Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate H281DRAFT_00426 H281DRAFT_00426 monosaccharide ABC transporter ATP-binding protein, CUT2 family
Query= TCDB::P0AAG8 (506 letters) >FitnessBrowser__Burk376:H281DRAFT_00426 Length = 503 Score = 439 bits (1128), Expect = e-127 Identities = 222/494 (44%), Positives = 336/494 (68%), Gaps = 5/494 (1%) Query: 13 LLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILF 72 L+ + ++KSFPGV+AL +V + +HALMGENGAGKSTL+K L G+Y +DSG IL Sbjct: 4 LISVKKLSKSFPGVRALHDVQFDLVEGEVHALMGENGAGKSTLMKILAGVYTRDSGEILL 63 Query: 73 QGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTK--GMFVDQDKMYRET 130 G+ ++ S ++A GI ++HQEL L+ +V N+++GR P G+F+D+DK+ + Sbjct: 64 GGQPVELQSPRDAQAAGIGIIHQELQLMNHLTVAQNIFIGREPRGRLGLFLDEDKLNAKA 123 Query: 131 KAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFT 190 + I + ++IDPRA VG L+V+ QM+EIAKA S++++++IMDEPTS+L + E+ LF Sbjct: 124 REILSRMHVNIDPRAMVGNLTVASQQMVEIAKALSFDSRVLIMDEPTSALNDAEIAELFR 183 Query: 191 IIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRSL 250 IIR+LK+RG G+VYISHKM+E+ Q+ D VTVLRDG+++AT A +++ II MMVGR+L Sbjct: 184 IIRELKQRGVGVVYISHKMDELKQIADRVTVLRDGEYVATVAAADTSVEAIIGMMVGRTL 243 Query: 251 NQRFP-DKENKPGEVILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETL 309 + P + GE+ LEVRNL + P +RDVSF L KGEILG AGL+GA RT++ + Sbjct: 244 SDVAPAGRAASQGEIALEVRNLHA--GPLVRDVSFTLRKGEILGFAGLMGAGRTEVARAV 301 Query: 310 FGIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRN 369 FG +G I + G + + ++A+ HG ++E+R+ G+ +D+ N ++SN+RN Sbjct: 302 FGADPVESGEIFVKGAKASIRTPSDAVAHGIGYLSEDRKRFGLATGMDVESNIVMSNLRN 361 Query: 370 YKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILM 429 + + L +RM+ I+ + ++TP Q+ LSGGNQQK++I +WL ++L Sbjct: 362 FLSLNFFLRRARMRRRASHFINLLAIRTPSAAQQVRLLSGGNQQKIVIAKWLERDCDVLF 421 Query: 430 LDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVD 489 DEPTRGIDVGAK EIY+L+ LA +GK I++ISSE+PE+L ++DR++VM G ++G + Sbjct: 422 FDEPTRGIDVGAKSEIYKLLRSLADEGKAIVMISSELPEILRMSDRVVVMCEGRITGELP 481 Query: 490 TKTTTQNEILRLAS 503 + TQ I+ LA+ Sbjct: 482 AEQATQERIMHLAT 495 Score = 75.9 bits (185), Expect = 3e-18 Identities = 63/250 (25%), Positives = 113/250 (45%), Gaps = 15/250 (6%) Query: 8 SSGEYLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDS 67 S GE LE+ ++ P V+ +V+ +R I G GAG++ + + +FG +S Sbjct: 254 SQGEIALEVRNLHAG-PLVR---DVSFTLRKGEILGFAGLMGAGRTEVARAVFGADPVES 309 Query: 68 GTILFQGKEIDFHSAKEALENGISMVHQELNL--------VLQRSVMDNMWLGRYPTKGM 119 G I +G + + +A+ +GI + ++ V VM N L + + Sbjct: 310 GEIFVKGAKASIRTPSDAVAHGIGYLSEDRKRFGLATGMDVESNIVMSN--LRNFLSLNF 367 Query: 120 FVDQDKMYRETKAIFDELDIDIDPRAR-VGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTS 178 F+ + +M R + L I A+ V LS Q I IAK + ++ DEPT Sbjct: 368 FLRRARMRRRASHFINLLAIRTPSAAQQVRLLSGGNQQKIVIAKWLERDCDVLFFDEPTR 427 Query: 179 SLTEKEVNHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTM 238 + + ++ ++R L + G IV IS ++ EI ++ D V V+ +G+ P T Sbjct: 428 GIDVGAKSEIYKLLRSLADEGKAIVMISSELPEILRMSDRVVVMCEGRITGELPAEQATQ 487 Query: 239 DKIIAMMVGR 248 ++I+ + R Sbjct: 488 ERIMHLATQR 497 Lambda K H 0.318 0.136 0.384 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: 570 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: 506 Length of database: 503 Length adjustment: 34 Effective length of query: 472 Effective length of database: 469 Effective search space: 221368 Effective search space used: 221368 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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