GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__SB2B:6937206
          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:

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