Alignments for a candidate for mglA in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments 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 SM_b20673 SM_b20673 sugar uptake ABC transporter ATP-binding protein

Query= TCDB::P0AAG8
         (506 letters)



>FitnessBrowser__Smeli:SM_b20673
          Length = 526

 Score =  401 bits (1030), Expect = e-116
 Identities = 225/509 (44%), Positives = 323/509 (63%), Gaps = 10/509 (1%)

Query: 4   STTPSSGEYLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIY 63
           S T  S   +L    I+KSF GV AL +V  ++R   IHALMGENGAGKSTL+K L G+Y
Sbjct: 9   SVTTESDRPILAAEAISKSFGGVAALKDVRFELRAGEIHALMGENGAGKSTLMKVLSGVY 68

Query: 64  QKDSGTILFQGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPT-KGMFVD 122
               G +   G+ + F + ++A   GI+++HQELNLV +  V DN++LGR     G+FVD
Sbjct: 69  TDYEGAVRVDGETVRFSNVRDAEAAGIAIIHQELNLVPELGVADNIFLGRERVIAGLFVD 128

Query: 123 QDKMYRETKAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTE 182
           +       + + + L I++DP ARVG L V + Q++EIAKA S  A+I+IMDEPTS+L+ 
Sbjct: 129 RKASLEAARGLLNRLGIELDPEARVGQLRVGEQQLVEIAKALSVEARILIMDEPTSALSP 188

Query: 183 KEVNHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKII 242
            E   LF I+R+L   G GI+YISH+++E+ QL D VTV RDG+ +   P+AGL  + II
Sbjct: 189 GECRRLFKIMRQLAADGVGIIYISHRIDEVMQLSDRVTVFRDGRHVWARPMAGLDENTII 248

Query: 243 AMMVGRS-LNQRFPDKENKPGEVILEVRNLTSL------RQPSIRDVSFDLHKGEILGIA 295
           A MVGR+ L+    D+    GE +L VR+L+         +  ++ VSFD+  GEILGI 
Sbjct: 249 AAMVGRNLLDAHRRDRGKGGGEPVLSVRDLSLAVSGRHGWRDVLKGVSFDVRAGEILGIG 308

Query: 296 GLVGAKRTDIVETLFGIRE-KSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYA 354
           GL+GA RT+I+ET+F   E    G I L G  +N  +  +A   GFALVTE+R++ G++ 
Sbjct: 309 GLLGAGRTEILETIFASNEGLRGGEIRLDGIAVNIRSPRDARRLGFALVTEDRKAKGLHL 368

Query: 355 YLDIGFNSLISNIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQK 414
           +  I  N  +  +     + GL      ++  +  +D++ V+  G     G+LSGGNQQK
Sbjct: 369 HESIRDNVALPLVGRLA-RFGLRSFEGERALAKGAVDALGVRCAGTGQAAGTLSGGNQQK 427

Query: 415 VIIGRWLLTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITD 474
           V+IG+WL T P +L+LDEPTRGIDVGAK EIY LI +LA  G  I+++SSE+PELL + D
Sbjct: 428 VVIGKWLATGPRVLLLDEPTRGIDVGAKREIYDLIFKLAGDGLAIVVVSSELPELLLLAD 487

Query: 475 RILVMSNGLVSGIVDTKTTTQNEILRLAS 503
           RILVM+ G  +G++  +  ++  I++LA+
Sbjct: 488 RILVMAEGRQTGLISREEASEERIMQLAA 516



 Score = 65.1 bits (157), Expect = 6e-15
 Identities = 57/233 (24%), Positives = 105/233 (45%), Gaps = 9/233 (3%)

Query: 29  LDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQK-DSGTILFQGKEIDFHSAKEALE 87
           L  V+  VR   I  + G  GAG++ +L+ +F   +    G I   G  ++  S ++A  
Sbjct: 292 LKGVSFDVRAGEILGIGGLLGAGRTEILETIFASNEGLRGGEIRLDGIAVNIRSPRDARR 351

Query: 88  NGISMVHQELN---LVLQRSVMDNMWL---GRYPTKGMFVDQDKMYRETKAIFDELDIDI 141
            G ++V ++     L L  S+ DN+ L   GR    G+   + +      A+ D L +  
Sbjct: 352 LGFALVTEDRKAKGLHLHESIRDNVALPLVGRLARFGLRSFEGERALAKGAV-DALGVRC 410

Query: 142 DPRARV-GTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTIIRKLKERGC 200
               +  GTLS    Q + I K  +   +++++DEPT  +       ++ +I KL   G 
Sbjct: 411 AGTGQAAGTLSGGNQQKVVIGKWLATGPRVLLLDEPTRGIDVGAKREIYDLIFKLAGDGL 470

Query: 201 GIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRSLNQR 253
            IV +S ++ E+  L D + V+ +G+          + ++I+ +   RS   R
Sbjct: 471 AIVVVSSELPELLLLADRILVMAEGRQTGLISREEASEERIMQLAAPRSARGR 523


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: 591
Number of extensions: 25
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: 526
Length adjustment: 35
Effective length of query: 471
Effective length of database: 491
Effective search space:   231261
Effective search space used:   231261
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources