLARWLEIAPKVLILDEPTRGVD----IYAKSEIYQLVHRLASQGVAVVV 456 LSGG QQ+V +AR + P VL+LDEP +D + ++E+ QL + G+ + Sbjct: 137 SLSGGQQQRVAIARAVVNRPLVLLLDEPLSALDYKLRVQMRTELKQLRREM---GITFIF 193 Query: 457 ISSELPEVIGICDRVLVMREGMI 479 ++ + E + DRV+VM EG + Sbjct: 194 VTHDQEEAFSMSDRVVVMNEGCV 216 Lambda K H 0.320 0.135 0.378 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: 454 Number of extensions: 25 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 521 Length of database: 370 Length adjustment: 32 Effective length of query: 489 Effective length of database: 338 Effective search space: 165282 Effective search space used: 165282 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: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. 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