GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acdH in Bacteroides thetaiotaomicron VPI-5482

Align short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) (characterized)
to candidate 351334 BT1806 acyl-CoA dehydrogenase (NCBI ptt file)

Query= metacyc::MONOMER-17424
         (375 letters)



>FitnessBrowser__Btheta:351334
          Length = 568

 Score =  174 bits (441), Expect = 5e-48
 Identities = 121/367 (32%), Positives = 185/367 (50%), Gaps = 39/367 (10%)

Query: 37  KEAIDEMAELGLFGMLVPEQWGGSDTGYVAYAMALEEIAAGDGACSTIMSVHNSVGCVPI 96
           KE +D M + GL GM +P ++GG +     Y M  E +AA D     I S+ +   C+  
Sbjct: 92  KENLDAMVKAGLNGMTMPRRFGGLNFPITPYTMCAEIVAAADAGFGNIWSLQD---CIET 148

Query: 97  L-RFGNEQQKEQFLTPLATGAMLGAFALTEPQAGSDASSLKTRARLEGDH--YVLNGSKQ 153
           L  FGN  Q  +F+  +  G  + +  LTEP AGSD  ++  +A        ++LNG K+
Sbjct: 149 LYEFGNADQHSRFIPRVCQGETM-SMDLTEPDAGSDLQAVMLKATYSEKDGCWLLNGVKR 207

Query: 154 FITSGQNAGVVIVFAVTDPEAGK-RGISAFIVPTDSPGYQVARVEDKLGQHASDTCQIVF 212
           FIT+G +A + +V A ++      RG+S FI      G  V R+E KLG H S TC++V+
Sbjct: 208 FITNG-DADIHLVLARSEEGTRDGRGLSMFIYDKRQGGVDVRRIEHKLGIHGSPTCELVY 266

Query: 213 DNVQVPVAN--RLGAEGEGYKIALANLEGGRIGIASQAVGMARAAFEVARDYANERQSFG 270
            N +  +    +LG      K  +A + G R+GIA+Q+VG+++AA+     YA +R+ FG
Sbjct: 267 KNAKAELCGDRKLGL----IKYVMALMNGARLGIAAQSVGLSQAAYNEGLAYAKDRKQFG 322

Query: 271 KPLIEHQAVAFRLADMATKISVARQMVLHAA-------ALRDAGRPALVE---------- 313
           K +I+  AV   LA M  K+   R ++   A       AL D  R   +           
Sbjct: 323 KAIIDFPAVYDMLAIMKGKLDAGRALLYQTARYVDIYKALDDISRERKLTPEERLEQKKY 382

Query: 314 -------ASMAKLFASEMAEKVCSDALQTLGGYGYLSDFPLERIYRDVRVCQIYEGTSDI 366
                    +AK   SE A +   D +Q  GG G++ ++  +RIYRD R+  IYEGT+ +
Sbjct: 383 AKLADSFTPLAKGMNSEYANQNAYDCIQIHGGSGFMMEYACQRIYRDARITSIYEGTTQL 442

Query: 367 QRMVIAR 373
           Q +   R
Sbjct: 443 QTVAAIR 449


Lambda     K      H
   0.319    0.134    0.382 

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: 435
Number of extensions: 28
Number of successful extensions: 6
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: 568
Length adjustment: 33
Effective length of query: 342
Effective length of database: 535
Effective search space:   182970
Effective search space used:   182970
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: 51 (24.3 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