Alignments for a candidate for mglA in Ruegeria conchae TW15

GapMind for catabolism of small carbon sources

Alignments for a candidate for mglA in Ruegeria conchae TW15

Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate WP_010437238.1 G7G_RS0100415 sugar ABC transporter ATP-binding protein

Query= TCDB::P0AAG8
         (506 letters)



>NCBI__GCF_000192475.1:WP_010437238.1
          Length = 521

 Score =  366 bits (940), Expect = e-106
 Identities = 188/491 (38%), Positives = 308/491 (62%), Gaps = 3/491 (0%)

Query: 13  LLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILF 72
           L+++  + KSF     LD V+ ++RP  +HAL GENGAGKST L   +G++Q  +G IL 
Sbjct: 15  LIQLDRVGKSFGTNIVLDGVDFELRPGEVHALCGENGAGKSTCLGLFYGLHQPSAGRILC 74

Query: 73  QGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYRETKA 132
            GKE    S   A   GI  V QEL+L    SV +N++ GR PT+   VD  ++ R  +A
Sbjct: 75  DGKEQRVESPSHAQSLGIGCVFQELSLAGALSVAENIYAGRVPTRFGVVDWPELRRRAQA 134

Query: 133 IFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTII 192
           +  E  +DID    V  L +S  Q++EIAKA S N++++++DEPTS+L   EV+ LF ++
Sbjct: 135 LLAEFGLDIDVSTPVENLPISSRQIVEIAKALSLNSRVLLLDEPTSALAPDEVDALFEVL 194

Query: 193 RKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRSLNQ 252
           + L ++G GIVY+SH M EIFQ+ D +TVLRDG+ I+T P++  + ++++A M+G +   
Sbjct: 195 KSLTKKGIGIVYVSHHMAEIFQISDRITVLRDGRHISTLPVSETSQEQVVAEMIGGAHPG 254

Query: 253 RFPDKENKPGEVILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETLFGI 312
                    GE +L V++LT        D+SF +  GEI+G+AGL+GA+R++IV ++ G+
Sbjct: 255 DVTRSGKINGEEVLHVQHLT--HPGEFEDISFSIKAGEIVGMAGLMGARRSEIVRSIVGL 312

Query: 313 REKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRNYKN 372
              + G I LHGK +N  +  +A+  G   V EER++ G++    +  N + +++ ++ +
Sbjct: 313 MHGATGEIRLHGKPVNFASLRQAMRAGVGFVPEERKTEGLFLEQSLSDNLIAASLSDHAS 372

Query: 373 KVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILMLDE 432
             G + +  +K+ +Q  ID+  VKT G    +G LSGGNQQK+++ +WL   P +L+++E
Sbjct: 373 -AGFMRSGSIKAASQTAIDAFSVKTSGINELVGDLSGGNQQKIMLAKWLKRAPALLIIEE 431

Query: 433 PTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVDTKT 492
           PT+G+DVGAKF+I+  +   A +G  I+++SS+ PEL+ ++ RILV+ +G + G +    
Sbjct: 432 PTKGVDVGAKFQIHTELLRRAAEGMAILVVSSDFPELVSLSTRILVVHDGHLMGDIAAAE 491

Query: 493 TTQNEILRLAS 503
            T+  +L++A+
Sbjct: 492 ATETTLLQMAA 502



 Score = 68.2 bits (165), Expect = 7e-16
 Identities = 56/248 (22%), Positives = 110/248 (44%), Gaps = 12/248 (4%)

Query: 9   SGEYLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSG 68
           +GE +L +  +  + PG    ++++  ++   I  + G  GA +S +++ + G+    +G
Sbjct: 263 NGEEVLHVQHL--THPG--EFEDISFSIKAGEIVGMAGLMGARRSEIVRSIVGLMHGATG 318

Query: 69  TILFQGKEIDFHSAKEALENGISMVHQELN---LVLQRSVMDNMW---LGRYPTKGMFVD 122
            I   GK ++F S ++A+  G+  V +E     L L++S+ DN+    L  + + G F+ 
Sbjct: 319 EIRLHGKPVNFASLRQAMRAGVGFVPEERKTEGLFLEQSLSDNLIAASLSDHASAG-FMR 377

Query: 123 QDKMYRETKAIFDELDIDIDP-RARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLT 181
              +   ++   D   +        VG LS    Q I +AK       ++I++EPT  + 
Sbjct: 378 SGSIKAASQTAIDAFSVKTSGINELVGDLSGGNQQKIMLAKWLKRAPALLIIEEPTKGVD 437

Query: 182 EKEVNHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKI 241
                 + T + +    G  I+ +S    E+  L   + V+ DG  +     A  T   +
Sbjct: 438 VGAKFQIHTELLRRAAEGMAILVVSSDFPELVSLSTRILVVHDGHLMGDIAAAEATETTL 497

Query: 242 IAMMVGRS 249
           + M  G S
Sbjct: 498 LQMAAGNS 505


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: 23
Number of successful extensions: 6
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: 521
Length adjustment: 35
Effective length of query: 471
Effective length of database: 486
Effective search space:   228906
Effective search space used:   228906
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 24 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