GapMind for catabolism of small carbon sources

 

Aligments for a candidate for liuA in Dechlorosoma suillum PS

Align acyl-CoA dehydrogenase subunit (EC 1.3.8.4; EC 1.3.8.5) (characterized)
to candidate Dsui_0977 Dsui_0977 acyl-CoA dehydrogenase

Query= metacyc::MONOMER-11693
         (386 letters)



>lcl|FitnessBrowser__PS:Dsui_0977 Dsui_0977 acyl-CoA dehydrogenase
          Length = 378

 Score =  273 bits (697), Expect = 8e-78
 Identities = 159/379 (41%), Positives = 230/379 (60%), Gaps = 7/379 (1%)

Query: 5   LTPELEELRRTVEEFAHDVVAPKIGDFYERHEFPYEIVREMGRMGLFGLPFPEEYGGMGG 64
           LT E E +R ++  FA + +AP   ++ + H FP E ++E+G +G  G+  PEE+GG G 
Sbjct: 3   LTQEQEMIRDSMRAFAQERLAPFAAEWDKNHTFPAEALKELGELGAMGMCVPEEWGGAGM 62

Query: 65  DYLALGIALEELARVDSSVAITLEAGVSLGAMPIHLFGTDAQKAEWLPRLCSGEILGAFG 124
           DY++L + LEE+A  D + +  +    SL       +GTD QK EWL  L  GE LG F 
Sbjct: 63  DYMSLVLTLEEIAAGDGATSTIVSVQNSLACGITQKYGTDQQKEEWLKPLARGEKLGCFC 122

Query: 125 LTEPDGGSDAGATRTTARLDESTNEWVINGTKCFITNSGTDITGLVTVTAVTGRKPDGKP 184
           LTEP  GSDA A   T R D   + +V+NG K FIT        +  V AVT  K  GK 
Sbjct: 123 LTEPHTGSDAAAI--TTRADRDGDHFVLNGVKQFITTGKH--AHMAIVFAVTD-KAAGKK 177

Query: 185 LISSIIVPSGTPGFTVAAPYSKVGWNASDTRELSFADVRVPAANLLGEQGRGYAQFLRIL 244
            IS  +VP+ T GF V     K+G +ASDT ++ F D RVPA+ LLG++G GY   L  L
Sbjct: 178 GISCFLVPTDTKGFIVGRTEEKMGQHASDTVQIIFEDCRVPASALLGKEGEGYKIALSNL 237

Query: 245 DEGRIAISALATGLAQGCVDESVKYAGERHAFGRNIGAYQAIQFKIADMEMKAHMARVG- 303
           + GRI I+A + G+A+   + +V+YA ER  FG+ I  +QA+ F++ADM      AR+  
Sbjct: 238 EAGRIGIAAQSIGMARAAFEAAVRYAKERVTFGQPIIEHQAVNFRLADMNTLLDAARLMV 297

Query: 304 WRDAASRLVAGEPFKKEAAIAKLYSSTVAVDNAREATQIHGGYGFMNEYPVARMWRDSKI 363
           WR AA +  AG+P  KEA++AK+++S  A   A +A QIHGG G+ +++PV R++RD +I
Sbjct: 298 WRAAALK-DAGKPCLKEASMAKMFASEAAEKIASDAIQIHGGVGYTSDFPVERIYRDVRI 356

Query: 364 LEIGEGTSEVQRMLIAREL 382
            +I EG +++QR++I R +
Sbjct: 357 SQIYEGANDIQRLVIGRSI 375


Lambda     K      H
   0.318    0.136    0.402 

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: 381
Number of extensions: 13
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: 386
Length of database: 378
Length adjustment: 30
Effective length of query: 356
Effective length of database: 348
Effective search space:   123888
Effective search space used:   123888
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 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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