GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mglA in Klebsiella michiganensis M5al

Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate BWI76_RS14860 BWI76_RS14860 ABC transporter

Query= TCDB::P0AAG8
         (506 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS14860 BWI76_RS14860 ABC
           transporter
          Length = 510

 Score =  390 bits (1001), Expect = e-113
 Identities = 198/488 (40%), Positives = 318/488 (65%), Gaps = 5/488 (1%)

Query: 13  LLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILF 72
           LL + GI+K +    AL+NV   +    +HALMGENGAGKSTL+K L G  Q+DSG I  
Sbjct: 9   LLRLEGISKRYGATLALNNVRFDLFAGEVHALMGENGAGKSTLMKILSGNEQRDSGVIFI 68

Query: 73  QGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTK-GMFVDQDKMYRETK 131
            G+ ID  + ++A + GI+++HQELN V   +V +N++LG+ PT     +D+ +M+RE K
Sbjct: 69  DGQAIDIRTPRDARKYGIAIIHQELNTVPDMTVAENLFLGQEPTSFAGILDRKRMHREAK 128

Query: 132 AIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTI 191
              + ++ DIDP+A +G+LS+ + QM+EIA+A S NAK++++DEPT++L+  E   L+ +
Sbjct: 129 EKLNRINADIDPQAPLGSLSIGRQQMVEIARAVSENAKVLVLDEPTAALSRAETLQLYRL 188

Query: 192 IRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRSLN 251
           I ++++ G G+VYISH+MEE++QL + VTV RDG WI TE L  ++   I+ MMVGR + 
Sbjct: 189 IAQMRQDGVGMVYISHRMEEVWQLANRVTVFRDGTWIGTENLGNVSTTDIVRMMVGRQIV 248

Query: 252 QRFPDKENKPGEVILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETLFG 311
             +  +   PG+V+LEVR+L      +   VSF++  GE++ ++GLVG+ RT++   LFG
Sbjct: 249 DLYQHEPRTPGDVLLEVRDLAG---SATGPVSFEVSAGEVVSMSGLVGSGRTEVARLLFG 305

Query: 312 IREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRNYK 371
              +S G++ L G++    +   AI  G  +VTE+R++ G++    +  N  IS++ N+ 
Sbjct: 306 ADPRSQGSVRLAGRESQPSDPTAAIADGIGMVTEDRKTQGLFLGHSVEHNIDISSLDNFV 365

Query: 372 NKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILMLD 431
              G++    +++     +  +R++       + +LSGGNQQK  + RWLL    +L+LD
Sbjct: 366 -AGGVVKRKTIRAAVLEQMRRLRLRENAVELPVSALSGGNQQKAALARWLLRDSRLLILD 424

Query: 432 EPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVDTK 491
           EPTRG+D+GAK EIY+LI  LA+ GK I++ISS++PE +GI+DR+LVM  G +   + + 
Sbjct: 425 EPTRGVDIGAKREIYELIDRLARAGKAILVISSDLPEAIGISDRVLVMRGGRIVHQLPSC 484

Query: 492 TTTQNEIL 499
           + T+ E++
Sbjct: 485 SATEEEVM 492



 Score = 91.7 bits (226), Expect = 6e-23
 Identities = 57/224 (25%), Positives = 115/224 (51%), Gaps = 6/224 (2%)

Query: 278 SIRDVSFDLHKGEILGIAGLVGAKRTDIVETLFGIREKSAGTITLHGKQINNHNANEAIN 337
           ++ +V FDL  GE+  + G  GA ++ +++ L G  ++ +G I + G+ I+     +A  
Sbjct: 24  ALNNVRFDLFAGEVHALMGENGAGKSTLMKILSGNEQRDSGVIFIDGQAIDIRTPRDARK 83

Query: 338 HGFALVTEERRSTGIYAYLDIGFNSLISNIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKT 397
           +G A++ +E  +      + +  N  +   +   +  G+LD  RM  + +  ++ +    
Sbjct: 84  YGIAIIHQELNTV---PDMTVAENLFLG--QEPTSFAGILDRKRMHREAKEKLNRINADI 138

Query: 398 PGHRTQIGSLSGGNQQKVIIGRWLLTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGK 457
              +  +GSLS G QQ V I R +    ++L+LDEPT  +      ++Y+LIA++ + G 
Sbjct: 139 DP-QAPLGSLSIGRQQMVEIARAVSENAKVLVLDEPTAALSRAETLQLYRLIAQMRQDGV 197

Query: 458 GIIIISSEMPELLGITDRILVMSNGLVSGIVDTKTTTQNEILRL 501
           G++ IS  M E+  + +R+ V  +G   G  +    +  +I+R+
Sbjct: 198 GMVYISHRMEEVWQLANRVTVFRDGTWIGTENLGNVSTTDIVRM 241



 Score = 63.5 bits (153), Expect = 2e-14
 Identities = 59/252 (23%), Positives = 114/252 (45%), Gaps = 17/252 (6%)

Query: 10  GEYLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGT 69
           G+ LLE+  +  S  G      V+ +V    + ++ G  G+G++ + + LFG   +  G+
Sbjct: 259 GDVLLEVRDLAGSATGP-----VSFEVSAGEVVSMSGLVGSGRTEVARLLFGADPRSQGS 313

Query: 70  ILFQGKEIDFHSAKEALENGISMVHQELN---LVLQRSVMDNMWLGRYPTKGMFVDQDKM 126
           +   G+E        A+ +GI MV ++     L L  SV  N+ +        FV    +
Sbjct: 314 VRLAGRESQPSDPTAAIADGIGMVTEDRKTQGLFLGHSVEHNIDISSLDN---FVAGGVV 370

Query: 127 YRET--KAIFDELD-IDIDPRA---RVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSL 180
            R+T   A+ +++  + +   A    V  LS    Q   +A+    +++++I+DEPT  +
Sbjct: 371 KRKTIRAAVLEQMRRLRLRENAVELPVSALSGGNQQKAALARWLLRDSRLLILDEPTRGV 430

Query: 181 TEKEVNHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDK 240
                  ++ +I +L   G  I+ IS  + E   + D V V+R G+ +   P    T ++
Sbjct: 431 DIGAKREIYELIDRLARAGKAILVISSDLPEAIGISDRVLVMRGGRIVHQLPSCSATEEE 490

Query: 241 IIAMMVGRSLNQ 252
           ++    G   +Q
Sbjct: 491 VMLHATGTFTSQ 502


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: 601
Number of extensions: 35
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 506
Length of database: 510
Length adjustment: 34
Effective length of query: 472
Effective length of database: 476
Effective search space:   224672
Effective search space used:   224672
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