GapMind for catabolism of small carbon sources

 

Aligments for a candidate for liuA in Bacteroides thetaiotaomicron VPI-5482

Align isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate 351334 BT1806 acyl-CoA dehydrogenase (NCBI ptt file)

Query= BRENDA::Q75N94
         (430 letters)



>lcl|FitnessBrowser__Btheta:351334 BT1806 acyl-CoA dehydrogenase
           (NCBI ptt file)
          Length = 568

 Score =  147 bits (371), Expect = 8e-40
 Identities = 125/423 (29%), Positives = 206/423 (48%), Gaps = 45/423 (10%)

Query: 32  RTFASKHPKGFVPPTEDELLELRERVQEFTRREITEEV----AAKTDAQNEFPA------ 81
           R +  K    + P   ++ L+  ++V E T  EIT E+    A   D +    A      
Sbjct: 29  RNYRDKDEFDYAPLDFEDALDSYDKVLEITG-EITGEIINANAEGVDEEGPHCANGRVEY 87

Query: 82  -----EMWKKLGDAGFLGITANEDYGGLGMGYQAHCIVMEELSRASGSIALSYAAHSQLC 136
                E    +  AG  G+T    +GGL      + +  E ++ A       ++   Q C
Sbjct: 88  ASGTKENLDAMVKAGLNGMTMPRRFGGLNFPITPYTMCAEIVAAADAGFGNIWSL--QDC 145

Query: 137 VNQLSLNGSPEQKERFLPGLLSGDKIGALAMSEHSAGSDV--VSMKTTAKEVDGGYVLNG 194
           +  L   G+ +Q  RF+P +  G+ + ++ ++E  AGSD+  V +K T  E DG ++LNG
Sbjct: 146 IETLYEFGNADQHSRFIPRVCQGETM-SMDLTEPDAGSDLQAVMLKATYSEKDGCWLLNG 204

Query: 195 TKMWITNGPDADFIVVYAKTEP-QKGSKGITAFVVEKTFDGFSCARKLDKLGMRGSNTGE 253
            K +ITNG DAD  +V A++E   +  +G++ F+ +K   G    R   KLG+ GS T E
Sbjct: 205 VKRFITNG-DADIHLVLARSEEGTRDGRGLSMFIYDKRQGGVDVRRIEHKLGIHGSPTCE 263

Query: 254 LIFEDVFVPKENVLGEVNRG-VKVLMEGLDLERLVLSAGPLGIMQAALDLVLPYTHVRKQ 312
           L++++    K  + G+   G +K +M  ++  RL ++A  +G+ QAA +  L Y   RKQ
Sbjct: 264 LVYKNA---KAELCGDRKLGLIKYVMALMNGARLGIAAQSVGLSQAAYNEGLAYAKDRKQ 320

Query: 313 FGTPIAHNQLIQGKLADMYTKLQASRAYTYSTARHIDNSASLSEVS----IRTQDCAGAI 368
           FG  I     +   LA M  KL A RA  Y TAR++D   +L ++S    +  ++     
Sbjct: 321 FGKAIIDFPAVYDMLAIMKGKLDAGRALLYQTARYVDIYKALDDISRERKLTPEERLEQK 380

Query: 369 LYA--------------AERATECALDAIQLMGGNGYINELPAGRLLRDAKLYEIGAGTS 414
            YA              +E A + A D IQ+ GG+G++ E    R+ RDA++  I  GT+
Sbjct: 381 KYAKLADSFTPLAKGMNSEYANQNAYDCIQIHGGSGFMMEYACQRIYRDARITSIYEGTT 440

Query: 415 EIR 417
           +++
Sbjct: 441 QLQ 443


Lambda     K      H
   0.317    0.134    0.380 

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: 532
Number of extensions: 28
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: 430
Length of database: 568
Length adjustment: 34
Effective length of query: 396
Effective length of database: 534
Effective search space:   211464
Effective search space used:   211464
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: 52 (24.6 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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