GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Burk376:H281DRAFT_00426 H281DRAFT_00426
           monosaccharide ABC transporter ATP-binding protein, CUT2
           family
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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