Align Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate 7024900 Shewana3_2074 ABC transporter related (RefSeq)
Query= TCDB::Q9X051 (523 letters) >FitnessBrowser__ANA3:7024900 Length = 499 Score = 361 bits (926), Expect = e-104 Identities = 192/503 (38%), Positives = 326/503 (64%), Gaps = 15/503 (2%) Query: 11 VLLEARNITKTFPGVIAVNNVTLQIYKGEVCALVGENGAGKSTLMKILAGVYPDYEGQIF 70 ++LE + I+K +PGV A+ +V+L+++ GEV AL+GENGAGKSTL+K++ G G I Sbjct: 3 LILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDIL 62 Query: 71 LEGKEVRFRNPREAQENGIALIPQELDLVPNLSSAENIFLSREPVNEFGVIEYQKMFEQA 130 G+ F P +AQ+ GI+ + QE++LVPNL+ A+N+FL EP G+I ++KM+ A Sbjct: 63 FLGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEP-RRLGLIHFKKMYADA 121 Query: 131 SKLFSKLGVNIDPKTKVEDLSTSQQQMVAIAKALSLDAKIIIMDEPTSAIGKRETEQLFN 190 + ++ ++ID + D S + QQ++AIA+ +++ AK++++DEPT+++ +E + LF Sbjct: 122 RAVLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFG 181 Query: 191 IIRSLKNEGKSVIYISHRLEEIFEIADRVVVMRDGRKVGEGPIEEFDHDKLVRLMVGRSI 250 I+ LK +G ++++I+H L+++++I+DR+ V+R+G+ +GE E KL+ M+GRS+ Sbjct: 182 ILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSL 241 Query: 251 DQFFI----KERATITDEIFRVEGIKLWSLDRK-KLLVDDVSFYVRKGEVLGIYGLVGAG 305 + + KER T+T R E + L D K + ++ V KG+ +G+ GL+G+G Sbjct: 242 QEQLVDKQEKER-TVT----RAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSG 296 Query: 306 RTELLEAIFGAHPGRTEGKVFIGGKEIKIHSPRDAVKNGIGLVPEDRKTAGLILQMSVLH 365 R+E+ A+FG + G + + G+++ + P DA+ GI L PEDRK G+I +S+ Sbjct: 297 RSEVCNAVFGLDLVDS-GSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRE 355 Query: 366 NITLPSVVMKLIVRKFGLIDSQLEKEIVRSFIEKLNIKTPSPYQIVENLSGGNQQKVVLA 425 NI L ++ + + + + ++EI + FI+KL I TP + +E LSGGNQQKV+LA Sbjct: 356 NIIL---ALQARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILA 412 Query: 426 KWLAIKPKVLLLDEPTRGIDVNAKSEIYKLISEMAVSGMGVVMVSSELPEILAMSDRILV 485 +WLAI+P +L+LDEPTRGID+ A +EI KLI + GM +++ SSEL E++A S++++V Sbjct: 413 RWLAIEPILLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVV 472 Query: 486 MSEGRKTAEFLREEVTEEDLLKA 508 + + E E+T + +++A Sbjct: 473 LRDRYAVRELSGAELTSQHVMQA 495 Score = 96.7 bits (239), Expect = 2e-24 Identities = 66/243 (27%), Positives = 128/243 (52%), Gaps = 14/243 (5%) Query: 283 VDDVSFYVRKGEVLGIYGLVGAGRTELLEAIFGAHPGRTEGKVFIGGKEIKIHSPRDAVK 342 ++DVS + GEV + G GAG++ L++ + GA + G + G+ ++P DA K Sbjct: 20 LEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQ-SKDMGDILFLGEPQHFNTPMDAQK 78 Query: 343 NGIGLVPEDRKTAGLILQMSVLHNITLPSVVMKLIVRKFGLIDSQLEKEIVRSFIE--KL 400 GI V ++ L+ ++V N+ L R+ GLI + R+ + KL Sbjct: 79 AGISTVYQE---VNLVPNLTVAQNLFLGYEP-----RRLGLIHFKKMYADARAVLTQFKL 130 Query: 401 NIKTPSPYQIVENLSGGNQQKVVLAKWLAIKPKVLLLDEPTRGIDVNAKSEIYKLISEMA 460 +I +P + + S QQ + +A+ +A+ KVL+LDEPT +D ++ +++++ Sbjct: 131 DIDVSAP---LSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGILNQLK 187 Query: 461 VSGMGVVMVSSELPEILAMSDRILVMSEGRKTAEFLREEVTEEDLLKAAIPRSVKVETTQ 520 G+ +V ++ L ++ +SDRI V+ G+ E+L E+ + L++A + RS++ + Sbjct: 188 AKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSLQEQLVD 247 Query: 521 REE 523 ++E Sbjct: 248 KQE 250 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: 583 Number of extensions: 30 Number of successful extensions: 9 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: 499 Length adjustment: 35 Effective length of query: 488 Effective length of database: 464 Effective search space: 226432 Effective search space used: 226432 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