Alignments for a candidate for mglA in Rhodobacter johrii JA192

GapMind for catabolism of small carbon sources

Alignments for a candidate for mglA in Rhodobacter johrii JA192

Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate WP_069332735.1 C8J29_RS16570 sugar ABC transporter ATP-binding protein

Query= TCDB::P0AAG8
         (506 letters)



>NCBI__GCF_003046325.1:WP_069332735.1
          Length = 499

 Score =  367 bits (941), Expect = e-106
 Identities = 192/492 (39%), Positives = 305/492 (61%), Gaps = 5/492 (1%)

Query: 11  EYLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTI 70
           E +L +  +++ F  V+ L +V+  +RP  +HAL+GENGAGKST +K L G     +G +
Sbjct: 3   EPVLAIRQVSRLFGPVQVLFDVDFDLRPGEVHALIGENGAGKSTTMKILAGYLAPSAGEV 62

Query: 71  LFQGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYRET 130
           L  G+ + F S++EA   G+ M+HQE NL    +V +N++LGR   +G F+D   M  E+
Sbjct: 63  LLDGRPVHFPSSREAEAAGVVMIHQEFNLATPLTVEENIFLGRELKRGPFLDHRAMQAES 122

Query: 131 KAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFT 190
           + + + L   +DPRARV TLSV   QM+EIAKA    A+++IMDEPT+ LT +E + L  
Sbjct: 123 RRLLERLHCAVDPRARVSTLSVPNRQMVEIAKALGLKARVLIMDEPTAVLTHRETDTLLE 182

Query: 191 IIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRSL 250
            + +L+  G  I+Y SHK++E+ ++ D VTVLRDG+ + T P  GL+ D++   MVGR L
Sbjct: 183 QVDRLRAAGTAILYTSHKLDEVARIADRVTVLRDGRRVMTAPAKGLSEDRMAETMVGREL 242

Query: 251 NQRFPDKENKPGEVILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETLF 310
           +  FP K +   E +LEV  LT      +RD SF L +GE+LG AGLVG+ RT+++E + 
Sbjct: 243 SGLFPPKSSPAPEPVLEVAGLTV--PGFVRDASFTLRRGEVLGFAGLVGSGRTELMEGIV 300

Query: 311 GIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRNY 370
           G+R  + G + + G  + + + + A   G   +TE+R+  G+     +G N  +  +  +
Sbjct: 301 GLR-PATGEVRMEGSPLPHASVSAARAAGLVYLTEDRKEKGLLLGKPLGENLTLLALDRF 359

Query: 371 KNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILML 430
                L+D +  +      I    ++        GSLSGGNQQK+++ + +L +P ++++
Sbjct: 360 GRV--LIDKAAEERALTQAISDFDIRVGDRGISAGSLSGGNQQKLLLAKTMLAEPRVVII 417

Query: 431 DEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVDT 490
           DEPTRGIDVG K +IY  IA LA +G+ +I++SSE+PE++G+ +R++VMS G ++G V+ 
Sbjct: 418 DEPTRGIDVGTKQQIYGFIARLAAEGRSVIVVSSELPEVIGLANRVVVMSAGRIAGEVEG 477

Query: 491 KTTTQNEILRLA 502
           +  T+  I+RLA
Sbjct: 478 EAITEENIVRLA 489



 Score = 63.5 bits (153), Expect = 2e-14
 Identities = 55/248 (22%), Positives = 114/248 (45%), Gaps = 12/248 (4%)

Query: 11  EYLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTI 70
           E +LE++G+  + PG   + + +  +R   +    G  G+G++ L++ + G+ +  +G +
Sbjct: 255 EPVLEVAGL--TVPGF--VRDASFTLRRGEVLGFAGLVGSGRTELMEGIVGL-RPATGEV 309

Query: 71  LFQGKEIDFHSAKEALENGISMV---HQELNLVLQRSVMDNMWLGRYPTKG-MFVDQDKM 126
             +G  +   S   A   G+  +    +E  L+L + + +N+ L      G + +D+   
Sbjct: 310 RMEGSPLPHASVSAARAAGLVYLTEDRKEKGLLLGKPLGENLTLLALDRFGRVLIDKAAE 369

Query: 127 YRETKAIFDELDIDIDPRA-RVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEV 185
            R       + DI +  R    G+LS    Q + +AK      ++VI+DEPT  +     
Sbjct: 370 ERALTQAISDFDIRVGDRGISAGSLSGGNQQKLLLAKTMLAEPRVVIIDEPTRGIDVGTK 429

Query: 186 NHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMM 245
             ++  I +L   G  ++ +S ++ E+  L + V V+  G+         +T + I+ + 
Sbjct: 430 QQIYGFIARLAAEGRSVIVVSSELPEVIGLANRVVVMSAGRIAGEVEGEAITEENIVRLA 489

Query: 246 VGRSLNQR 253
           +G  LN R
Sbjct: 490 MG--LNHR 495


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: 579
Number of extensions: 22
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: 499
Length adjustment: 34
Effective length of query: 472
Effective length of database: 465
Effective search space:   219480
Effective search space used:   219480
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