Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate 16017 b1900 fused L-arabinose transporter subunits of ABC superfamily: ATP-binding components (NCBI)
Query= uniprot:D8IZC7 (521 letters) >FitnessBrowser__Keio:16017 Length = 504 Score = 374 bits (959), Expect = e-108 Identities = 205/497 (41%), Positives = 304/497 (61%), Gaps = 9/497 (1%) Query: 4 TPLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEI 63 TP L RGI K+F AL+D+ G++HALMGENGAGKSTL+K+LSG +AP G + Sbjct: 5 TPYLSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSV 64 Query: 64 LLDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSR 123 +++G+ ++ D A+ AG+ +IYQEL + P ++VA N+++G +L + G+++ + + Sbjct: 65 VINGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLG-QLPHKGGIVNRSLLNYE 123 Query: 124 TDAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLF 183 L+ LG LSI + Q VEIA+AL ++I+ DEPT++LS RE + LF Sbjct: 124 AGLQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLF 183 Query: 184 NVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELV-RDEIDSERIVQMMVGR 242 V+R LR EG I+Y+SHRM E++AL+D +TV +DG +V ++D + +VQ MVGR Sbjct: 184 RVIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGR 243 Query: 243 SLSEFYQHQ-RIAPADAAQLPTVMQVRALAGGKIRPASFDVRAGEVLGFAGLVGAGRTEL 301 + + Y Q R + +L V A G P S VR+GE++G GLVGAGR+EL Sbjct: 244 DIGDIYGWQPRSYGEERLRLDAVK-----APGVRTPISLAVRSGEIVGLFGLVGAGRSEL 298 Query: 302 ARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMN 361 + +FG + G + ++ +P+ I +P A+ AG+ PEDRK +G+ +V N ++ Sbjct: 299 MKGMFGGTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINIS 358 Query: 362 VASRHTRLGLVRSRSLG-GVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAP 420 +H G V + A I+ LN+K E + LSGGNQQK +L RWL Sbjct: 359 ARRKHVLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEM 418 Query: 421 KVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMIT 480 KV++LDEPTRG+D+ AK EIY +++ LA+QGVAV+ SS+LPEV+G+ DR++VMREG I Sbjct: 419 KVILLDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIA 478 Query: 481 GELAGAAITQENIMRLA 497 GEL + + LA Sbjct: 479 GELLHEQADERQALSLA 495 Lambda K H 0.320 0.135 0.378 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: 710 Number of extensions: 40 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: 521 Length of database: 504 Length adjustment: 35 Effective length of query: 486 Effective length of database: 469 Effective search space: 227934 Effective search space used: 227934 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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