Align Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate 5208462 Shew_0974 spermidine/putrescine ABC transporter ATPase subunit (RefSeq)
Query= TCDB::Q9X051 (523 letters) >FitnessBrowser__PV4:5208462 Length = 378 Score = 121 bits (303), Expect = 5e-32 Identities = 87/271 (32%), Positives = 149/271 (54%), Gaps = 21/271 (7%) Query: 5 TEKEREVLLEARNITKTFPGVIAVNNVTLQIYKGEVCALVGENGAGKSTLMKILAGVYPD 64 T+ + EVLL+ ++K F V AV++V+L I +GE+ AL+G +G+GKSTL+++LAG Sbjct: 13 TKTQGEVLLKIERVSKLFDDVRAVDDVSLNINRGEIFALLGGSGSGKSTLLRMLAGFEKP 72 Query: 65 YEGQIFLEGKEVRFRNPREAQENGIALIPQELDLVPNLSSAENIFLSREPVNEFGVIEYQ 124 EG+I+L+G+++ P E I ++ Q L P+++ A+NI FG ++ Sbjct: 73 TEGRIYLDGQDITDMPP---YERPINMMFQSYALFPHMTVAQNI--------AFG-LKQD 120 Query: 125 KM----FEQASKLFSKLGVNIDP--KTKVEDLSTSQQQMVAIAKALSLDAKIIIMDEPTS 178 KM EQ K KL V+++P K K LS Q+Q VA+A++L+ K++++DEP Sbjct: 121 KMPKAEIEQRVKEMLKL-VHMEPYAKRKPNQLSGGQRQRVALARSLAKRPKLLLLDEPMG 179 Query: 179 AIGKR-ETEQLFNIIRSLKNEGKSVIYISHRLEEIFEIADRVVVMRDGRKVGEGPIEEFD 237 A+ K+ T+ ++ L+ G + + ++H EE +A+R+ +M DG G + Sbjct: 180 ALDKKLRTQMQLEVVDILEAVGVTCVMVTHDQEEAMTMAERIAIMNDGWIAQTGSPMDI- 238 Query: 238 HDKLVRLMVGRSIDQFFIKERATITDEIFRV 268 ++ MV I + E + DE+ V Sbjct: 239 YESPANRMVAEFIGSVNLFEGDIVEDEVDHV 269 Score = 88.6 bits (218), Expect = 4e-22 Identities = 64/211 (30%), Positives = 111/211 (52%), Gaps = 23/211 (10%) Query: 283 VDDVSFYVRKGEVLGIYGLVGAGRTELLEAIFGAHPGRTEGKVFIGGKEIKIHSPRDAVK 342 VDDVS + +GE+ + G G+G++ LL + G TEG++++ G++I P + Sbjct: 36 VDDVSLNINRGEIFALLGGSGSGKSTLLRMLAGFEKP-TEGRIYLDGQDITDMPPYERPI 94 Query: 343 NGIGLVPEDRKTAGLILQMSVLHNITLPSVVMKLIVRKFGLIDSQLEK-EIVRSFIEKLN 401 N + ++ L M+V NI FGL ++ K EI + E L Sbjct: 95 NMMF------QSYALFPHMTVAQNIA------------FGLKQDKMPKAEIEQRVKEMLK 136 Query: 402 IKTPSPY--QIVENLSGGNQQKVVLAKWLAIKPKVLLLDEPTRGIDVNAKSEI-YKLISE 458 + PY + LSGG +Q+V LA+ LA +PK+LLLDEP +D ++++ +++ Sbjct: 137 LVHMEPYAKRKPNQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRTQMQLEVVDI 196 Query: 459 MAVSGMGVVMVSSELPEILAMSDRILVMSEG 489 + G+ VMV+ + E + M++RI +M++G Sbjct: 197 LEAVGVTCVMVTHDQEEAMTMAERIAIMNDG 227 Lambda K H 0.317 0.137 0.372 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: 406 Number of extensions: 22 Number of successful extensions: 5 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: 523 Length of database: 378 Length adjustment: 32 Effective length of query: 491 Effective length of database: 346 Effective search space: 169886 Effective search space used: 169886 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 51 (24.3 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