Align Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate Ac3H11_609 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)
Query= TCDB::Q9X051 (523 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_609 Length = 505 Score = 394 bits (1011), Expect = e-114 Identities = 224/512 (43%), Positives = 323/512 (63%), Gaps = 16/512 (3%) Query: 11 VLLEARNITKTFPGVIAVNNVTLQIYKGEVCALVGENGAGKSTLMKILAGVYP--DYEGQ 68 +LLE RNI KTFPGV+A+N V LQ+ GE+ A+VGENGAGKSTLMK+L+GVYP Y GQ Sbjct: 1 MLLEMRNIRKTFPGVVALNQVNLQVQAGEIHAIVGENGAGKSTLMKVLSGVYPHGSYSGQ 60 Query: 69 IFLEGKEVRFRNPREAQENGIALIPQELDLVPNLSSAENIFLSREPVNEFGVIEYQKMFE 128 I +G+E F R+++ GI +I QEL LVP LS AENIFL E GVI++ Sbjct: 61 ILFDGQEREFAGIRDSEHLGIIIIHQELALVPLLSIAENIFLGNETARH-GVIDWMAAHS 119 Query: 129 QASKLFSKLGVNIDPKTKVEDLSTSQQQMVAIAKALSLDAKIIIMDEPTSAIGKRETEQL 188 +A L K+G+ P T V L +QQ+V IAKALS +++I+DEPT+++ + +++ L Sbjct: 120 RAQALLHKVGLGESPDTPVGQLGVGKQQLVEIAKALSRKVRLLILDEPTASLNENDSQAL 179 Query: 189 FNIIRSLKNEGKSVIYISHRLEEIFEIADRVVVMRDGRKVG-----EGPIEEFDHDKLVR 243 +++ LK +G + I ISH+L EI +AD + V+RDG V EGP+ E D++++ Sbjct: 180 LDLLLELKAQGITCILISHKLNEISRVADAITVLRDGSTVQMLDCREGPVSE---DRVIQ 236 Query: 244 LMVGRSIDQFFIKERATITDEIFRVEGIKLWSLDRK-KLLVDDVSFYVRKGEVLGIYGLV 302 MVGR + + + + + + +F V + R + + + VR+GE++GI GL+ Sbjct: 237 AMVGREMSDRYPQRQPQVGEIVFEVRNWRAHHPQRSDREHLKGIDLNVRRGEIVGIAGLM 296 Query: 303 GAGRTELLEAIFGAHPG-RTEGKVFIGGKEIKIHSPRDAVKNGIGLVPEDRKTAGLILQM 361 GAGRTEL +IFG G R G+V + G+ I + + AV +G+ V EDRK GL+L Sbjct: 297 GAGRTELAMSIFGRSWGQRISGEVRLHGQPIDVSTVEKAVSHGLAYVTEDRKGNGLVLNE 356 Query: 362 SVLHNITLPSVVMKLIVRKFGLIDSQLEKEIVRSFIEKLNIKTPSPYQIVENLSGGNQQK 421 + N +L ++ V +IDS E + + + EKL I+ Q NLSGGNQQK Sbjct: 357 DIQFNTSLANLPG---VSFASVIDSGQEHRVAQDYREKLRIRCSGVDQKTLNLSGGNQQK 413 Query: 422 VVLAKWLAIKPKVLLLDEPTRGIDVNAKSEIYKLISEMAVSGMGVVMVSSELPEILAMSD 481 VVL+KWL P+VL+LDEPTRGIDV AK EIY LI+++A G V+++SSE+PE+L ++D Sbjct: 414 VVLSKWLFTSPEVLILDEPTRGIDVGAKYEIYTLIAQLAAEGKCVIVISSEMPELLGITD 473 Query: 482 RILVMSEGRKTAEFLREEVTEEDLLKAAIPRS 513 RI VM+EGR AE E ++E +++A + S Sbjct: 474 RIYVMNEGRFVAEMPTSEASQEKIMRAIVKAS 505 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: 619 Number of extensions: 36 Number of successful extensions: 10 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: 523 Length of database: 505 Length adjustment: 35 Effective length of query: 488 Effective length of database: 470 Effective search space: 229360 Effective search space used: 229360 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 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