GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA in Pseudomonas fluorescens FW300-N1B4

Align Methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial; MMSDH; Malonate-semialdehyde dehydrogenase [acylating]; Aldehyde dehydrogenase family 6 member A1; EC 1.2.1.18; EC 1.2.1.27 (characterized)
to candidate Pf1N1B4_2417 Betaine aldehyde dehydrogenase (EC 1.2.1.8)

Query= SwissProt::Q02253
         (535 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2417
          Length = 490

 Score =  227 bits (579), Expect = 7e-64
 Identities = 136/437 (31%), Positives = 225/437 (51%), Gaps = 7/437 (1%)

Query: 41  KLFIDGKFVESKSDKWIDIHNPATNEVVGRVPQSTKAEMEAAVAACKRAFPAWADTSILS 100
           KL+IDG + ++ SD   +  NPA  EV+  V ++TK ++E AV + ++    WA  + + 
Sbjct: 8   KLYIDGGYSDASSDATFEAINPANGEVLATVQRATKEDVERAVVSAEKGQKIWAAMTAME 67

Query: 101 RQQVLLRYQQLIKENLKEIARLITLEQGKTLADAEG-DVFRGLQVVEHACSVTSLMLGET 159
           R ++L R   +++E   E+A L TL+ GK  ++    D+  G  V+E+   +   + GE 
Sbjct: 68  RSRILRRAVDILRERNDELAALETLDTGKAYSETRYVDIVTGADVLEYYAGLVPAIEGEQ 127

Query: 160 MPSITKDMDLYSYRLPLGVCAGIAPFNFPAMIPLWMFPMAMVCGNTFLMKPSERVPGATM 219
           +P  T    +Y+ R PLG+ AGI  +N+P  I LW    A+  GN  + KPSE     T+
Sbjct: 128 IPLRTTSF-VYTRREPLGIVAGIGAWNYPIQIALWKSAPALAAGNAMIFKPSEVTSLTTL 186

Query: 220 LLAKLLQDSGAPDGTLNIIHGQ-HEAVNFICDHPDIKAISFVGSNQAGEYIFERGSRNG- 277
            LA++  ++G P G  N++ G   E   ++ +HP I+ ISF G    G+ +    S +  
Sbjct: 187 KLAEIYTEAGLPAGVFNVLTGSGREVGTWLTEHPRIEKISFTGGTDTGKKVMASASGSSL 246

Query: 278 KRVQANMGAKNHGVVMPDANKENTLNQLVGAAFGAAGQRCMALSTAVLVGEAKK--WLPE 335
           K V   +G K+  ++  DA+ +   +  + A F ++GQ C    T V V    K  +  +
Sbjct: 247 KDVTMELGGKSPLIIFDDADLDRAADTAMMANFYSSGQVCTN-GTRVFVPSHLKAAFEAK 305

Query: 336 LVERAKNLRVNAGDQPGADLGPLITPQAKERVCNLIDSGAKEGASILLDGRKIKVKGYEN 395
           +VER   +RV   +    + GPL++    E V   I  G +EGA +L  G ++    +  
Sbjct: 306 IVERVARIRVGNPEDENTNFGPLVSFAHMESVLGYIAKGKEEGARLLCGGDRLTDGEFAK 365

Query: 396 GNFVGPTIISNVKPSMTCYKEEIFGPVLVVLETETLDEAIKIVNDNPYGNGTAIFTTNGA 455
           G FV PT+ ++    MT  +EEIFGPV+ +L  ET +E I+  ND  +G    + T +  
Sbjct: 366 GAFVAPTVFTDCTDEMTIVREEIFGPVMSILTYETEEEVIRRANDTEFGLAAGVVTKDLN 425

Query: 456 IARKYAHMVDVGQVGVN 472
            A +  H ++ G   +N
Sbjct: 426 RAHRVIHQLEAGICWIN 442


Lambda     K      H
   0.318    0.133    0.389 

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: 560
Number of extensions: 28
Number of successful extensions: 5
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: 490
Length adjustment: 35
Effective length of query: 500
Effective length of database: 455
Effective search space:   227500
Effective search space used:   227500
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