Align Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 (characterized)
to candidate AZOBR_RS31245 AZOBR_RS31245 ABC transporter ATP-binding protein
Query= SwissProt::P23924 (506 letters) >FitnessBrowser__azobra:AZOBR_RS31245 Length = 518 Score = 357 bits (915), Expect = e-103 Identities = 198/498 (39%), Positives = 303/498 (60%), Gaps = 12/498 (2%) Query: 13 LLEMRGINKSFPGVKALDNVNLNVRPHSIHALMGENGAGKSTLLKCLFGIYQKDS--GSI 70 +LEM+GI K+FPGVKALD+VNL+VR IHAL+GENGAGKSTL+K L G+Y + S G I Sbjct: 5 ILEMKGITKTFPGVKALDDVNLSVREGEIHALIGENGAGKSTLMKVLSGVYPQGSFDGEI 64 Query: 71 VFQGKEVDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYQDT 130 F+G+ F ++ GI ++HQEL LV S+ +N++LG +D D Sbjct: 65 RFRGQPQAFRGIADSERLGIIIIHQELALVPLLSITENLFLGNEQASRGVIDWDAATLRA 124 Query: 131 KAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFT 190 + + + + P + + V + Q++EIAKA S K++I+DEPT+SL E + + L Sbjct: 125 RELLRLVGLHDPPETLITDIGVGKQQLVEIAKALSKEVKLLILDEPTASLNESDSDALLE 184 Query: 191 IIRKLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIATQPLEG--LDMDKIIAMMVGR 248 ++ + K RG + ISHK+ EI ++ D +TILRDG + T + D+II MVGR Sbjct: 185 LLLQFKARGIASILISHKLNEIAKVADRVTILRDGTTVETLDCREAVVSQDRIIRGMVGR 244 Query: 249 SLNQRFPDKENKPGDVILEVR-----HLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRT 303 +L+ R+P + PGDV+ EV+ H + +RDV+ + +GE++GIAGL+GA RT Sbjct: 245 ALSDRYPRRTTVPGDVLFEVKGWSADHPAHPGRRVVRDVNLTVRRGEVVGIAGLMGAGRT 304 Query: 304 DIVETLFG--IREKSSGTITLHGKKINNHTANEAINHGFALVTEERRSTGIYAYLDIGFN 361 + +LFG G L G++I+ T + A+ +G A TE+R+ G+ DI N Sbjct: 305 EFAMSLFGRSYGRNIRGQAFLDGREIDVSTISRAMANGLAYATEDRKHLGLVLDNDIRHN 364 Query: 362 SLISNIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWL 421 ++N+R + ++D+ R + +R++ + +LSGGNQQKV++ +WL Sbjct: 365 VTLANLRGVAKR-WVIDHEREVQVAEEFRRRLRIRCADVFQETVNLSGGNQQKVVLSKWL 423 Query: 422 LTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSN 481 P++L+LDEPTRGIDVGAK+EIY +I +L +G+G+++ISSEMPELLG+ DRI VM+ Sbjct: 424 FADPQVLILDEPTRGIDVGAKYEIYTIINQLVAEGRGVVLISSEMPELLGVADRIYVMNA 483 Query: 482 GLVSGIVDTKTTTQNEIL 499 G + + +Q +I+ Sbjct: 484 GEMVAEMPAAEASQEKIM 501 Score = 89.7 bits (221), Expect = 2e-22 Identities = 66/248 (26%), Positives = 118/248 (47%), Gaps = 11/248 (4%) Query: 10 GEYLLEMRGINK---SFPGVKALDNVNLNVRPHSIHALMGENGAGKSTLLKCLFG-IYQK 65 G+ L E++G + + PG + + +VNL VR + + G GAG++ LFG Y + Sbjct: 258 GDVLFEVKGWSADHPAHPGRRVVRDVNLTVRRGEVVGIAGLMGAGRTEFAMSLFGRSYGR 317 Query: 66 D-SGSIVFQGKEVDFHSAKEALENGISMVHQE---LNLVLQRSVMDNMWLG--RYPTKGM 119 + G G+E+D + A+ NG++ ++ L LVL + N+ L R K Sbjct: 318 NIRGQAFLDGREIDVSTISRAMANGLAYATEDRKHLGLVLDNDIRHNVTLANLRGVAKRW 377 Query: 120 FVDQDKMYQDTKAIFDELDIDI-DPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTS 178 +D ++ Q + L I D LS Q + ++K + +++I+DEPT Sbjct: 378 VIDHEREVQVAEEFRRRLRIRCADVFQETVNLSGGNQQKVVLSKWLFADPQVLILDEPTR 437 Query: 179 SLTEKEVNHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIATQPLEGLDM 238 + ++TII +L G G+V IS +M E+ + D I ++ G+ +A P Sbjct: 438 GIDVGAKYEIYTIINQLVAEGRGVVLISSEMPELLGVADRIYVMNAGEMVAEMPAAEASQ 497 Query: 239 DKIIAMMV 246 +KI+ ++ Sbjct: 498 EKIMGAIM 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: 679 Number of extensions: 35 Number of successful extensions: 11 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: 518 Length adjustment: 35 Effective length of query: 471 Effective length of database: 483 Effective search space: 227493 Effective search space used: 227493 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