GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acdH in Dinoroseobacter shibae DFL-12

Align Short-chain acyl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate 3607889 Dshi_1297 acyl-CoA dehydrogenase domain protein (RefSeq)

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



>FitnessBrowser__Dino:3607889
          Length = 387

 Score =  287 bits (735), Expect = 3e-82
 Identities = 149/371 (40%), Positives = 223/371 (60%)

Query: 5   DDQQQIRDMARDFAQERLKPFAAEWDREHRFPKEAIGEMAGLGFFGMLVPEQWGGCDTGY 64
           ++ + +R+M   +AQER+KP AAE DR + FP     EM  LG  G+ V E +GG   GY
Sbjct: 12  EEVEALREMVHRWAQERVKPLAAETDRSNAFPNALWPEMGELGLLGITVDEAYGGAGMGY 71

Query: 65  LAYAMALEEIAAGDGACSTIMSVHNSVGCVPILNYGTDEQKERFLKPLASGAMLGAFALT 124
           LA+ +A+EEI+    +       H+++    I   GTD QKE++L  L SGA +GA A++
Sbjct: 72  LAHTVAVEEISRASASIGLSYGAHSNLCVNQIKLNGTDAQKEKYLPKLVSGAHVGALAMS 131

Query: 125 EPQAGSDASGLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFIV 184
           E  AGSD  G+K RA    DHY LNG K +IT+G +A  ++V+A TDP AG +GI+AF++
Sbjct: 132 EAGAGSDVVGMKLRAEKRNDHYRLNGTKYWITNGPDADTLVVYAKTDPEAGSKGITAFLI 191

Query: 185 PTDSPGYKVARVEDKLGQHASDTCQILFEDVKVPLANRLGEEGEGYRIALANLEGGRVGI 244
             +  G+  +   DKLG   S+T +++FEDV+VP  N LGEEG G  + ++ L+  RV +
Sbjct: 192 EKEMAGFSTSPHFDKLGMRGSNTAELIFEDVEVPFENVLGEEGRGVAVLMSGLDYERVVL 251

Query: 245 ASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAALR 304
           +  ++G+     +    Y  ER  FG+PI   Q +  ++ADM T +  AR   +  A   
Sbjct: 252 SGVNIGIMAGCLDEVMPYMTERRQFGEPIGNFQLMQGKIADMYTAMNSARAYAYEVAKAC 311

Query: 305 DSGKPALVEASMAKLFASEMAEKVCSSALQTLGGYGYLNDFPVERIYRDVRVCQIYEGTS 364
           D G+    +A+   L+ASE   KV   A+Q +GG G+LND PV R++RD ++ +I  GTS
Sbjct: 312 DRGEVTRQDAAACVLYASEEGMKVAHQAVQAMGGAGFLNDSPVARMFRDAKLMEIGAGTS 371

Query: 365 DIQRMVISRNL 375
           +I+RM++ R L
Sbjct: 372 EIRRMLVGREL 382


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: 351
Number of extensions: 14
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: 387
Length adjustment: 30
Effective length of query: 345
Effective length of database: 357
Effective search space:   123165
Effective search space used:   123165
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