Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate WP_012042345.1 BBTA_RS09915 sugar ABC transporter ATP-binding protein
Query= CharProtDB::CH_014279 (504 letters) >NCBI__GCF_000015165.1:WP_012042345.1 Length = 516 Score = 332 bits (852), Expect = 1e-95 Identities = 181/480 (37%), Positives = 298/480 (62%), Gaps = 10/480 (2%) Query: 8 LSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVVIN 67 L RG+ K+F +KAL D+ F G++HAL+GENGAGKSTL+K+++G +A G+V + Sbjct: 15 LEIRGLTKSFGALKALQDVDFTLGEGEIHALLGENGAGKSTLIKVVTGVFARDAGTVRLA 74 Query: 68 GQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLLNYEAGLQ 127 G E++ A+ AG+A +YQE++L+P ++VA+N+YLG+ P + G+V ++ + A Sbjct: 75 GDEIAPRSAKDAVEAGIATVYQEVNLLPNLSVAQNLYLGRQPTRFGVVRQAEMRRRAHAL 134 Query: 128 LKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFRVIR 187 L G+DID PL S+ + IA+A+ +A+++ DEPT+SL E++ LFRV+R Sbjct: 135 LLDYGLDIDVGAPLASYSVAVQHITAIARAVDLSARVLILDEPTASLDRHEVEILFRVMR 194 Query: 188 ELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKT--FTDMQQVDHDALVQAMVGRDI 245 +L +G I++VSH +++++ + D +TV ++GR + T TD+ ++D L++ M+GR++ Sbjct: 195 KLAADGIGIVFVSHFLDQVYEICDRVTVLRNGRLIGTRDITDLPRLD---LIRMMLGREL 251 Query: 246 GDI----YGWQPRSYGEERLRLDAVKAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMKG 301 + QP + E + G P L +R GE+VGL GL+G+GR+E + Sbjct: 252 AETTHERAASQPDTAREVCVSFKGFGKQGYVAPFDLELRRGEVVGLAGLLGSGRTETARL 311 Query: 302 MFGGTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISARR 361 +FG + +G+ + + + + P A G CPE+RK EGI+ +VR+NI ++ + Sbjct: 312 VFGAERADSGEASVAGKAVRLNSPRDAAGLGFGYCPEERKTEGIVADLTVRENIVLALQA 371 Query: 362 KHVLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKVI 421 + L ++ ++ A +IR L+I+ P E+ I LSGGNQQKA+L RWL+ K++ Sbjct: 372 RRGLHR-PLSRREQDEIAMRYIRMLDIRPPDPERPIGLLSGGNQQKALLARWLATSPKLL 430 Query: 422 LLDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAGEL 481 +LDEPTRGIDVGA EI ++ L QG+A+L SS+L E++ ++R+VV+R+ EL Sbjct: 431 VLDEPTRGIDVGAHAEIIRLVRDLCEQGLALLVISSELDEIVTYSNRVVVLRDRAHVEEL 490 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: 631 Number of extensions: 28 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: 516 Length adjustment: 34 Effective length of query: 470 Effective length of database: 482 Effective search space: 226540 Effective search space used: 226540 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