GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA in Shewanella loihica PV-4

Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate 5209190 Shew_1668 methylmalonate-semialdehyde dehydrogenase (RefSeq)

Query= BRENDA::Q02252
         (535 letters)



>FitnessBrowser__PV4:5209190
          Length = 501

 Score =  564 bits (1453), Expect = e-165
 Identities = 272/481 (56%), Positives = 351/481 (72%)

Query: 40  VKLFIGGKFVESKSDKWIDIHNPATNEVIGRVPQATKAEMDAAIASCKRAFPAWADTSVL 99
           VK +I G+F+     + I + NPA NEVI  +  AT  E++ AIAS K+AF  W +  V 
Sbjct: 5   VKHYIDGQFILGSGQQQISVTNPANNEVIATINAATVEEVETAIASAKQAFATWKEVPVS 64

Query: 100 SRQQVLLRYQQLIKENLKEIAKLITLEQGKTLADAEGDVFRGLQVVEHACSVTSLMMGET 159
            R +V+ RYQ L+K +  EIA ++  E GKT  DA+GDV+RG++V EHAC++ SL+MGET
Sbjct: 65  ERARVMFRYQHLLKLHHDEIATILAQETGKTFEDAKGDVWRGIEVAEHACNIASLIMGET 124

Query: 160 MPSITKDMDLYSYRLPLGVCAGIAPFNFPAMIPLWMFPMAMVCGNTFLMKPSERVPGATM 219
           + ++ + +D YSY  PLGVCAGI PFNFPAMIPLWMFP+A+ CGNTF++KPSE+ P    
Sbjct: 125 VENVARSIDTYSYTQPLGVCAGITPFNFPAMIPLWMFPLAIACGNTFVLKPSEQDPLTPQ 184

Query: 220 LLAKLLQDSGAPDGTLNIIHGQHEAVNFICDHPDIKAISFVGSNKAGEYIFERGSRHGKR 279
            L +L +++GAP G L ++HG   AV+ +  H DIKAISFVGS   G+YI++ G+ + KR
Sbjct: 185 RLVELFEEAGAPKGVLQLVHGDKTAVDVLLSHQDIKAISFVGSVGVGQYIYKTGTDNLKR 244

Query: 280 VQANMGAKNHGVVMPDANKENTLNQLVGAAFGAAGQRCMALSTAVLVGEAKKWLPELVEH 339
           VQA  GAKNH V+MPDANK+  +N LVGA+ GAAGQRCMALS AV VGEAKKW+PEL + 
Sbjct: 245 VQAFAGAKNHCVIMPDANKQQVINNLVGASVGAAGQRCMALSVAVFVGEAKKWIPELRDA 304

Query: 340 AKNLRVNAGDQPGADLGPLITPQAKERVCNLIDSGTKEGASILLDGRKIKVKGYENGNFV 399
              +R    D   A  GP+I+P AK RV  LI  G +EGA  LLDG    V+GYENGN+V
Sbjct: 305 IAKVRPGVWDDKDAAYGPVISPAAKARVLKLIAQGKEEGAECLLDGSDFTVEGYENGNWV 364

Query: 400 GPTIISNVKPNMTCYKEEIFGPVLVVLETETLDEAIQIVNNNPYGNGTAIFTTNGATARK 459
           GPT+ +NV  +M+ YKEEIFGPVL  +E E+L+EAI++VNN+PYGNGT+IFT  GA ARK
Sbjct: 365 GPTMFTNVTTDMSIYKEEIFGPVLCCMEVESLEEAIELVNNSPYGNGTSIFTACGAAARK 424

Query: 460 YAHLVDVGQVGVNVPIPVPLPMFSFTGSRSSFRGDTNFYGKQGIQFYTQLKTITSQWKEE 519
           Y H ++VGQVG+NVPIPVPLP FSFTG + SF GD + YGKQ ++FYT+ KTIT++W E 
Sbjct: 425 YQHNIEVGQVGINVPIPVPLPFFSFTGWKGSFYGDQHAYGKQAVRFYTETKTITARWFET 484

Query: 520 D 520
           D
Sbjct: 485 D 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: 695
Number of extensions: 20
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: 501
Length adjustment: 35
Effective length of query: 500
Effective length of database: 466
Effective search space:   233000
Effective search space used:   233000
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