GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mglA in Sinorhizobium meliloti 1021

Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate SMc02337 SMc02337 ABC transporter ATP-binding protein

Query= TCDB::P0AAG8
         (506 letters)



>lcl|FitnessBrowser__Smeli:SMc02337 SMc02337 ABC transporter
           ATP-binding protein
          Length = 501

 Score =  380 bits (976), Expect = e-110
 Identities = 201/491 (40%), Positives = 304/491 (61%), Gaps = 7/491 (1%)

Query: 13  LLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILF 72
           L+ +SGI+K+F GV+AL  V+  +R   +HAL+GENGAGKSTL++ L G  +  SGT+  
Sbjct: 4   LVSLSGISKNFSGVQALKGVDFDLRAGEVHALVGENGAGKSTLMRVLAGEMKPTSGTVSI 63

Query: 73  QGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYRETKA 132
            G+ +     + A   GIS++HQEL L    +V +N++LGR P     V+  ++ +    
Sbjct: 64  HGETMQHSGPRGAAGRGISVIHQELALAPDLTVAENIFLGRLPR---IVNHRRLRKAASE 120

Query: 133 IFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTII 192
           I + L  DIDP    G L+V+  Q++EIAKA S  A+I++ DEPT+ L   +   L  II
Sbjct: 121 ILERLGFDIDPAIHAGRLTVAHQQVVEIAKALSNRARIIVFDEPTAVLANTDAERLLAII 180

Query: 193 RKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRSLNQ 252
           R+L+  G G VYISH++ E+F L D +TV++DG  + T   +   +D +IA MVGR ++ 
Sbjct: 181 RELRAGGTGAVYISHRLNEVFDLSDRITVMKDGSHVETLETSATDVDAVIARMVGRQMSA 240

Query: 253 RFPDKENK-PGEVILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETLFG 311
            FP K  + PGEV++ VRN++  R   +RDVSF +  GE++G+ GLVG+ RT++   +FG
Sbjct: 241 LFPSKAGRVPGEVVVRVRNVS--RGRKVRDVSFSVRAGEVVGLGGLVGSGRTEVARLVFG 298

Query: 312 IREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRNYK 371
             +  +GT+ L+GK ++  +  EA+     LV E+R+  G+     I  N+ ++ IR+  
Sbjct: 299 ADKMDSGTVELNGKPLHLSSPREAVRARIGLVPEDRKQQGVILDAPIRINTTLAKIRSI- 357

Query: 372 NKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILMLD 431
           +++G LD  + +     +   MR+K       + SLSGGNQQKV + +W     ++L+LD
Sbjct: 358 SRLGFLDAGKERQVAVALGAEMRLKASSVDAPVSSLSGGNQQKVALAKWFHADCDLLILD 417

Query: 432 EPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVDTK 491
           EPTRG+DVGAK EIY LI +LAK GK I++ISSE  EL GI DR+LVM+ G + G +   
Sbjct: 418 EPTRGVDVGAKGEIYNLINDLAKAGKAILVISSEHQELFGICDRVLVMAEGAIVGELTES 477

Query: 492 TTTQNEILRLA 502
             T+ ++L LA
Sbjct: 478 KFTEQQLLTLA 488



 Score = 86.7 bits (213), Expect = 2e-21
 Identities = 60/250 (24%), Positives = 122/250 (48%), Gaps = 10/250 (4%)

Query: 10  GEYLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGT 69
           GE ++ +  +++     + + +V+  VR   +  L G  G+G++ + + +FG  + DSGT
Sbjct: 251 GEVVVRVRNVSRG----RKVRDVSFSVRAGEVVGLGGLVGSGRTEVARLVFGADKMDSGT 306

Query: 70  ILFQGKEIDFHSAKEALENGISMV---HQELNLVLQRSVMDNMWLGRYPTKGM--FVDQD 124
           +   GK +   S +EA+   I +V    ++  ++L   +  N  L +  +     F+D  
Sbjct: 307 VELNGKPLHLSSPREAVRARIGLVPEDRKQQGVILDAPIRINTTLAKIRSISRLGFLDAG 366

Query: 125 KMYRETKAIFDELDIDIDP-RARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEK 183
           K  +   A+  E+ +      A V +LS    Q + +AK F  +  ++I+DEPT  +   
Sbjct: 367 KERQVAVALGAEMRLKASSVDAPVSSLSGGNQQKVALAKWFHADCDLLILDEPTRGVDVG 426

Query: 184 EVNHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIA 243
               ++ +I  L + G  I+ IS + +E+F +CD V V+ +G  +     +  T  +++ 
Sbjct: 427 AKGEIYNLINDLAKAGKAILVISSEHQELFGICDRVLVMAEGAIVGELTESKFTEQQLLT 486

Query: 244 MMVGRSLNQR 253
           + + RS  +R
Sbjct: 487 LAMTRSARER 496


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: 575
Number of extensions: 23
Number of successful extensions: 10
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: 501
Length adjustment: 34
Effective length of query: 472
Effective length of database: 467
Effective search space:   220424
Effective search space used:   220424
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