Align Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 (characterized)
to candidate 206505 DVU1070 branched chain amino acid ABC transporter, ATP-binding protein (TIGR)
Query= SwissProt::P23924 (506 letters) >FitnessBrowser__DvH:206505 Length = 524 Score = 259 bits (663), Expect = 1e-73 Identities = 158/490 (32%), Positives = 264/490 (53%), Gaps = 9/490 (1%) Query: 13 LLEMRGINKSFPGVKALDNVNLNVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGSIVF 72 ++ + GI KSF V+A ++ L++ P I AL+GENGAGKSTL+ L G +D+G I Sbjct: 34 VVRLEGIGKSFGPVRANHDITLDIVPGRIKALLGENGAGKSTLMSILSGRLAQDTGIIHV 93 Query: 73 QGKEVDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYQDTKA 132 G+ V F S K+AL+ GI MV+Q LV +V +N+ LG+ G ++ M + Sbjct: 94 DGEAVRFRSPKDALKAGIGMVYQHFMLVDSMTVAENVLLGQ---SGAWLSPVHMSRVVAE 150 Query: 133 IFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTII 192 + +DIDP ARV LS+ + Q +EI K +++++I+DEPT+ LT E LF + Sbjct: 151 LAARYGLDIDPAARVCDLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPGETEQLFEAL 210 Query: 193 RKLKERGCGIVYISHKMEEIFQLCDEITILRDGQWI-ATQPLEGLDMDKIIAMMVGRSLN 251 ++ E G IV+ISHKM+E+ L DEI ILR G+ + E ++ MVGR + Sbjct: 211 HRMAENGKAIVFISHKMQEVLALADEIAILRRGEVVDEFHESEVPGEAELANRMVGREVI 270 Query: 252 QRFPDKENKPGDVILEVRHLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETLFG 311 + +PGD +L H+ L ++ +SF++ KGE+ IAG+ G + ++VE + G Sbjct: 271 LEVAAEPLEPGDRVL---HVDGLAGDGLKGLSFEVRKGEVFAIAGVAGNGQRELVECVTG 327 Query: 312 IREKSSGTITLHGKKINNHTANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRNYK 371 +R + G + L G G A + E+R+ LD+ N L++ R Sbjct: 328 LRRPAEGEVELLGIPWRQFFTKAPRQGGLAYIPEDRQGLATCLSLDLVDNFLLT-ARGCF 386 Query: 372 NKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILMLD 431 + LD + + ++ V+ SLSGGN QK+++GR +P +++ + Sbjct: 387 TRGPFLDRKSADAAARDILAEYNVQPGRAEAPARSLSGGNLQKLVVGREFYRKPSLIVAE 446 Query: 432 EPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVDTK 491 PT+G+D+ A E++ + E+ + G++++S ++ E+L + DR+ VM G G++D Sbjct: 447 NPTQGLDIAATEEVWARLLEV-RSHAGVLLVSGDLNEVLALADRVAVMYRGCFIGLLDRS 505 Query: 492 TTTQNEILRL 501 T + + + L Sbjct: 506 DTNKVDAIGL 515 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: 577 Number of extensions: 31 Number of successful extensions: 5 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 Apr 09 2024. 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