Align Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate WP_046008336.1 OLEAN_RS05080 ABC transporter ATP-binding protein
Query= TCDB::Q9X051 (523 letters) >NCBI__GCF_000967895.1:WP_046008336.1 Length = 303 Score = 102 bits (255), Expect = 1e-26 Identities = 70/215 (32%), Positives = 118/215 (54%), Gaps = 11/215 (5%) Query: 12 LLEARNITKTFPGVIAVNNVTLQIYKGEVCALVGENGAGKSTLMKILAGVYPDYEGQIFL 71 L+E +N+TK + A+NN++ +I G+ ALVG NGAGKSTL ILAG P G+ + Sbjct: 4 LIECQNLTKAYGNKKALNNISFEIQSGQPIALVGPNGAGKSTLFGILAGYIPATSGEAKI 63 Query: 72 EGKEVRFRNPREAQENGIALIPQELDLVPNLSSAENI-FLSREPVNEFGVIEYQKMFEQA 130 G V +P I +PQ+ PNL+ + + FL+R + FG K F++A Sbjct: 64 LGHNV--GSPELI--GRIGALPQDALFNPNLTIQQQLSFLAR--LQGFG---RSKAFKEA 114 Query: 131 SKLFSKLGVNIDPKTKVEDLSTSQQQMVAIAKALSLDAKIIIMDEPTSAIGKRETEQLFN 190 +++ + + K K+ LS ++ VAIA+AL + +++++DEPT+ + + Sbjct: 115 ARVLELMQLADTAKEKITALSHGMKKRVAIAQALMGEPELVLLDEPTAGLDPENARNIRQ 174 Query: 191 IIRSLKNEGKSVIYISHRLEEIFEIADRVVVMRDG 225 + +L +E VI SH LEE+ + ++V+ + G Sbjct: 175 QVMALSDETTFVI-SSHNLEELERLCEQVLYLDQG 208 Score = 62.4 bits (150), Expect = 2e-14 Identities = 63/241 (26%), Positives = 115/241 (47%), Gaps = 22/241 (9%) Query: 280 KLLVDDVSFYVRKGEVLGIYGLVGAGRTELLEAIFGAHPGRTEGKVFIGGKEIKIHSPRD 339 K ++++SF ++ G+ + + G GAG++ L + G P T G+ I G + SP Sbjct: 17 KKALNNISFEIQSGQPIALVGPNGAGKSTLFGILAGYIPA-TSGEAKILGHNVG--SPE- 72 Query: 340 AVKNGIGLVPEDRK-TAGLILQMSVLHNITLPSVVMKLIVRKFGLIDSQLEKEIVRSFIE 398 + IG +P+D L +Q + + R G S+ KE R +E Sbjct: 73 -LIGRIGALPQDALFNPNLTIQQQ-----------LSFLARLQGFGRSKAFKEAAR-VLE 119 Query: 399 KLNIKTPSPYQIVENLSGGNQQKVVLAKWLAIKPKVLLLDEPTRGIDVNAKSEIYKLISE 458 + + + +I LS G +++V +A+ L +P+++LLDEPT G+D I + + Sbjct: 120 LMQLADTAKEKITA-LSHGMKKRVAIAQALMGEPELVLLDEPTAGLDPENARNIRQQV-- 176 Query: 459 MAVSGMGVVMVSS-ELPEILAMSDRILVMSEGRKTAEFLREEVTEEDLLKAAIPRSVKVE 517 MA+S ++SS L E+ + +++L + +G A+ + + TE+ L R V Sbjct: 177 MALSDETTFVISSHNLEELERLCEQVLYLDQGELKAQHIIGQQTEQQTLSYLTVRLVVKN 236 Query: 518 T 518 T Sbjct: 237 T 237 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: 314 Number of extensions: 21 Number of successful extensions: 4 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: 303 Length adjustment: 31 Effective length of query: 492 Effective length of database: 272 Effective search space: 133824 Effective search space used: 133824 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: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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