Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_012385743.1 BIND_RS14235 sugar ABC transporter ATP-binding protein
Query= uniprot:D8IZC7 (521 letters) >NCBI__GCF_000019845.1:WP_012385743.1 Length = 511 Score = 398 bits (1023), Expect = e-115 Identities = 208/495 (42%), Positives = 314/495 (63%), Gaps = 7/495 (1%) Query: 6 LLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILL 65 LL IRK F LAL + L +R +HALMGENGAGKSTLMK+++G++ PD G I L Sbjct: 21 LLTAENIRKEFPGVLALDGVELKLRRSSVHALMGENGAGKSTLMKIIAGIYKPDAGRIRL 80 Query: 66 DGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRTD 125 G ++ + P + +GI++I+QEL + ++VA N+++ E R G +DH MR T Sbjct: 81 KGNEISFQSPLDALESGISMIHQELNLMDYMTVAENIWIRREPLNRFGFVDHDEMRRMTQ 140 Query: 126 AVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNV 185 A+ R+L LS+A +Q VEIA+A+ + S ++IMDEPT+AL+ERE + LF + Sbjct: 141 ALFRRLRIDLDPDAEVRDLSVANRQIVEIAKAVSYGSDVLIMDEPTSALTEREVDHLFEI 200 Query: 186 VRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRSLS 245 +R LR +G+ I+YI+H+M E++ +AD ++ RDG ++ ++ + I++MMVGR L+ Sbjct: 201 IRDLRAQGIGIVYITHKMNELFEIADEFSIFRDGRYISTHAACDVTCDDIIRMMVGRELT 260 Query: 246 EFYQHQRIAPADAAQLPTVMQVRALA-GGKIRPASFDVRAGEVLGFAGLVGAGRTELARL 304 + + + + D A + V+ + G + +FD+RAGE+LG AGL+G+GR+ LA Sbjct: 261 QMFPKEEVPIGDVA-----LSVKNVGLDGVFQGVNFDLRAGEILGIAGLIGSGRSSLAAT 315 Query: 305 LFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNV-A 363 LFG P + G I + G V ID P AMR +A++ EDRK G L +++ N + V Sbjct: 316 LFGVTPATSGSIAIAGNDVVIDSPATAMRHQMAFLTEDRKVSGCLLSLSILENLQLAVLQ 375 Query: 364 SRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKVL 423 ++ G V + L ++L VK + + +G LSGGNQQKVL+ RWL P++L Sbjct: 376 DKYVTNGFVHEKELFSACDEMARKLRVKTPNLQEIIGNLSGGNQQKVLIGRWLLNKPRIL 435 Query: 424 ILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITGEL 483 ILDEPTRG+D+ AK+EI++LV LA +GVA+++ISSE+PEV+G+ DR++VM EG +TG L Sbjct: 436 ILDEPTRGIDVGAKAEIHRLVTELAREGVAIILISSEMPEVLGMSDRIMVMHEGRMTGIL 495 Query: 484 AGAAITQENIMRLAT 498 + TQ IM LA+ Sbjct: 496 DRSEATQVKIMELAS 510 Score = 83.2 bits (204), Expect = 2e-20 Identities = 57/226 (25%), Positives = 107/226 (47%), Gaps = 5/226 (2%) Query: 282 VRAGEVLGFAGLVGAGRTELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPE 341 +R V G GAG++ L +++ G G I L+G + P A+ +GI+ + + Sbjct: 44 LRRSSVHALMGENGAGKSTLMKIIAGIYKPDAGRIRLKGNEISFQSPLDALESGISMIHQ 103 Query: 342 DRKGQGLFLQMAVAANATMNVASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGK 401 + L M VA N + + R G V + + +A +RL + + P+ V Sbjct: 104 ELN---LMDYMTVAENIWIRREPLN-RFGFVDHDEMRRMTQALFRRLRIDL-DPDAEVRD 158 Query: 402 LSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSEL 461 LS N+Q V +A+ + VLI+DEPT + +++++ L +QG+ +V I+ ++ Sbjct: 159 LSVANRQIVEIAKAVSYGSDVLIMDEPTSALTEREVDHLFEIIRDLRAQGIGIVYITHKM 218 Query: 462 PEVIGICDRVLVMREGMITGELAGAAITQENIMRLATDTNVPRTAP 507 E+ I D + R+G A +T ++I+R+ + + P Sbjct: 219 NELFEIADEFSIFRDGRYISTHAACDVTCDDIIRMMVGRELTQMFP 264 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: 669 Number of extensions: 28 Number of successful extensions: 7 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: 511 Length adjustment: 35 Effective length of query: 486 Effective length of database: 476 Effective search space: 231336 Effective search space used: 231336 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: 52 (24.6 bits)
This GapMind analysis is from Sep 24 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