Align Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate WP_068005521.1 PsAD2_RS10155 ABC transporter ATP-binding protein
Query= TCDB::Q9X051 (523 letters) >NCBI__GCF_001623255.1:WP_068005521.1 Length = 515 Score = 282 bits (721), Expect = 2e-80 Identities = 167/499 (33%), Positives = 285/499 (57%), Gaps = 13/499 (2%) Query: 12 LLEARNITKTFPGVIAVNNVTLQIYKGEVCALVGENGAGKSTLMKILAGVYPDYEGQIFL 71 LL +NITK F ++A NV L ++ GE+ AL+GENGAGK+TLM IL G Y EG++ + Sbjct: 10 LLSLQNITKIFGDLVANGNVNLDLHAGEIVALLGENGAGKTTLMNILFGHYVADEGRVMV 69 Query: 72 EGK-----EVRFRNPREAQENGIALIPQELDLVPNLSSAENIFLSREPVNEFGVIEYQKM 126 ++ P+ A E GI ++ Q L NL+ ENI L E + K Sbjct: 70 RTSSGTLVDLEPGAPQAALEAGIGMVHQHFTLAENLTGLENIVLGTESLFA-RKFSRSKA 128 Query: 127 FEQASKLFSKLGVNIDPKTKVEDLSTSQQQMVAIAKALSLDAKIIIMDEPTSAIGKRETE 186 + +L G+ +D +V L+ ++Q V I KAL DA+I+++DEPT+ + +E++ Sbjct: 129 RAKLQELMQSSGLEVDLDLRVSKLAVGERQRVEILKALYRDARILVLDEPTAVLTPQESD 188 Query: 187 QLFNIIRSLKNEGKSVIYISHRLEEIFEIADRVVVMRDGRKVGEGPIEEFDHDKLVRLMV 246 LFN ++ L +G ++I+ISH++ E+ +DRV V+R GR V + P + D KL LMV Sbjct: 189 SLFNTLKLLAAKGMAIIFISHKMAEVLGASDRVAVLRGGRIVADLPTSQCDRHKLAELMV 248 Query: 247 GRSIDQFFIKERATITDEIFRVEGIKLWSLDRKKLLVDDVSFYVRKGEVLGIYGLVGAGR 306 G ++ Q +E +EI +G+ S + L+++V+ +RKGE++G+ G+ G G+ Sbjct: 249 GHAV-QMAEREPGNPGEEILVFKGV---SAGEGRELIENVNLSLRKGEIIGLAGVSGNGQ 304 Query: 307 TELLEAIFGAHPGRTEGKVFIGGKEIKIHSPRDAVKNGIGLVPEDRKTAGLILQMSVLHN 366 + L + + G T G V +G + +K ++ A+++G+ +PEDR G++ MSV N Sbjct: 305 SMLAKVLSGLEE-PTAGAVTLGSQPLKANAAA-AIQSGVARIPEDRHHDGIVGAMSVEEN 362 Query: 367 ITLPSVVMKLIVRKFGLIDSQLEKEIVRSFIEKLNIKTPSPYQIVENLSGGNQQKVVLAK 426 + L + K ++FGL+ ++ + I+ +I+ P + LSGGN QK+VLA+ Sbjct: 363 LVLEE-IRKPAYQRFGLLRFNEIRKRAQEAIKAYDIRCSGPLAVSRLLSGGNIQKIVLAR 421 Query: 427 WLAIKPKVLLLDEPTRGIDVNAKSEIYKLISEMAVSGMGVVMVSSELPEILAMSDRILVM 486 L +P ++L +P+RG+DV A +++++ + E G GV+++S +L E+ +SDRI V+ Sbjct: 422 TLDQEPAIVLAAQPSRGLDVGATADVHRRLQEARDRGAGVLLISEDLDELFQLSDRIAVI 481 Query: 487 SEGRKTAEFLREEVTEEDL 505 G + EE+ ++ + Sbjct: 482 HRGHVSEPMASEELDKKQV 500 Score = 89.0 bits (219), Expect = 4e-22 Identities = 59/229 (25%), Positives = 115/229 (50%), Gaps = 8/229 (3%) Query: 28 VNNVTLQIYKGEVCALVGENGAGKSTLMKILAGVYPDYEGQIFLEGKEVRFRNPREAQEN 87 + NV L + KGE+ L G +G G+S L K+L+G+ G + L + ++ N A ++ Sbjct: 281 IENVNLSLRKGEIIGLAGVSGNGQSMLAKVLSGLEEPTAGAVTLGSQPLK-ANAAAAIQS 339 Query: 88 GIALIPQELD---LVPNLSSAENIFLS--REPVNE-FGVIEYQKMFEQASKLFSKLGVNI 141 G+A IP++ +V +S EN+ L R+P + FG++ + ++ ++A + + Sbjct: 340 GVARIPEDRHHDGIVGAMSVEENLVLEEIRKPAYQRFGLLRFNEIRKRAQEAIKAYDIRC 399 Query: 142 DPKTKVEDL-STSQQQMVAIAKALSLDAKIIIMDEPTSAIGKRETEQLFNIIRSLKNEGK 200 V L S Q + +A+ L + I++ +P+ + T + ++ ++ G Sbjct: 400 SGPLAVSRLLSGGNIQKIVLARTLDQEPAIVLAAQPSRGLDVGATADVHRRLQEARDRGA 459 Query: 201 SVIYISHRLEEIFEIADRVVVMRDGRKVGEGPIEEFDHDKLVRLMVGRS 249 V+ IS L+E+F+++DR+ V+ G EE D ++ +M G S Sbjct: 460 GVLLISEDLDELFQLSDRIAVIHRGHVSEPMASEELDKKQVGLMMAGHS 508 Score = 80.5 bits (197), Expect = 1e-19 Identities = 60/238 (25%), Positives = 121/238 (50%), Gaps = 17/238 (7%) Query: 285 DVSFYVRKGEVLGIYGLVGAGRTELLEAIFGAHPGRTEGKVFIGGK-----EIKIHSPRD 339 +V+ + GE++ + G GAG+T L+ +FG H EG+V + +++ +P+ Sbjct: 28 NVNLDLHAGEIVALLGENGAGKTTLMNILFG-HYVADEGRVMVRTSSGTLVDLEPGAPQA 86 Query: 340 AVKNGIGLVPEDRKTAGLILQMSVLHNITLPSVVMKLIVRKFGLIDSQLE-KEIVRSFIE 398 A++ GIG+V + A ++ L NI L + L RKF ++ + +E+++S Sbjct: 87 ALEAGIGMVHQHFTLAE---NLTGLENIVLGTE--SLFARKFSRSKARAKLQELMQSSGL 141 Query: 399 KLNIKTPSPYQIVENLSGGNQQKVVLAKWLAIKPKVLLLDEPTRGIDVNAKSEIYKLISE 458 ++++ V L+ G +Q+V + K L ++L+LDEPT + ++ + Sbjct: 142 EVDLDLR-----VSKLAVGERQRVEILKALYRDARILVLDEPTAVLTPQESDSLFNTLKL 196 Query: 459 MAVSGMGVVMVSSELPEILAMSDRILVMSEGRKTAEFLREEVTEEDLLKAAIPRSVKV 516 +A GM ++ +S ++ E+L SDR+ V+ GR A+ + L + + +V++ Sbjct: 197 LAAKGMAIIFISHKMAEVLGASDRVAVLRGGRIVADLPTSQCDRHKLAELMVGHAVQM 254 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: 595 Number of extensions: 31 Number of successful extensions: 10 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 523 Length of database: 515 Length adjustment: 35 Effective length of query: 488 Effective length of database: 480 Effective search space: 234240 Effective search space used: 234240 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: 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