Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate BWI76_RS19640 BWI76_RS19640 galactose/methyl galactoside ABC transporter ATP-binding protein MglA
Query= uniprot:B2SYR5 (512 letters) >FitnessBrowser__Koxy:BWI76_RS19640 Length = 506 Score = 389 bits (1000), Expect = e-112 Identities = 211/494 (42%), Positives = 310/494 (62%), Gaps = 10/494 (2%) Query: 5 LRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVMID 64 L NI K FPGV+ALD V+ V +H LMGENGAGKSTLLK L G YQ DSG ++ Sbjct: 14 LEMTNINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGSILFQ 73 Query: 65 GNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNSLGWVNKREAKRFVRER 124 G E+ F SA ++ GI+++HQEL V +V +N+ LG+ P +V++ + R + Sbjct: 74 GQEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGVFVDQDKMYRDTKAI 133 Query: 125 LEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFKLVR 184 + + + +DP A++ LS++Q QM+EI KA NA+++ +DEPTSSL+ +E LFK++R Sbjct: 134 FDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFKIIR 193 Query: 185 DLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGREISD 244 L+ ++YISH+M+EI++LCD TI RDG+ IA+ P LEG+ D I++ MVGR ++ Sbjct: 194 KLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIATQP-LEGLDMDKIIAMMVGRSLNQ 252 Query: 245 IYNYSARPLGEVRFAAKGIEGHALAQPA----SFEVRRGEIVGFFGLVGAGRSELMHLVY 300 + GEV + + +L QP+ SF++ +GEI+G GLVGA R++++ ++ Sbjct: 253 RFPNKENKPGEVILEVRNLT--SLRQPSIRDISFDLHKGEILGIAGLVGAKRTDIVETLF 310 Query: 301 GADHKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHY 360 G K GG + L GK I SA EAI HG L E+R+ GI A + N IS + Y Sbjct: 311 GIREKAGGTIRLHGKKINNHSANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIKKY 370 Query: 361 LRVGMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRW-LAEPDLKVV 419 LD + I +++KTP + +I LSGGNQQK I+ RW L +P+ ++ Sbjct: 371 KNKVGLLDNSRMKSDTQWVIDSMRVKTPGQHTQIGSLSGGNQQKVIIGRWLLTQPE--IL 428 Query: 420 ILDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGEL 479 +LDEPTRGIDVGAK EIY +I +LA++ I++ISSE+PE+LG++DRI+VM G ++G + Sbjct: 429 MLDEPTRGIDVGAKFEIYQLIAELAKKDKGIIIISSEMPELLGITDRILVMSNGLVAGIV 488 Query: 480 TRKDATEQSVLSLA 493 K T+ +L LA Sbjct: 489 ETKTTTQNEILRLA 502 Score = 85.9 bits (211), Expect = 3e-21 Identities = 64/233 (27%), Positives = 109/233 (46%), Gaps = 8/233 (3%) Query: 242 ISDIYNYSARPLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYG 301 +S+ S L E+ K G + +VR I G GAG+S L+ ++G Sbjct: 2 VSNNSERSGEYLLEMTNINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFG 61 Query: 302 ADHKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYL 361 K G +L G+ I SA EA+ +GI + +E +V +V +N+ + Y Sbjct: 62 IYQKDSGSILFQGQEIDFHSAKEALENGISMV---HQELNLVLQRSVMDNMWLG---RYP 115 Query: 362 RVGMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVIL 421 G+F+D+ K L I R ++ LS Q +++ + + K+VI+ Sbjct: 116 TKGVFVDQDKMYRDTKAIFDELDIDI-DPRARVGTLSVSQMQMIEIAKAFSY-NAKIVIM 173 Query: 422 DEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGR 474 DEPT + + ++ +I +L ERGC IV IS ++ E+ + D I ++R G+ Sbjct: 174 DEPTSSLTEKEVNHLFKIIRKLKERGCGIVYISHKMEEIFQLCDEITILRDGQ 226 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: 590 Number of extensions: 24 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 512 Length of database: 506 Length adjustment: 34 Effective length of query: 478 Effective length of database: 472 Effective search space: 225616 Effective search space used: 225616 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