GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Paraburkholderia bryophila 376MFSha3.1

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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