Align Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 (characterized)
to candidate Ac3H11_609 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)
Query= SwissProt::P23924 (506 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_609 Length = 505 Score = 382 bits (980), Expect = e-110 Identities = 207/499 (41%), Positives = 319/499 (63%), Gaps = 12/499 (2%) Query: 13 LLEMRGINKSFPGVKALDNVNLNVRPHSIHALMGENGAGKSTLLKCLFGIYQKDS--GSI 70 LLEMR I K+FPGV AL+ VNL V+ IHA++GENGAGKSTL+K L G+Y S G I Sbjct: 2 LLEMRNIRKTFPGVVALNQVNLQVQAGEIHAIVGENGAGKSTLMKVLSGVYPHGSYSGQI 61 Query: 71 VFQGKEVDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYQDT 130 +F G+E +F +++ GI ++HQEL LV S+ +N++LG + +D + Sbjct: 62 LFDGQEREFAGIRDSEHLGIIIIHQELALVPLLSIAENIFLGNETARHGVIDWMAAHSRA 121 Query: 131 KAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFT 190 +A+ ++ + P VG L V + Q++EIAKA S +++I+DEPT+SL E + L Sbjct: 122 QALLHKVGLGESPDTPVGQLGVGKQQLVEIAKALSRKVRLLILDEPTASLNENDSQALLD 181 Query: 191 IIRKLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIATQPL-EG-LDMDKIIAMMVGR 248 ++ +LK +G + ISHK+ EI ++ D IT+LRDG + EG + D++I MVGR Sbjct: 182 LLLELKAQGITCILISHKLNEISRVADAITVLRDGSTVQMLDCREGPVSEDRVIQAMVGR 241 Query: 249 SLNQRFPDKENKPGDVILEVR-----HLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRT 303 ++ R+P ++ + G+++ EVR H + ++ + ++ +GEI+GIAGL+GA RT Sbjct: 242 EMSDRYPQRQPQVGEIVFEVRNWRAHHPQRSDREHLKGIDLNVRRGEIVGIAGLMGAGRT 301 Query: 304 DIVETLFGIR--EKSSGTITLHGKKINNHTANEAINHGFALVTEERRSTGIYAYLDIGFN 361 ++ ++FG ++ SG + LHG+ I+ T +A++HG A VTE+R+ G+ DI FN Sbjct: 302 ELAMSIFGRSWGQRISGEVRLHGQPIDVSTVEKAVSHGLAYVTEDRKGNGLVLNEDIQFN 361 Query: 362 SLISNIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWL 421 + ++N+ + ++D+ + Q + +R++ G + +LSGGNQQKV++ +WL Sbjct: 362 TSLANLPGV-SFASVIDSGQEHRVAQDYREKLRIRCSGVDQKTLNLSGGNQQKVVLSKWL 420 Query: 422 LTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSN 481 T PE+L+LDEPTRGIDVGAK+EIY LIA+LA +GK +I+ISSEMPELLGITDRI VM+ Sbjct: 421 FTSPEVLILDEPTRGIDVGAKYEIYTLIAQLAAEGKCVIVISSEMPELLGITDRIYVMNE 480 Query: 482 GLVSGIVDTKTTTQNEILR 500 G + T +Q +I+R Sbjct: 481 GRFVAEMPTSEASQEKIMR 499 Score = 83.6 bits (205), Expect = 2e-20 Identities = 63/256 (24%), Positives = 123/256 (48%), Gaps = 15/256 (5%) Query: 7 PPSGEYLLEMRGINKSFP---GVKALDNVNLNVRPHSIHALMGENGAGKSTLLKCLFGIY 63 P GE + E+R P + L ++LNVR I + G GAG++ L +FG Sbjct: 252 PQVGEIVFEVRNWRAHHPQRSDREHLKGIDLNVRRGEIVGIAGLMGAGRTELAMSIFGRS 311 Query: 64 --QKDSGSIVFQGKEVDFHSAKEALENGISMVHQELN---LVLQRSVMDNMWLGRYP--T 116 Q+ SG + G+ +D + ++A+ +G++ V ++ LVL + N L P + Sbjct: 312 WGQRISGEVRLHGQPIDVSTVEKAVSHGLAYVTEDRKGNGLVLNEDIQFNTSLANLPGVS 371 Query: 117 KGMFVDQDKMYQDTKAIFDELDI---DIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIM 173 +D + ++ + ++L I +D + LS Q + ++K + +++I+ Sbjct: 372 FASVIDSGQEHRVAQDYREKLRIRCSGVDQKTL--NLSGGNQQKVVLSKWLFTSPEVLIL 429 Query: 174 DEPTSSLTEKEVNHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIATQPL 233 DEPT + ++T+I +L G ++ IS +M E+ + D I ++ +G+++A P Sbjct: 430 DEPTRGIDVGAKYEIYTLIAQLAAEGKCVIVISSEMPELLGITDRIYVMNEGRFVAEMPT 489 Query: 234 EGLDMDKIIAMMVGRS 249 +KI+ +V S Sbjct: 490 SEASQEKIMRAIVKAS 505 Lambda K H 0.319 0.137 0.388 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: 623 Number of extensions: 25 Number of successful extensions: 9 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: 506 Length of database: 505 Length adjustment: 34 Effective length of query: 472 Effective length of database: 471 Effective search space: 222312 Effective search space used: 222312 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