GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acdH in Shewanella oneidensis MR-1

Align Short-chain acyl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate 201059 SO1897 isovaleryl-CoA dehydrogenase (NCBI ptt file)

Query= reanno::pseudo13_GW456_L13:PfGW456L13_2983
         (375 letters)



>FitnessBrowser__MR1:201059
          Length = 389

 Score =  276 bits (706), Expect = 7e-79
 Identities = 145/371 (39%), Positives = 220/371 (59%)

Query: 5   DDQQQIRDMARDFAQERLKPFAAEWDREHRFPKEAIGEMAGLGFFGMLVPEQWGGCDTGY 64
           +D   +RD   DFAQ  + P AA+ D ++ FP E    + G+G  G+ VPE++GG + GY
Sbjct: 14  EDVDMLRDAVHDFAQHEIAPIAAKVDHDNAFPNEIWPVLGGMGLLGVTVPEEYGGANMGY 73

Query: 65  LAYAMALEEIAAGDGACSTIMSVHNSVGCVPILNYGTDEQKERFLKPLASGAMLGAFALT 124
           LA+ +A+EEI+    +       H+++    I   G   QK ++L  L SG  +GA A++
Sbjct: 74  LAHVVAMEEISRASASIGLSYGAHSNLCVNQINRNGNAAQKAKYLPKLVSGEHIGALAMS 133

Query: 125 EPQAGSDASGLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFIV 184
           EP AGSD   +K  AR EGD Y+LNG K +IT+G +A   +++A TD + G  GI+AFIV
Sbjct: 134 EPNAGSDVVSMKLHARKEGDRYILNGNKMWITNGPDANTYVIYAKTDLTKGAHGITAFIV 193

Query: 185 PTDSPGYKVARVEDKLGQHASDTCQILFEDVKVPLANRLGEEGEGYRIALANLEGGRVGI 244
                G+  A+  DKLG   S+TC+++FEDV+VP  N LG    G ++ ++ L+  RV +
Sbjct: 194 ERGFKGFSQAQKLDKLGMRGSNTCELVFEDVEVPEENILGGLNNGVKVLMSGLDYERVVL 253

Query: 245 ASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAALR 304
           +   +G+  A  +    Y  ERE FGK I E Q V  +LADM T +  A+  V+  A   
Sbjct: 254 SGGPLGIMNACMDIVVPYIHEREQFGKSIGEFQLVQGKLADMYTGMNAAKAYVYSVAKSC 313

Query: 305 DSGKPALVEASMAKLFASEMAEKVCSSALQTLGGYGYLNDFPVERIYRDVRVCQIYEGTS 364
           D G+    +A+ A L+++E+A K+   A+Q LGG GY+N++   R+ RD ++ +I  GTS
Sbjct: 314 DRGETTRKDAAGAILYSAELATKMALDAIQLLGGNGYVNEYATGRLLRDAKLYEIGAGTS 373

Query: 365 DIQRMVISRNL 375
           +I+RM+I R L
Sbjct: 374 EIRRMLIGREL 384


Lambda     K      H
   0.320    0.135    0.394 

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: 336
Number of extensions: 13
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: 375
Length of database: 389
Length adjustment: 30
Effective length of query: 345
Effective length of database: 359
Effective search space:   123855
Effective search space used:   123855
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 (21.8 bits)
S2: 50 (23.9 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