Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate WP_084931762.1 HA51_RS02835 sugar ABC transporter ATP-binding protein
Query= uniprot:B2SYR5 (512 letters) >NCBI__GCF_002095475.1:WP_084931762.1 Length = 500 Score = 380 bits (976), Expect = e-110 Identities = 216/495 (43%), Positives = 323/495 (65%), Gaps = 12/495 (2%) Query: 5 LRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVMID 64 L I K + AL V F V G+VH L+GENGAGKSTLL IL G DSG + ++ Sbjct: 6 LMMRGITKTYGSAIALQDVDFMVRPGEVHALIGENGAGKSTLLNILSGVRPADSGAIHVN 65 Query: 65 GNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNSLG--WVNKREAKRFVR 122 G +V+ + S+ AGIA+IHQELQ+VP+L+VA+N+ LG+ +L +V+KR Sbjct: 66 GEQVQMKNPLSARHAGIAMIHQELQHVPELSVAQNMFLGRPLTTLNGLFVDKRAQLARAT 125 Query: 123 ERLEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFKL 182 L+ + +++P ++ L ++Q+Q+VEI +ALL A++IA+DEPTSSL+ RE E L +L Sbjct: 126 HILKQLDPSINPAEPIKNLKVSQQQIVEIARALLDEAKIIAMDEPTSSLTPREFERLAEL 185 Query: 183 VRDLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGREI 242 + DL++ ++IY+SH+M+EI+++CD TI RDGR++ + T +TIV++MVGR+I Sbjct: 186 IADLKSTGVSLIYVSHKMNEIFQVCDRATIMRDGRQVGV-VNICDETEETIVAKMVGRKI 244 Query: 243 SDIYNYS---ARPLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLV 299 + S R + +V A+G E +PASF V GE++G GLVGAGR+EL+ L+ Sbjct: 245 DKQAHQSWATDRKVLQVENVARGTE----IKPASFSVCAGEVLGVAGLVGAGRTELLKLI 300 Query: 300 YGADHKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRH 359 G D + GE+ ++G+ ++ + AIR GI L PEDRK+EGI+ V N+ + R+ Sbjct: 301 AGIDKRSAGEVRVNGQLVRNHNVSAAIRAGIGLVPEDRKKEGIIKARAVKVNMALPSMRN 360 Query: 360 YLRVGMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVV 419 + G+ K A A + LK++ + + I LSGGNQQK I+ RW+A D +V Sbjct: 361 FTLAGVIRKVKLNA-VAQEVMSDLKLRPLNIEKPIGTLSGGNQQKVIIGRWVA-ADAEVF 418 Query: 420 ILDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGEL 479 + DEPTRGID+GAK EIYN+I +LA++G AIV++SSE+ E+L VSDR++VMR+G+I+ EL Sbjct: 419 LFDEPTRGIDIGAKAEIYNLIEKLAQQGKAIVVVSSEMTEILRVSDRVLVMREGKITREL 478 Query: 480 TRKDATEQSVLSLAL 494 T D TE+++ A+ Sbjct: 479 TGDDITEENIARFAI 493 Lambda K H 0.320 0.136 0.385 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: 648 Number of extensions: 37 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: 512 Length of database: 500 Length adjustment: 34 Effective length of query: 478 Effective length of database: 466 Effective search space: 222748 Effective search space used: 222748 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 24 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