GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acdH in Sphingomonas koreensis DSMZ 15582

Align Short/branched chain specific acyl-CoA dehydrogenase, mitochondrial; SBCAD; 2-methyl branched chain acyl-CoA dehydrogenase; 2-MEBCAD; 2-methylbutyryl-coenzyme A dehydrogenase; 2-methylbutyryl-CoA dehydrogenase; EC 1.3.8.5 (characterized)
to candidate Ga0059261_4052 Ga0059261_4052 Acyl-CoA dehydrogenases

Query= SwissProt::P45954
         (432 letters)



>FitnessBrowser__Korea:Ga0059261_4052
          Length = 385

 Score =  255 bits (651), Expect = 2e-72
 Identities = 139/368 (37%), Positives = 219/368 (59%), Gaps = 4/368 (1%)

Query: 63  MIKSSVKKFAQEQIAPLVSTMDENSKMEKSVI-QGLFQQGLMGIEVDPEYGGTGASFLST 121
           MI+ + ++FA+E+I PL + +D      +  +   + + GL GI VD E+GG G  +L  
Sbjct: 16  MIRDTTQRFAKERIEPLAAKIDAEDWFPRDELWTAMGELGLHGITVDEEFGGLGLGYLEH 75

Query: 122 VLVIEELAKVDASVAVFCEIQNTLINTLIRKHGTEEQKATYLPQLTT-EKVGSFCLSEAG 180
           V+  EE+++  AS+ +     + L    I +  +  QKA YLP+L + E VGS  +SEAG
Sbjct: 76  VIACEEVSRASASIGLSYGAHSNLCVNQISRWASPAQKAKYLPRLISGEHVGSLAMSEAG 135

Query: 181 AGSDSFALKTRADKEGDYYVLNGSKMWISSAEHAGLFLVMANVDPTIGYKGITSFLVDRD 240
           AGSD  ++K RA+ +GD YVLNG+K WI++A +A   +V A      G +GIT+FL+++D
Sbjct: 136 AGSDVVSMKLRAEHKGDRYVLNGTKFWITNAAYADTLVVYAKTGE--GSRGITTFLIEKD 193

Query: 241 TPGLHIGKPENKLGLRASSTCPLTFENVKVPEANILGQIGHGYKYAIGSLNEGRIGIAAQ 300
            PG  IG+  +K+G+R S T  L F++ +VPE N++G +  G    +  L+  R  +A  
Sbjct: 194 MPGFSIGQKIDKMGMRGSPTAELVFDDCEVPEENVMGPLNGGVGVLMSGLDYERTVLAGI 253

Query: 301 MLGLAQGCFDYTIPYIKERIQFGKRLFDFQGLQHQVAHVATQLEAARLLTYNAARLLEAG 360
            LG+ Q C D  +PY++ER QFG+ +  FQ +Q +VA +   L +AR   Y  A+  +AG
Sbjct: 254 QLGIMQACLDVVLPYLRERKQFGQAIGSFQLMQAKVADMYVALNSARAYVYAVAQACDAG 313

Query: 361 KPFIKEASMAKYYASEIAGQTTSKCIEWMGGVGYTKDYPVEKYFRDAKIGTIYEGASNIQ 420
           K    +A+ A   ASE A +   + ++ +GG GYTKD+PVE++ RDAK+  I  G + I+
Sbjct: 314 KTTRFDAAGAILLASENAFRVAGEAVQALGGAGYTKDWPVERFLRDAKLLDIGAGTNEIR 373

Query: 421 LNTIAKHI 428
              I + +
Sbjct: 374 RMLIGREL 381


Lambda     K      H
   0.318    0.134    0.385 

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: 393
Number of extensions: 12
Number of successful extensions: 4
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: 432
Length of database: 385
Length adjustment: 31
Effective length of query: 401
Effective length of database: 354
Effective search space:   141954
Effective search space used:   141954
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: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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