Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate HSERO_RS03640 HSERO_RS03640 D-ribose transporter ATP-binding protein
Query= CharProtDB::CH_014279 (504 letters) >FitnessBrowser__HerbieS:HSERO_RS03640 Length = 502 Score = 374 bits (959), Expect = e-108 Identities = 205/497 (41%), Positives = 304/497 (61%), Gaps = 9/497 (1%) Query: 5 TPYLSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSV 64 TP L RGI K+F AL+D+ G++HALMGENGAGKSTL+K+LSG +AP G + Sbjct: 8 TPLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEI 67 Query: 65 VINGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLG-QLPHKGGIVNRSLLNYE 123 +++G+ ++ D A+ AG+ +IYQEL + P ++VA N+++G +L + G+++ + + Sbjct: 68 LLDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSR 127 Query: 124 AGLQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLF 183 L+ LG LSI + Q VEIA+AL ++I+ DEPT++LS RE + LF Sbjct: 128 TDAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLF 187 Query: 184 RVIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGR 243 V+R LR EG I+Y+SHRM E++AL+D +TV +DG +V ++D + +VQ MVGR Sbjct: 188 NVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELV-RDEIDSERIVQMMVGR 246 Query: 244 DIGDIYGWQPRSYGEERLRLDAVK-----APGVRTPISLAVRSGEIVGLFGLVGAGRSEL 298 + + Y Q R + +L V A G P S VR+GE++G GLVGAGR+EL Sbjct: 247 SLSEFYQHQ-RIAPADAAQLPTVMQVRALAGGKIRPASFDVRAGEVLGFAGLVGAGRTEL 305 Query: 299 MKGMFGGTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINIS 358 + +FG + G + ++ +P+ I +P A+ AG+ PEDRK +G+ +V N ++ Sbjct: 306 ARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMN 365 Query: 359 ARRKHVLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEM 418 +H G V + A I+ LN+K E + LSGGNQQK +L RWL Sbjct: 366 VASRHTRLGLVRSRSLG-GVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAP 424 Query: 419 KVILLDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIA 478 KV++LDEPTRG+D+ AK EIY +++ LA+QGVAV+ SS+LPEV+G+ DR++VMREG I Sbjct: 425 KVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMIT 484 Query: 479 GELLHEQADERQALSLA 495 GEL + + LA Sbjct: 485 GELAGAAITQENIMRLA 501 Lambda K H 0.319 0.136 0.391 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: 687 Number of extensions: 39 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: 504 Length of database: 502 Length adjustment: 34 Effective length of query: 470 Effective length of database: 468 Effective search space: 219960 Effective search space used: 219960 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 (21.7 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