Alignments for a candidate for mglA in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for mglA in Halomonas desiderata SP1

Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate WP_086510989.1 BZY95_RS16555 L-arabinose ABC transporter ATP-binding protein AraG

Query= TCDB::P0AAG8
         (506 letters)



>NCBI__GCF_002151265.1:WP_086510989.1
          Length = 497

 Score =  373 bits (958), Expect = e-108
 Identities = 207/496 (41%), Positives = 306/496 (61%), Gaps = 8/496 (1%)

Query: 11  EYLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTI 70
           E  L   GI+  FPGV+ALD V+       +HALMGENGAGKSTLLK L G+     G +
Sbjct: 3   EPYLRFDGISMVFPGVRALDGVSFGAHAGQVHALMGENGAGKSTLLKVLSGVNHPSEGAL 62

Query: 71  LFQGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYRET 130
              G+   F +A+EAL  GI++++QEL L    +V +N+ LG+ PT+  F+ + ++    
Sbjct: 63  WIDGERHVFANAREALAQGIAIIYQELTLSPNMTVAENLLLGQLPTRHGFIKRRQLRERA 122

Query: 131 KAIFDEL-DIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLF 189
            AI  +L + DI P  +V  LS+ Q QMIEI +A   NA+I+  DEPTSSL+ +E   L 
Sbjct: 123 LAILADLGEGDIHPSTKVRELSIGQQQMIEIGRALLRNARIIAFDEPTSSLSVQETRQLK 182

Query: 190 TIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEP-LAGLTMDKIIAMMVGR 248
            II +L+E G  ++Y++H+MEE+F +CD VTV RDG+ I T   LA L  D +++ MVGR
Sbjct: 183 RIISRLREEGRVVLYVTHRMEEVFDMCDAVTVFRDGKHIRTHASLAALDHDTLVSEMVGR 242

Query: 249 SLNQRFPDKENKPGEVILEVRNLTS--LRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIV 306
            +   +  +E + GEVILE+  +    L+ P    VSF++ +GE+ G+ GLVGA R++++
Sbjct: 243 DIEDVYGYRERERGEVILEIDAIEGRGLKAP----VSFEVRRGEVFGLFGLVGAGRSELM 298

Query: 307 ETLFGIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISN 366
             + G    SAG +   G+     +  EAI  G A+  E+R+S GI+    +  N  IS 
Sbjct: 299 RLVCGAERASAGEVRFQGQARRFASPGEAIRMGIAMCPEDRKSQGIFPVASVADNLNISC 358

Query: 367 IRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPE 426
            R ++    L D  R +++ +  I  + +KTPG RT IG+LSGGNQQKVI+ RWL  + E
Sbjct: 359 RRFFRRWGVLRDTRRERANAEAYIQRLSIKTPGPRTAIGTLSGGNQQKVILARWLAEKIE 418

Query: 427 ILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSG 486
           + ++DEPTRGIDVGA+ +IY L+ +L ++GK +++ISS++ E+  I DRI VM +G +  
Sbjct: 419 LFVVDEPTRGIDVGARRDIYTLLFDLTEQGKSVVVISSDLAEVSSICDRIGVMRDGALVE 478

Query: 487 IVDTKTTTQNEILRLA 502
           +V     TQ  +L LA
Sbjct: 479 VVPRHEATQERLLGLA 494


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: 569
Number of extensions: 27
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 506
Length of database: 497
Length adjustment: 34
Effective length of query: 472
Effective length of database: 463
Effective search space:   218536
Effective search space used:   218536
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 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