Align Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate GFF2651 PGA1_c26910 ABC transporter, ATP-binding protein
Query= TCDB::Q9X051 (523 letters) >FitnessBrowser__Phaeo:GFF2651 Length = 522 Score = 263 bits (673), Expect = 9e-75 Identities = 165/504 (32%), Positives = 266/504 (52%), Gaps = 26/504 (5%) Query: 12 LLEARNITKTFPGVIAVNNVTLQIYKGEVCALVGENGAGKSTLMKILAGVYPDYEGQIFL 71 +L +NITK F V A ++V+ ++ GEV AL+GENGAGK+TLM IL G Y G + L Sbjct: 15 VLRLQNITKRFGSVTANDDVSFDLFPGEVIALLGENGAGKTTLMNILFGQYMADTGGVEL 74 Query: 72 EGKEVRFRNPREAQENGIALIPQELDLVPNLSSAENIFLSREPVNEFGVIEYQKMFEQAS 131 G + PR A + G+ ++ Q L NL+ ENI L EP+ G + + Sbjct: 75 FGAPLPPGAPRAALDGGVGMVHQHFTLADNLTVWENITLGVEPLLGLG-LRAGPAKARIR 133 Query: 132 KLFSKLGVNIDPKTKVEDLSTSQQQMVAIAKALSLDAKIIIMDEPTSAIGKRETEQLFNI 191 L + + +DP KV L+ ++Q V I KAL DA+I+I+DEPT+ + +E++ LF Sbjct: 134 ALAEQFHLKVDPNAKVSRLTVGERQRVEILKALYRDARILILDEPTAVLTPQESDALFAT 193 Query: 192 IRSLKNEGKSVIYISHRLEEIFEIADRVVVMRDGRKVGEGPIEEFDHDKLVRLMVGRSI- 250 +R N G SVI+ISH+L E+ I+DRV+V+R G+ V E + D D L LMVG + Sbjct: 194 LREAINRGLSVIFISHKLHEVMAISDRVLVLRHGKLVAERQTADTDSDALAALMVGADVV 253 Query: 251 ---------DQFFIKERATITDEIFRVEGIKLWSLDRKKLLVDDVSFYVRKGEVLGIYGL 301 ++ R T G++ SLD + G++ G+ G+ Sbjct: 254 PAKFAANTPGPALLQLRDVTTPSAGASPGLRHVSLD------------LAAGQITGLAGV 301 Query: 302 VGAGRTELLEAIFGAHPGRTEGKVFIGGKEIKIHSPRDAVKNGIGLVPEDRKTAGLILQM 361 G G+ L + + G ++ G + + G SPR+A+ GI +PEDR G I Sbjct: 302 SGNGQAALSDLVSGLITPQS-GSLTLNGAAPAGWSPREAITAGIARIPEDRHKTGTIADF 360 Query: 362 SVLHNITLPSVVMKLIVRKFGLIDSQLEKEIVRSFIEKLNIKTPSPYQIVENLSGGNQQK 421 + N L + + R G +D + ++ ++ I +++ P P + LSGGN QK Sbjct: 361 DLTENAILETYATRFSHR--GWLDWRAARDFAKTVITGYDVRCPGPDTRIRLLSGGNMQK 418 Query: 422 VVLAKWLAIKPKVLLLDEPTRGIDVNAKSEIYKLISEMAVSGMGVVMVSSELPEILAMSD 481 ++L + L P+++L ++P RG+D+ A + +++ +++ G V+++S +L EI+ +SD Sbjct: 419 LILGRVLEQSPQIILANQPVRGLDIGAVTYVHEQLAKACARGAAVLLISEDLDEIMQLSD 478 Query: 482 RILVMSEGRKTAEFLREEVTEEDL 505 I V+SEGR + F R E+L Sbjct: 479 VIHVISEGRLSPGFARGSKQPEEL 502 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: 548 Number of extensions: 27 Number of successful extensions: 8 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: 522 Length adjustment: 35 Effective length of query: 488 Effective length of database: 487 Effective search space: 237656 Effective search space used: 237656 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