GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Smeli:SMa1328
          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:

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