Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate WP_078427103.1 BK574_RS00955 ABC transporter ATP-binding protein
Query= CharProtDB::CH_014279 (504 letters) >NCBI__GCF_002019605.1:WP_078427103.1 Length = 509 Score = 276 bits (705), Expect = 2e-78 Identities = 162/489 (33%), Positives = 269/489 (55%), Gaps = 7/489 (1%) Query: 8 LSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVVIN 67 + + I K FPG+ A +++ G++HAL+GENGAGKSTL+ +L G Y P G +++ Sbjct: 5 IEMKDIRKEFPGIVANDNVTLQVKQGEIHALLGENGAGKSTLMNVLFGLYQPEKGEILVK 64 Query: 68 GQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLLNYEAGLQ 127 G+ + +D A G+ +++Q LV + TV ENI LG+ P GG +N Sbjct: 65 GKPVKITDPNVANRLGIGMVHQHFMLVEKFTVTENIILGKEPTAGGKINIKKAAKAVETI 124 Query: 128 LKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFRVIR 187 K G+ +DP ++ +S+G Q VEI K L R A+I+ FDEPT++L+ +EI L ++++ Sbjct: 125 SKQYGLAVDPYAKIQDISVGMQQRVEILKTLYRGAEILIFDEPTAALTPQEITELIQIMK 184 Query: 188 ELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGRDIGD 247 +L EG+ I+ ++H+++EI + D TV + GR + T D+ + D+L MVGR++ Sbjct: 185 KLVSEGKSIILITHKLKEIMEVCDRCTVIRRGRGIGT-VDISESTPDSLAAMMVGREVNF 243 Query: 248 IYGWQPRSYGEERLRLDAVKAPGVR-----TPISLAVRSGEIVGLFGLVGAGRSELMKGM 302 P + L++ + R + L V +GEI+G+ G+ G G++EL++ + Sbjct: 244 SVEKDPAQPKDAVLQIKDLVVKDSRDITAVNDLHLEVHAGEILGVAGVDGNGQTELIEAI 303 Query: 303 FGGTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISA-RR 361 G + T G + ++ Q I P AG+ P+DR G++ +V +NI + + Sbjct: 304 TGLRKPTGGNIQLNGQDITGLTPRKITGAGVGHIPQDRHKHGLVLDFTVGENIVLQTYYQ 363 Query: 362 KHVLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKVI 421 K V+N A+ I +++TP L LSGGNQQKAI+ R + ++ Sbjct: 364 KPYSTSGVLNFNEIYKKANELIEDYDVRTPSEHTLARALSGGNQQKAIIAREVDRSPDLL 423 Query: 422 LLDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAGEL 481 + +PTRG+DVGA I++ + +G AVL S +L EVL V+DRI V+ EG+I + Sbjct: 424 IAAQPTRGLDVGAIESIHHRLVKERDKGKAVLLISLELDEVLNVSDRIAVIYEGKIVAIV 483 Query: 482 LHEQADERQ 490 ++ +E + Sbjct: 484 DADKTNENE 492 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: 659 Number of extensions: 36 Number of successful extensions: 7 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: 509 Length adjustment: 34 Effective length of query: 470 Effective length of database: 475 Effective search space: 223250 Effective search space used: 223250 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 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