GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Paucidesulfovibrio gracilis DSM 16080

Align Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 (characterized)
to candidate WP_078716498.1 B5D49_RS04560 ABC transporter ATP-binding protein

Query= SwissProt::P23924
         (506 letters)



>NCBI__GCF_900167125.1:WP_078716498.1
          Length = 514

 Score =  275 bits (702), Expect = 4e-78
 Identities = 163/479 (34%), Positives = 274/479 (57%), Gaps = 12/479 (2%)

Query: 7   PPSGEYLLEMRGINKSFPGVKALDNVNLNVRPHSIHALMGENGAGKSTLLKCLFGIYQKD 66
           PP G  L+ ++G+ K F  V A D+++LN+ P  + AL+GENGAGKSTL+  L G YQ D
Sbjct: 18  PPQGIPLVSIKGLTKRFGKVVANDDISLNIYPGRVKALLGENGAGKSTLMSMLAGRYQPD 77

Query: 67  SGSIVFQGKEVDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKM 126
           +G+I   GK V F SA++A+E GI MV+Q   LV   +V +N+ LG+      F++  +M
Sbjct: 78  AGTIALDGKPVRFSSARDAIEAGIGMVYQHFMLVESMTVAENVLLGQ--EGSFFLNPKEM 135

Query: 127 YQDTKAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVN 186
               + +     +DIDP ARV  LS+ + Q +EI K    +++++I DEPT+ LT +E  
Sbjct: 136 RNRVQELSVRYGLDIDPAARVSDLSMGEKQRVEILKLLYRDSRVLIFDEPTAVLTPRETF 195

Query: 187 HLFTIIRKLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIAT-QPLEGLDMDKIIAMM 245
           HLF  + K+ E+G  IV+ISHK+EE+  + DEI ILR G+        E      +   M
Sbjct: 196 HLFEALWKIAEQGKSIVFISHKLEEVLAVADEIAILRQGRIEGEFSESEVTSKADLACRM 255

Query: 246 VGRSLNQRFPDKENKP-GDVILEVRHLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTD 304
           VG+ +     D+E  P GD +L+VR+LT +    + D++FDLH+GE++ + G+ G  +  
Sbjct: 256 VGKEVLLEV-DREAMPHGDAVLQVRNLTGI---GLEDITFDLHQGEVVAVVGVAGNGQKA 311

Query: 305 IVETLFGIREKSSGTITLHGKKINNHTANEAINHGFALVTEERRSTGIYAYLDIGFNSLI 364
           +VE + G+R+    T+ + GK+  +  A  +  +  A + E+R        L++  N L+
Sbjct: 312 LVEAICGLRKPPVDTMFIMGKRWRDFYAKPSWKNSLAYIPEDRLGLATCRNLNLVDNLLL 371

Query: 365 SNIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIG-SLSGGNQQKVIIGRWLLT 423
           +  + +  +   LD  +   DT  +I    ++ PG    +   LSGGN QK ++ R L  
Sbjct: 372 TTRQGFA-RGPWLDKKKAARDTTELIKKFDIR-PGRIAALAWQLSGGNLQKSVLARELYR 429

Query: 424 QPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNG 482
            P +++ ++PT+G+D+ A  +++  +   A++  GI++++ ++ E L + DR+ V+  G
Sbjct: 430 CPRLIVAEQPTQGLDIAATEQVWNHLL-AAREMAGILLVTGDLNEALQLADRVAVIYRG 487



 Score = 78.2 bits (191), Expect = 7e-19
 Identities = 50/206 (24%), Positives = 101/206 (49%), Gaps = 9/206 (4%)

Query: 281 DVSFDLHKGEILGIAGLVGAKRTDIVETLFGIREKSSGTITLHGKKINNHTANEAINHGF 340
           D+S +++ G +  + G  GA ++ ++  L G  +  +GTI L GK +   +A +AI  G 
Sbjct: 42  DISLNIYPGRVKALLGENGAGKSTLMSMLAGRYQPDAGTIALDGKPVRFSSARDAIEAGI 101

Query: 341 ALVTEERRSTGIYAYLDIGFNSLISNIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGH 400
            +V +      +   + +  N L+    ++      + N   +   ++ +D      P  
Sbjct: 102 GMVYQHFM---LVESMTVAENVLLGQEGSFFLNPKEMRNRVQELSVRYGLDI----DPAA 154

Query: 401 RTQIGSLSGGNQQKVIIGRWLLTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGII 460
           R  +  LS G +Q+V I + L     +L+ DEPT  +     F +++ + ++A++GK I+
Sbjct: 155 R--VSDLSMGEKQRVEILKLLYRDSRVLIFDEPTAVLTPRETFHLFEALWKIAEQGKSIV 212

Query: 461 IISSEMPELLGITDRILVMSNGLVSG 486
            IS ++ E+L + D I ++  G + G
Sbjct: 213 FISHKLEEVLAVADEIAILRQGRIEG 238


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: 562
Number of extensions: 28
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: 514
Length adjustment: 34
Effective length of query: 472
Effective length of database: 480
Effective search space:   226560
Effective search space used:   226560
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:

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:

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:

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:

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