GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA in Marinobacter algicola DG893

Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate WP_007152784.1 MDG893_RS05705 CoA-acylating methylmalonate-semialdehyde dehydrogenase

Query= BRENDA::Q9EQ20
         (535 letters)



>NCBI__GCF_000170835.1:WP_007152784.1
          Length = 496

 Score =  563 bits (1451), Expect = e-165
 Identities = 264/482 (54%), Positives = 359/482 (74%)

Query: 40  VKLFIDGKFVESKSDKWIDIHNPATNEVVGRVPQSTKAEMDAAVESCKRAFPAWADTSIL 99
           V L+I G+FV+S++D+WID+ +PATNEV+ R P +T AEM  A+E+    F  W +  + 
Sbjct: 4   VPLYIAGEFVQSQTDQWIDVTDPATNEVIARAPCTTDAEMRRAIENAGEVFKTWKEVPVS 63

Query: 100 SRQQVLLRYQQLIKENLKEIARLITLEQGKTLADAEGDVFRGLQVVEHACSVTSLMLGET 159
            R +V++RYQ L+KE+  EIA +++ E GKT  DA+GDV+RG++VVEHA ++ SLM+GET
Sbjct: 64  ERARVMMRYQALLKEHHDEIAEILSSETGKTFEDAKGDVWRGIEVVEHAANIPSLMMGET 123

Query: 160 MPSITKDMDLYSYRLPLGVCAGIAPFNFPAMIPLWMFPMAMVCGNTFLMKPSERVPGATM 219
           + ++ +++D YSY  PLGVCAGI PFNFPAMIPLWMFPMA+  GNTF++KPSE+ P   M
Sbjct: 124 VENVAREIDTYSYTQPLGVCAGITPFNFPAMIPLWMFPMAIASGNTFILKPSEQDPLTPM 183

Query: 220 LLAKLLQDSGAPDGTLNIIHGQHDAVNFICDHPDIKAISFVGSNQAGEYIFERGSRNGKR 279
            LA+L +++GAP G L ++HG  + V+ +   P IKA+SFVGS   G YI+E G+RN KR
Sbjct: 184 RLAELFEEAGAPKGVLQVVHGGKEQVDVLLTDPAIKAVSFVGSVPVGRYIYETGTRNMKR 243

Query: 280 VQANMGAKNHGVVMPDANKENTLNQLVGAAFGAAGQRCMALSTAILVGEAKKWLPELVDR 339
           VQ+  GAKNH V++PDA+K   +  LVGA+ GAAGQRCMA+S A+ VGEA++W+PE+ + 
Sbjct: 244 VQSFAGAKNHMVILPDADKNQVVKALVGASVGAAGQRCMAISVAVFVGEAQEWIPEVKEA 303

Query: 340 AKNLRVNAGDQPGADLGPLITPQAKERVCNLIDSGTKEGASILLDGRRIKVKGYENGNFV 399
              +R  A +   A  GP+I+ QAK+RV +LI  G +EGA +LLDGR   V G  +GN+V
Sbjct: 304 LAAVRPGAWNDKEASYGPIISKQAKQRVESLITRGEEEGAKLLLDGRNCTVDGLPDGNWV 363

Query: 400 GPTIISNVKPSMTCYKEEIFGPVLVVLETETLDEAIKIVNDNPYGNGTAIFTTNGATARK 459
           GPT+ + VKP M  YKEEIFGPVL  +E +TL++AI +VND+PYGNGT+IFT++G  AR+
Sbjct: 364 GPTLFAGVKPEMDVYKEEIFGPVLACMEVDTLEDAINLVNDSPYGNGTSIFTSSGGAARR 423

Query: 460 YAHMVDVGQVGVNVPIPVPLPMFSFTGSRSSFRGDTNFYGKQGIQFYTQLKTITSQWKEE 519
           Y H ++VGQVG+NVPIPVPLP FSFTG + SF GD + YGKQ ++FYT+ KTIT +W   
Sbjct: 424 YQHEIEVGQVGINVPIPVPLPFFSFTGWKGSFYGDQHAYGKQAVKFYTETKTITCRWFSS 483

Query: 520 DA 521
           DA
Sbjct: 484 DA 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: 727
Number of extensions: 25
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: 496
Length adjustment: 35
Effective length of query: 500
Effective length of database: 461
Effective search space:   230500
Effective search space used:   230500
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 24 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