Alignments for a candidate for mglA in Maridesulfovibrio bastinii DSM 16055

GapMind for catabolism of small carbon sources

Alignments for a candidate for mglA in Maridesulfovibrio bastinii DSM 16055

Align Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 (characterized)
to candidate WP_027178119.1 G496_RS0103835 ABC transporter ATP-binding protein

Query= SwissProt::P23924
         (506 letters)



>NCBI__GCF_000429985.1:WP_027178119.1
          Length = 513

 Score =  266 bits (681), Expect = 1e-75
 Identities = 156/482 (32%), Positives = 270/482 (56%), Gaps = 8/482 (1%)

Query: 2   GSTISPPSGEYLLEMRGINKSFPGVKALDNVNLNVRPHSIHALMGENGAGKSTLLKCLFG 61
           GS     S   ++ ++GI K F  V A + + L++ P  I AL+GENGAGKSTL+  L G
Sbjct: 13  GSPAEYASSSPIVSLKGITKRFGKVVANNKIVLDLYPGRIKALLGENGAGKSTLMSMLAG 72

Query: 62  IYQKDSGSIVFQGKEVDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFV 121
            +Q D G I   GK VDF S+K+A+  GI MV+Q   LV   +V +N+ LG+    G FV
Sbjct: 73  RFQPDEGHIEVDGKRVDFSSSKDAINAGIGMVYQHFMLVDSMTVTENVLLGQ--EGGFFV 130

Query: 122 DQDKMYQDTKAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLT 181
           +  +M +  K + ++ +++IDP AR+  LS+ + Q +EI K     ++++I DEPT+ LT
Sbjct: 131 NPKEMSRRVKKLAEDYELEIDPDARINQLSMGEKQRVEILKLLYRESRVLIFDEPTAVLT 190

Query: 182 EKEVNHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIATQPLEGLDMDKI 241
            +E   LF  +  +  +G  IV+ISHK+EE+  + DE+ ILR G   +  P E +     
Sbjct: 191 PRETFRLFEALWAMTRQGKSIVFISHKLEEVMAIADEVAILRRGCVDSEVPREKITSKAD 250

Query: 242 IA-MMVGRSLNQRFPDKENKPGDVILEVRHLTSLRQPSIRDVSFDLHKGEILGIAGLVGA 300
           +A  MVG+ +       E + GD +LEV+ L  L    +++++ ++H+GE++GI G+ G 
Sbjct: 251 LACRMVGKEVLLEIDRNEVEIGDKVLEVKSLNGL---GLKNINIEVHRGEVVGIVGVAGN 307

Query: 301 KRTDIVETLFGIREKSSGTITLHGKKINNHTANEAINHGFALVTEERRSTGIYAYLDIGF 360
            +  +VE + G+R     ++ + GK      A    NH  + + E+R        LD+  
Sbjct: 308 GQQALVEGVCGLRMPPKDSVFIMGKAWREFFAKMTWNHSLSYIPEDRLDLATARELDLVD 367

Query: 361 NSLISNIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRW 420
           N L++  + + +   +L   +     + +++   V+    +     LSGGN QK+++ R 
Sbjct: 368 NLLLTTRQGFCSG-PVLHRDKAAEVAKKLVEDHDVRPGRIQALAWQLSGGNLQKLVLARE 426

Query: 421 LLTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMS 480
           L  +P +++ ++PT+G+D+ A  E++  + E A+K  G+++++ ++ E L ++DRI VM 
Sbjct: 427 LYREPHLIVAEQPTQGLDISATEEVWNRLLE-ARKMAGVLLVTGDLNEALQLSDRIAVMY 485

Query: 481 NG 482
            G
Sbjct: 486 RG 487



 Score = 71.2 bits (173), Expect = 8e-17
 Identities = 46/213 (21%), Positives = 101/213 (47%), Gaps = 9/213 (4%)

Query: 282 VSFDLHKGEILGIAGLVGAKRTDIVETLFGIREKSSGTITLHGKKINNHTANEAINHGFA 341
           +  DL+ G I  + G  GA ++ ++  L G  +   G I + GK+++  ++ +AIN G  
Sbjct: 43  IVLDLYPGRIKALLGENGAGKSTLMSMLAGRFQPDEGHIEVDGKRVDFSSSKDAINAGIG 102

Query: 342 LVTEERRSTGIYAYLDIGFNSLISNIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHR 401
           +V +         ++ +   ++  N+   +     ++   M    + + +   ++     
Sbjct: 103 MVYQH--------FMLVDSMTVTENVLLGQEGGFFVNPKEMSRRVKKLAEDYELEIDPD- 153

Query: 402 TQIGSLSGGNQQKVIIGRWLLTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIII 461
            +I  LS G +Q+V I + L  +  +L+ DEPT  +     F +++ +  + ++GK I+ 
Sbjct: 154 ARINQLSMGEKQRVEILKLLYRESRVLIFDEPTAVLTPRETFRLFEALWAMTRQGKSIVF 213

Query: 462 ISSEMPELLGITDRILVMSNGLVSGIVDTKTTT 494
           IS ++ E++ I D + ++  G V   V  +  T
Sbjct: 214 ISHKLEEVMAIADEVAILRRGCVDSEVPREKIT 246


Lambda     K      H
   0.319    0.137    0.388 

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: 574
Number of extensions: 26
Number of successful extensions: 7
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: 513
Length adjustment: 34
Effective length of query: 472
Effective length of database: 479
Effective search space:   226088
Effective search space used:   226088
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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 Apr 09 2024. 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