Aligments for a candidate for mglA in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Aligments for a candidate for mglA in Pseudomonas stutzeri RCH2

Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate GFF1357 Psest_1392 ABC-type uncharacterized transport systems, ATPase components

Query= TCDB::P0AAG8
         (506 letters)



>FitnessBrowser__psRCH2:GFF1357
          Length = 518

 Score =  272 bits (696), Expect = 2e-77
 Identities = 172/505 (34%), Positives = 271/505 (53%), Gaps = 17/505 (3%)

Query: 7   PSSGEYLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKD 66
           P S    L++ GI K +PG  A D ++L ++P  IHAL+GENGAGKSTL+K ++G+ Q D
Sbjct: 2   PDSQTARLQLCGITKQYPGCLANDRIDLSIQPGEIHALLGENGAGKSTLMKIIYGVTQPD 61

Query: 67  SGTILFQGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKM 126
           +G I +QG+ +      +A E GI MV Q  +L    SV +N+ L      G     +  
Sbjct: 62  AGEIHWQGERVTMRDPAQARERGIGMVFQHFSLFETLSVAENIALALGAKAGTPKQLEPK 121

Query: 127 YRETKAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVN 186
            RE   +     + ++P+  V +LS+ + Q +EI +    + +++I+DEPTS LT +E +
Sbjct: 122 IRE---VSQRYGMPLEPQRLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEAD 178

Query: 187 HLFTIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIA-MM 245
            LF  +R+L   GC I++ISHK+ E+  LC   TVLR G+ ++ E +     D  +A +M
Sbjct: 179 ELFVTLRRLAAEGCSILFISHKLNEVRALCQSATVLRAGR-VSGECIPAECSDLELARLM 237

Query: 246 VG--RSLNQRFPDKENKPGEVILEVRNLTSLRQP----SIRDVSFDLHKGEILGIAGLVG 299
           VG    L   +P  E +     L V  L+         S+++V  ++  GEI+GIAG+ G
Sbjct: 238 VGDAEGLEAEYPKSEGRAP--FLRVERLSWHNADPFGVSLKEVDLEVRAGEIVGIAGVAG 295

Query: 300 AKRTDIVETLFG---IREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYL 356
             + +++  L G   ++   A  I   G  + +        HG A V  ER   G    +
Sbjct: 296 NGQDELLALLSGEQRLQAAQAMRIRFLGDDVAHLRPGARRRHGMAFVPAERLGHGAVPSM 355

Query: 357 DIGFNSLISNIRNYKN-KVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKV 415
            +  N L++  +     + GL+   R+++  + VI    VKTP  +T   SLSGGN QK 
Sbjct: 356 SLADNGLLTAYQQTGMVEQGLIRRGRVRAFAEQVIQRFAVKTPDAQTPAASLSGGNLQKF 415

Query: 416 IIGRWLLTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDR 475
           I+GR +L QP++L+   PT G+DVGA   I++ + EL   G  I++IS ++ EL  I+DR
Sbjct: 416 ILGREILQQPKLLIAAHPTWGVDVGAAAAIHRALIELRDAGAAILVISEDLEELFQISDR 475

Query: 476 ILVMSNGLVSGIVDTKTTTQNEILR 500
           I  +S+G +S    T +T   E+ R
Sbjct: 476 IAALSDGRLSPQRATASTCPVEVGR 500



 Score = 60.1 bits (144), Expect = 2e-13
 Identities = 51/221 (23%), Positives = 100/221 (45%), Gaps = 12/221 (5%)

Query: 282 VSFDLHKGEILGIAGLVGAKRTDIVETLFGIREKSAGTITLHGKQINNHNANEAINHGFA 341
           +   +  GEI  + G  GA ++ +++ ++G+ +  AG I   G+++   +  +A   G  
Sbjct: 27  IDLSIQPGEIHALLGENGAGKSTLMKIIYGVTQPDAGEIHWQGERVTMRDPAQARERGIG 86

Query: 342 LVTEERRSTGIYAYLDIGFNSLISNIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHR 401
           +V +      ++  L +  N  ++        +G    +  + + +    S R   P   
Sbjct: 87  MVFQH---FSLFETLSVAENIALA--------LGAKAGTPKQLEPKIREVSQRYGMPLEP 135

Query: 402 TQ-IGSLSGGNQQKVIIGRWLLTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGII 460
            + + SLS G +Q+V I R L+    +L+LDEPT  +      E++  +  LA +G  I+
Sbjct: 136 QRLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADELFVTLRRLAAEGCSIL 195

Query: 461 IISSEMPELLGITDRILVMSNGLVSGIVDTKTTTQNEILRL 501
            IS ++ E+  +     V+  G VSG       +  E+ RL
Sbjct: 196 FISHKLNEVRALCQSATVLRAGRVSGECIPAECSDLELARL 236


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: 563
Number of extensions: 32
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: 518
Length adjustment: 35
Effective length of query: 471
Effective length of database: 483
Effective search space:   227493
Effective search space used:   227493
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 17 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, or view the source code.

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