GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acdH in Sphingobium czechense LL01

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 WP_066607952.1 V473_RS17395 isovaleryl-CoA dehydrogenase

Query= SwissProt::P45954
         (432 letters)



>NCBI__GCF_001046645.1:WP_066607952.1
          Length = 381

 Score =  259 bits (662), Expect = 1e-73
 Identities = 143/371 (38%), Positives = 219/371 (59%), Gaps = 3/371 (0%)

Query: 59  DEEMMIKSSVKKFAQEQIAPLVSTMDENSKMEKSVIQGLFQQGLMGIEVDPEYGGTGASF 118
           D   MI+ S  +F+ ++IAPL + +D      + +   + + GL GI V  E GG G  +
Sbjct: 10  DNADMIRDSAARFSADRIAPLAAEIDAKDWFPRELWPAMGELGLHGITVSEEDGGLGLGY 69

Query: 119 LSTVLVIEELAKVDASVAVFCEIQNTLINTLIRKHGTEEQKATYLPQLTT-EKVGSFCLS 177
           L  V+  EE+A+  AS+ +     + L    IR+ G  EQKA YLP+L + + VGS  +S
Sbjct: 70  LEHVVAQEEVARASASIGLSYGAHSNLCVNQIRRWGNAEQKAKYLPKLISGDHVGSLAMS 129

Query: 178 EAGAGSDSFALKTRADKEGDYYVLNGSKMWISSAEHAGLFLVMANVDPTIGYKGITSFLV 237
           EAGAGSD  ++K +A+K+GD Y+LNG+K WI++A +A   +V A      G KGIT+FL+
Sbjct: 130 EAGAGSDVVSMKLKAEKKGDRYILNGTKFWITNAPYADTLVVYAKTGE--GSKGITTFLI 187

Query: 238 DRDTPGLHIGKPENKLGLRASSTCPLTFENVKVPEANILGQIGHGYKYAIGSLNEGRIGI 297
           ++D  G  IG+  +K+G+R S T  L F++ +VPE NI+G +  G    +  L+  R  +
Sbjct: 188 EKDMKGFSIGQKIDKMGMRGSPTAELVFDDCEVPEENIMGPLNGGVGILMSGLDYERTVL 247

Query: 298 AAQMLGLAQGCFDYTIPYIKERIQFGKRLFDFQGLQHQVAHVATQLEAARLLTYNAARLL 357
           A   LG+ Q C D  +PY++ER QFG+ +  FQ +Q +VA +   L +AR   Y  AR  
Sbjct: 248 AGIQLGIMQACLDTVLPYVRERQQFGRPIGAFQLMQAKVADMYVALNSARAYVYAVARAC 307

Query: 358 EAGKPFIKEASMAKYYASEIAGQTTSKCIEWMGGVGYTKDYPVEKYFRDAKIGTIYEGAS 417
           ++GK    +A+ A   ASE A +   + ++ +GG GYTKD+PVE+Y RDAK+  I  G +
Sbjct: 308 DSGKTTRFDAAGAILLASENAMKVALEAVQALGGAGYTKDWPVERYMRDAKLLDIGAGTN 367

Query: 418 NIQLNTIAKHI 428
            I+   I + +
Sbjct: 368 EIRRMLIGREL 378


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: 361
Number of extensions: 12
Number of successful extensions: 3
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: 381
Length adjustment: 31
Effective length of query: 401
Effective length of database: 350
Effective search space:   140350
Effective search space used:   140350
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 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