GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA 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:

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