Align Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 (characterized)
to candidate PP_2455 PP_2455 ribose ABC transporter - ATP-binding subunit
Query= SwissProt::P23924 (506 letters) >FitnessBrowser__Putida:PP_2455 Length = 524 Score = 326 bits (835), Expect = 1e-93 Identities = 184/497 (37%), Positives = 299/497 (60%), Gaps = 7/497 (1%) Query: 9 SGEYLLEMRGINKSFPGVKALDNVNLNVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSG 68 + E +L G+ K++ L V+L++R + AL GENGAGKSTL K + G+ +G Sbjct: 12 ANEVVLAASGLGKTY-AQPVLGEVSLSLRAGEVLALTGENGAGKSTLSKLISGLEVPTTG 70 Query: 69 SIVFQGKEVDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYQ 128 + ++G+ S EA G+ MV QELNL+ +V +N++L P++ ++ ++ Q Sbjct: 71 HMTYRGQAYAPGSRGEAERLGVRMVMQELNLLPTLTVAENLFLDNLPSRFGWISHKRLRQ 130 Query: 129 DTKAIFDELDID-IDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNH 187 A + +D IDP VG L + QM+EIA+ + ++I+DEPT+ LT +EV Sbjct: 131 LATAAMARVGLDAIDPDTPVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVAL 190 Query: 188 LFTIIRKLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIATQPLEGLDMDKIIAMMVG 247 LFT I +L+ RG IVYISH++EE+ ++ I +LRDG+ + +P++ +++ +MVG Sbjct: 191 LFTQIERLRARGVAIVYISHRLEELQRVAQRIVVLRDGKLVCDEPIQRYSSAELVNLMVG 250 Query: 248 RSLNQRFPDKENKPGDVILEVRHLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVE 307 R L + + G +L+V L R +R+VSF++ GEI GI+GL+GA RT+++ Sbjct: 251 RELGEHIDLGRRQLGAPLLKVDKLC--RGDKVREVSFEVRAGEIFGISGLIGAGRTELLR 308 Query: 308 TLFGIREKSSGTITLHG--KKINNHTANEAINHGFALVTEERRSTGIYAYLDIGFNSLIS 365 ++G SG I L + ++ + A+ G AL+TE+R+ G+ I N + Sbjct: 309 LIYGADRADSGGIALGQPPQAVSIDSPKAAVRAGIALITEDRKGEGLLLTQSISANIALG 368 Query: 366 NIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQP 425 N+ ++ G+LD+ K+ + I +MR+++ G + +G LSGGNQQKV+IGRWL Sbjct: 369 NL-GAVSRAGVLDSEAEKALAERQIQAMRIRSAGAQQVVGELSGGNQQKVVIGRWLERDC 427 Query: 426 EILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVS 485 ++L+ DEPTRGIDVGAKF+IY L+AELA++GK ++++SS++ EL+ I DRI V+S G + Sbjct: 428 QVLLFDEPTRGIDVGAKFDIYGLLAELARQGKALVVVSSDLRELMLICDRIAVLSAGRLI 487 Query: 486 GIVDTKTTTQNEILRLA 502 +Q+++L A Sbjct: 488 DTFARDHWSQDQLLAAA 504 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: 567 Number of extensions: 23 Number of successful extensions: 9 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: 506 Length of database: 524 Length adjustment: 35 Effective length of query: 471 Effective length of database: 489 Effective search space: 230319 Effective search space used: 230319 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