Alignments for a candidate for mglA in Phyllobacterium brassicacearum STM 196

GapMind for catabolism of small carbon sources

Alignments for a candidate for mglA in Phyllobacterium brassicacearum STM 196

Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate WP_106709787.1 CU102_RS04475 sugar ABC transporter ATP-binding protein

Query= TCDB::P0AAG8
         (506 letters)



>NCBI__GCF_003010955.1:WP_106709787.1
          Length = 514

 Score =  385 bits (990), Expect = e-111
 Identities = 209/497 (42%), Positives = 305/497 (61%), Gaps = 7/497 (1%)

Query: 11  EYLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTI 70
           E +L +  + K F  VKAL NVN  +    +HAL GENGAGKSTL+  + G+ Q D G I
Sbjct: 3   EPVLSIRNVTKHFGAVKALTNVNFALERGEVHALCGENGAGKSTLMNIIAGVLQPDEGEI 62

Query: 71  LFQGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPT-KGMFVDQDKMYRE 129
           +  GK +   S   A   G+ +VHQE+ L    SV +N+++      + + ++  K+ RE
Sbjct: 63  VLDGKTVRIGSPAAAQSLGLGLVHQEIALCPDASVAENIFMASISRQRSLLMNYRKLERE 122

Query: 130 TKAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLF 189
            +A+   L   ID R +VG L +S  Q++EIAKA + + +++I DEPT++LTE E   LF
Sbjct: 123 AQAVMSRL-APIDVRRKVGELPISSQQLVEIAKALTLDCRVLIFDEPTAALTEAEARILF 181

Query: 190 TIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRS 249
            IIR LK  G  IVYISH+M EIF+LCD VTVLRDG++++T+ +A LT D ++  MVGR 
Sbjct: 182 EIIRDLKANGISIVYISHRMAEIFELCDRVTVLRDGRYVSTDRVADLTPDDVVRRMVGRE 241

Query: 250 LNQRFPDKE---NKPGEVILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIV 306
           + Q +P K+    +P EV+  VR L        RDV  DL +GEILGI GL+G+ RT+I 
Sbjct: 242 ITQLYPPKQPAGERPQEVVFSVRGLGD--NERFRDVDIDLTRGEILGIGGLIGSGRTEIA 299

Query: 307 ETLFGIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISN 366
           E + G+R  + G I +HGKQ       +A+  G   ++E+R+ +G++  L I  N  + N
Sbjct: 300 EGICGLRATTNGQILIHGKQQAIGTYADAVKAGLVYLSEDRKGSGLFLDLSIAKNISVLN 359

Query: 367 IRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPE 426
           +      +GL+D        +     + ++       + SLSGGNQQKV I + L  QP+
Sbjct: 360 LDALTGHLGLIDTVGEGDLARDFAQRLNIRMGSIGAPVSSLSGGNQQKVAIAKQLAIQPK 419

Query: 427 ILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSG 486
           ++++DEPTRGIDVGAK EI+ L+ ELA+ G GII+ISSE+PELLG+ DR++V+  G V+G
Sbjct: 420 VILMDEPTRGIDVGAKSEIHALLRELAQSGIGIIVISSELPELLGLCDRVIVIREGEVAG 479

Query: 487 IVDTKTTTQNEILRLAS 503
            +     T+  ++RLAS
Sbjct: 480 ELGMDDMTEERVIRLAS 496



 Score = 72.4 bits (176), Expect = 4e-17
 Identities = 56/231 (24%), Positives = 111/231 (48%), Gaps = 21/231 (9%)

Query: 31  NVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILFQGKEIDFHSAKEALENGI 90
           +V++ +    I  + G  G+G++ + + + G+    +G IL  GK+    +  +A++ G+
Sbjct: 274 DVDIDLTRGEILGIGGLIGSGRTEIAEGICGLRATTNGQILIHGKQQAIGTYADAVKAGL 333

Query: 91  SMVHQELN---LVLQRSVMDNM----------WLGRYPTKGMFVDQDKMYRETKAIFDEL 137
             + ++     L L  S+  N+           LG   T G    +  + R+       L
Sbjct: 334 VYLSEDRKGSGLFLDLSIAKNISVLNLDALTGHLGLIDTVG----EGDLARD---FAQRL 386

Query: 138 DIDIDP-RARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTIIRKLK 196
           +I +    A V +LS    Q + IAK  +   K+++MDEPT  +     + +  ++R+L 
Sbjct: 387 NIRMGSIGAPVSSLSGGNQQKVAIAKQLAIQPKVILMDEPTRGIDVGAKSEIHALLRELA 446

Query: 197 ERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVG 247
           + G GI+ IS ++ E+  LCD V V+R+G+      +  +T +++I +  G
Sbjct: 447 QSGIGIIVISSELPELLGLCDRVIVIREGEVAGELGMDDMTEERVIRLASG 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: 615
Number of extensions: 29
Number of successful extensions: 9
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: 514
Length adjustment: 34
Effective length of query: 472
Effective length of database: 480
Effective search space:   226560
Effective search space used:   226560
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.

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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:

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 2024 update 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