GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mmsA in Sphingomonas koreensis DSMZ 15582

Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate Ga0059261_3677 Ga0059261_3677 methylmalonic acid semialdehyde dehydrogenase

Query= reanno::Smeli:SMc00781
         (498 letters)



>FitnessBrowser__Korea:Ga0059261_3677
          Length = 503

 Score =  652 bits (1681), Expect = 0.0
 Identities = 320/496 (64%), Positives = 379/496 (76%), Gaps = 1/496 (0%)

Query: 3   ELGHFIDGKRVAGTSGRVSNIFNPATGEVQGTVALASDADLAAAVESAKAAQPKWAATNP 62
           E+ HFI     AGT  R S++F+P TG VQ  V L + ADL AA+ +A  AQ  WAATNP
Sbjct: 7   EISHFIGNAATAGTGTRRSDVFDPNTGAVQAQVTLGAQADLDAAMANAVRAQISWAATNP 66

Query: 63  QRRARVFMKFVQLLNDNMNELAEMLSREHGKTIDDAKGDIVRGLEVCEFVIGIPHLQKSE 122
           QRRARV   F  L+  NM ELA +LS EHGK I DAKGDI RGLEV EFV GIPH+ K E
Sbjct: 67  QRRARVMFNFKALIEKNMEELAHLLSSEHGKVIADAKGDIQRGLEVIEFVCGIPHVLKGE 126

Query: 123 FTEGAGPGIDMYSIRQPVGIGAGITPFNFPGMIPMWMFAPAIACGNAFILKPSERDPSVP 182
           +T+GAGPGID+YS+RQP+G+ AGITPFNFP MIPMWMF  AIACGNAFILKPSERDPSVP
Sbjct: 127 YTQGAGPGIDVYSMRQPLGVVAGITPFNFPAMIPMWMFGVAIACGNAFILKPSERDPSVP 186

Query: 183 IRLAELMIEAGLPAGILNVVNGDKGAVDAILTHPDIAAVSFVGSTPIARYVYGTAAMNGK 242
           +RLAELM+EAGLP G+L VV GDK  VDAIL HP+I AVSFVGS+ IA YVY      GK
Sbjct: 187 VRLAELMLEAGLPEGVLQVVQGDKEMVDAILDHPEIKAVSFVGSSDIAHYVYRRGVAAGK 246

Query: 243 RAQCFGGAKNHMIIMPDADLDQAANALIGAGYGSAGERCMAISVAVPVGEETANRLIDKL 302
           R Q  GGAKNH I+MPDADLDQ  N L GA +GSAGERCMA+ V VPVG++TA+ L  KL
Sbjct: 247 RVQAMGGAKNHGIVMPDADLDQVVNDLAGAAFGSAGERCMALPVVVPVGDKTADALRAKL 306

Query: 303 VPMVESLRIGPYTDEKADMGPVVTKEAEQRIRSLIDSGIEQGAKLVVDGRDFKLQGYENG 362
           +P +E+LR+G  TD  A  GPVVT   + +I S I  G+++GA+LVVDGR F LQG+E G
Sbjct: 307 LPAIEALRVGVSTDAGAHYGPVVTAAHKAKIESYIQMGVDEGAELVVDGRGFTLQGHEQG 366

Query: 363 HFIGGCLFDDVTPDMDIYKTEIFGPVLSVVRARNYEEALSLPMKHEYGNGVAIYTRDGDA 422
            F+G  LFD VTP M  Y+ EIFGPVL +VRA ++E AL LP +H+YGNGVAI+TR+G A
Sbjct: 367 FFVGPTLFDRVTPQMQSYQEEIFGPVLQIVRAPDFETALRLPSEHQYGNGVAIFTRNGHA 426

Query: 423 ARDFASRINIGMVGVNVPIPVPLAYHSFGGWKSSSFGDLNQHGTDSIKFWTRTKTITSRW 482
           AR+FA+R+N+GMVG+NVPIPVP+AYH+FGGWK S+FGD NQHG + IKF+T+ KT+T RW
Sbjct: 427 AREFAARVNVGMVGINVPIPVPVAYHTFGGWKRSAFGDTNQHGMEGIKFFTKVKTVTQRW 486

Query: 483 PSGIKDGAE-FSIPTM 497
           P G  DG   F IPTM
Sbjct: 487 PDGSPDGGNAFVIPTM 502


Lambda     K      H
   0.319    0.137    0.409 

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: 806
Number of extensions: 24
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: 498
Length of database: 503
Length adjustment: 34
Effective length of query: 464
Effective length of database: 469
Effective search space:   217616
Effective search space used:   217616
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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 paper from 2022 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