GapMind for catabolism of small carbon sources

 

Aligments for a candidate for iolA in Shewanella amazonensis SB2B

Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate 6937206 Sama_1376 methylmalonate-semialdehyde dehydrogenase (RefSeq)

Query= BRENDA::Q02252
         (535 letters)



>lcl|FitnessBrowser__SB2B:6937206 Sama_1376
           methylmalonate-semialdehyde dehydrogenase (RefSeq)
          Length = 497

 Score =  556 bits (1432), Expect = e-163
 Identities = 266/484 (54%), Positives = 350/484 (72%)

Query: 37  VPTVKLFIGGKFVESKSDKWIDIHNPATNEVIGRVPQATKAEMDAAIASCKRAFPAWADT 96
           +  VK +I G+F   + ++ I + NPA N+ I  V  A+  E+  AIAS K AF +W + 
Sbjct: 2   ITQVKHYIDGEFTTGQGERIITVTNPANNQPIAEVRCASDEEVHGAIASAKAAFQSWKEV 61

Query: 97  SVLSRQQVLLRYQQLIKENLKEIAKLITLEQGKTLADAEGDVFRGLQVVEHACSVTSLMM 156
            V  R +V+LRYQ L+KE+  E+A ++  E GKT  DA+GDV+RG++V EHAC++ SL+M
Sbjct: 62  PVSERARVMLRYQALLKEHHDELATILAKETGKTFEDAKGDVWRGIEVAEHACNIASLLM 121

Query: 157 GETMPSITKDMDLYSYRLPLGVCAGIAPFNFPAMIPLWMFPMAMVCGNTFLMKPSERVPG 216
           GET+ ++ + +D YSY  PLGVCAGI PFNFPAMIPLWMFP+A+ CGNTF++KPSE+ P 
Sbjct: 122 GETVENVARKIDTYSYTQPLGVCAGITPFNFPAMIPLWMFPLAVACGNTFVLKPSEQDPM 181

Query: 217 ATMLLAKLLQDSGAPDGTLNIIHGQHEAVNFICDHPDIKAISFVGSNKAGEYIFERGSRH 276
             + LA+L + +GAP G L ++HG   AV+ +  HPDIKAISFVGS   G+Y+++ G+ +
Sbjct: 182 TPLRLAELFEQAGAPKGVLQLVHGDKSAVDILLTHPDIKAISFVGSVGVGQYVYKTGTDN 241

Query: 277 GKRVQANMGAKNHGVVMPDANKENTLNQLVGAAFGAAGQRCMALSTAVLVGEAKKWLPEL 336
            KRVQA  GAKNH V+MPDANK+  +N LVGA+ GAAGQRCMA+S AV VG AK+W+PEL
Sbjct: 242 LKRVQAFAGAKNHCVIMPDANKQQVINNLVGASVGAAGQRCMAISVAVFVGAAKEWIPEL 301

Query: 337 VEHAKNLRVNAGDQPGADLGPLITPQAKERVCNLIDSGTKEGASILLDGRKIKVKGYENG 396
            E    +R    D   A  GPLI+P AK RV  LI+ G  EGA  LLDG    V GYE+G
Sbjct: 302 KEALAKVRPGLWDDKDAGYGPLISPAAKARVLKLIEQGKAEGAECLLDGSDFTVPGYESG 361

Query: 397 NFVGPTIISNVKPNMTCYKEEIFGPVLVVLETETLDEAIQIVNNNPYGNGTAIFTTNGAT 456
           N+VGPT+   V  +M+ YKEEIFGPVL  +E + L++AI++VN +PYGNGT+IFT +GA 
Sbjct: 362 NWVGPTMFDKVTTDMSIYKEEIFGPVLCCMEVDELEDAIELVNKSPYGNGTSIFTASGAA 421

Query: 457 ARKYAHLVDVGQVGVNVPIPVPLPMFSFTGSRSSFRGDTNFYGKQGIQFYTQLKTITSQW 516
           ARKY H ++VGQVG+NVPIPVPLP FSFTG + SF GD + YGKQ I+F+T+ KTIT +W
Sbjct: 422 ARKYQHEIEVGQVGINVPIPVPLPFFSFTGWKGSFYGDQHAYGKQAIRFFTETKTITCRW 481

Query: 517 KEED 520
            E+D
Sbjct: 482 FEDD 485


Lambda     K      H
   0.318    0.133    0.391 

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: 710
Number of extensions: 27
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 535
Length of database: 497
Length adjustment: 35
Effective length of query: 500
Effective length of database: 462
Effective search space:   231000
Effective search space used:   231000
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:

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 preprint 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