GapMind for catabolism of small carbon sources

 

Aligments for a candidate for proP in Sinorhizobium meliloti 1021

Align Glycine betaine/proline/ectoine/pipecolic acid transporter OusA; Osmoprotectant uptake system A (characterized)
to candidate SMa1328 SMa1328 MtbA protein

Query= SwissProt::Q47421
         (501 letters)



>lcl|FitnessBrowser__Smeli:SMa1328 SMa1328 MtbA protein
          Length = 440

 Score =  200 bits (508), Expect = 1e-55
 Identities = 136/430 (31%), Positives = 217/430 (50%), Gaps = 24/430 (5%)

Query: 25  RKAITAAALGNAMEWFDFGVYGFVAYALGQVFFPGADPGVQMIAALATFSVPFLIRPLGG 84
           R+ I AA++GN +EW+DF ++G +A  L   FF  + P   +++ +A F+  FLIRPLG 
Sbjct: 10  RRVIVAASVGNIIEWYDFYIFGSLAAVLSVKFFEQSHPVAALLSTIALFTAGFLIRPLGA 69

Query: 85  VFFGALGDKYGRQKILAITIIIMSISTFCIGLIPSYERIGIWAPILLLLAKMAQGFSVGG 144
             FG +GD+ GR+    IT+  M + T  IGLIP+YE IG+ A  LL   +M QG  +GG
Sbjct: 70  FLFGWMGDRVGRKYTFLITLTGMGLGTGAIGLIPTYESIGLTAAFLLFSLRMIQGLCLGG 129

Query: 145 EYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVLISTLIGEQAFLAWGWRLP 204
           EY GA  +VAE+ PD +RG+   WL      G V+   V++   T  G +AF AW WR+P
Sbjct: 130 EYGGAITYVAEHVPDERRGYYTGWLQTSPTLGIVVSLAVIIAARTYFGSEAFDAWAWRVP 189

Query: 205 FFLALPLGLIGLYLRHALEETPAFRQHVEK--LEQNDRDGLKAGPGVSFREIATHHWKSL 262
           F ++  L  I +Y+R  L+ETP F++   K  + QN          + +  IAT      
Sbjct: 190 FLVSFLLVGIAIYIRLQLQETPIFQEIKAKGQMTQNPWREAFLSSNIKYVGIAT------ 243

Query: 263 LVCIGLVIATNVTYYMLLTYMPSYLS-HSLHYSENHGVLIIIAIMIGMLFVQPVMGLLSD 321
           +V IG  +      +  L ++        L+ +   G  +++A    +LF     G LSD
Sbjct: 244 IVLIGQGVVWYSGQFWALYFLQQVSKVDPLNSAYIVGAALLLATPSLILF-----GWLSD 298

Query: 322 RFGRKPFVVIGSVAMFFLAVPSFMLI-------NSDIIGLIFLGLLMLAVILNAFTGVMA 374
             GRKP ++ G +       P ++ +       N +    IF+ + +L   +    G + 
Sbjct: 299 IIGRKPVILGGMLLAALTYYPLYLWLGAVTQPDNINYPIAIFI-IFILVCYVGMVYGPVG 357

Query: 375 STLPALFPTHIRYSALASAFNI-SVLIAGLTPTVAAWLVESSQNL-YMPAYYLMVIAVIG 432
           + L   FP  IRY++++  ++I +    GL P + +    ++ ++ Y   Y + V AV  
Sbjct: 358 AFLAEYFPGRIRYTSVSVPYHIGNGWGGGLVPFITSAAFAATGSIGYALIYPIAVPAVCF 417

Query: 433 LLTGLFMKET 442
           +L    M ET
Sbjct: 418 VLAIFLMPET 427


Lambda     K      H
   0.327    0.142    0.427 

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: 603
Number of extensions: 27
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 501
Length of database: 440
Length adjustment: 33
Effective length of query: 468
Effective length of database: 407
Effective search space:   190476
Effective search space used:   190476
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 51 (24.3 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:

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 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