Alignments for a candidate for mglA in Dethiosulfovibrio salsuginis USBA 82

GapMind for catabolism of small carbon sources

Alignments for a candidate for mglA in Dethiosulfovibrio salsuginis USBA 82

Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate WP_085545256.1 B9Y55_RS10130 ABC transporter ATP-binding protein

Query= TCDB::P0AAG8
         (506 letters)



>NCBI__GCF_900177735.1:WP_085545256.1
          Length = 503

 Score =  322 bits (826), Expect = 2e-92
 Identities = 174/484 (35%), Positives = 284/484 (58%), Gaps = 9/484 (1%)

Query: 16  MSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILFQGK 75
           M GI KSF G+KA D ++L ++   + AL+GENGAGKSTL+  L GIY  D GTI   G 
Sbjct: 1   MKGITKSFQGIKANDQIDLTLKKGEVLALLGENGAGKSTLMNVLSGIYLPDGGTIDIGGT 60

Query: 76  EIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYRETKAIFD 135
            + F S  +A+  GI MVHQ   LV  ++V +NM LG  P     + + K+  E  AI  
Sbjct: 61  RLSFRSPNDAISAGIGMVHQHFMLVPSQTVWENMVLG-LPDLPQILPKGKIISEITAISK 119

Query: 136 ELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTIIRKL 195
           +  +++DP A +  LS+ + Q +EI K    NA+++I+DEPT+ LT +E   LF  I+++
Sbjct: 120 QYGLEVDPEAIIWQLSIGEQQRVEILKTLYRNAQVLILDEPTAVLTPQEARSLFNTIKRM 179

Query: 196 KERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRSLNQRFP 255
            E G GI++ISHK++E+ ++ D VTVLR G+ I T      + +KI  MMVG+ +N    
Sbjct: 180 TEEGRGIIFISHKLDEVMEISDRVTVLRKGKLIGTVDRENASKEKIAEMMVGKRINLDLD 239

Query: 256 DKENKPGEVILEVRNLTSLRQPSIR---DVSFDLHKGEILGIAGLVGAKRTDIVETLFGI 312
            K+  PGEV+  +    ++    ++    VS +L +G+ILG+AG+ G  +T++ + + G+
Sbjct: 240 KKDITPGEVVYSLSQANAISDRGLKALDQVSLELREGQILGLAGVAGNGQTELCQVMAGL 299

Query: 313 REKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRNYKN 372
           R+ ++G + L GK++ + +  E I+ G   +  +R+ TG+ + +D+  NS +   R ++ 
Sbjct: 300 RKMTSGKLILKGKEVTDSSPRELIDGGIRYIPADRKGTGMVSNMDVRENSTLK--RYWRR 357

Query: 373 KVG---LLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILM 429
            V    L+D   +      ++ +  V TP   T + +LSGGN QK+++GR L   P++L+
Sbjct: 358 PVARGVLIDWKAVLKHALGIVKNFNVDTPSVETPVRNLSGGNIQKLMLGRELSDIPKVLI 417

Query: 430 LDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVD 489
              PT G+DV A   + + + E  +KG  I +IS ++ EL+ ++DRI VM  G + G+V+
Sbjct: 418 AMNPTWGLDVAATRFVREQLLEEREKGAAIFLISEDLDELMSLSDRIAVMYRGKIMGLVE 477

Query: 490 TKTT 493
              T
Sbjct: 478 DPNT 481



 Score = 82.0 bits (201), Expect = 4e-20
 Identities = 57/223 (25%), Positives = 109/223 (48%), Gaps = 14/223 (6%)

Query: 282 VSFDLHKGEILGIAGLVGAKRTDIVETLFGIREKSAGTITLHGKQINNHNANEAINHGFA 341
           +   L KGE+L + G  GA ++ ++  L GI     GTI + G +++  + N+AI+ G  
Sbjct: 17  IDLTLKKGEVLALLGENGAGKSTLMNVLSGIYLPDGGTIDIGGTRLSFRSPNDAISAGIG 76

Query: 342 LVTEERR---STGIYAYLDIGFNSLISNIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTP 398
           +V +      S  ++  + +G   L            +L   ++ S+   +     ++  
Sbjct: 77  MVHQHFMLVPSQTVWENMVLGLPDLPQ----------ILPKGKIISEITAISKQYGLEVD 126

Query: 399 GHRTQIGSLSGGNQQKVIIGRWLLTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKG 458
                I  LS G QQ+V I + L    ++L+LDEPT  +       ++  I  + ++G+G
Sbjct: 127 PEAI-IWQLSIGEQQRVEILKTLYRNAQVLILDEPTAVLTPQEARSLFNTIKRMTEEGRG 185

Query: 459 IIIISSEMPELLGITDRILVMSNGLVSGIVDTKTTTQNEILRL 501
           II IS ++ E++ I+DR+ V+  G + G VD +  ++ +I  +
Sbjct: 186 IIFISHKLDEVMEISDRVTVLRKGKLIGTVDRENASKEKIAEM 228


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: 572
Number of extensions: 27
Number of successful extensions: 8
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: 503
Length adjustment: 34
Effective length of query: 472
Effective length of database: 469
Effective search space:   221368
Effective search space used:   221368
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