GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fadB in Pseudomonas fluorescens GW456-L13

Align 3-hydroxyadipyl-CoA dehydrogenase; EC 1.1.1.- (characterized)
to candidate PfGW456L13_2432 3-hydroxyacyl-CoA dehydrogenase PaaC (EC 1.1.1.-)

Query= SwissProt::P76083
         (475 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2432
           3-hydroxyacyl-CoA dehydrogenase PaaC (EC 1.1.1.-)
          Length = 505

 Score =  408 bits (1048), Expect = e-118
 Identities = 239/488 (48%), Positives = 309/488 (63%), Gaps = 30/488 (6%)

Query: 8   VAVIGSGTMGAGIAEVAASHGHQVLLYDISAEALTRAIDGIHARLNSRVTRGKLTAETCE 67
           +AVIG+G MGAGIA+VAA  GH VLL D    A  +AI+GI  +L  RV  GKL+AE+  
Sbjct: 10  IAVIGAGAMGAGIAQVAAQAGHPVLLLDNRPGAAAQAIEGIDRQLGKRVENGKLSAESRS 69

Query: 68  RTLKRLIPVTDIHALAAADLVIEAASERLEVKKALFAQLAEVCPPQTLLTTNTSSISITA 127
            T+ RL  V  I  LA  DL+IEA  E LEVK+ALF QL  +C    +L +NTSS+SIT+
Sbjct: 70  ATVARLQAVEVIETLADCDLIIEAIVENLEVKRALFRQLEGICGEHCILASNTSSLSITS 129

Query: 128 IAAEIKNPERVAGLHFFNPAPVMKLVEVVSGLATAAEVVEQLCELTLSWGKQPVRCHSTP 187
           IAA++ +P+R+ GLHFFNPAPVM LVEVVSGLA+   + E L +   +WGK+PV   STP
Sbjct: 130 IAAQLDHPQRLLGLHFFNPAPVMALVEVVSGLASDPALAECLYDTARAWGKKPVHTRSTP 189

Query: 188 GFIVNRVARPYYSEAWRALEEQVAAPEVIDAALRDGAGFPMGPLELTDLIGQDVNFAVTC 247
           GFIVNRVARP+Y+E+ R L+E  A    +DA +R+  GF MG  ELTDLIG DVN+AVTC
Sbjct: 190 GFIVNRVARPFYAESLRMLQEGAADCPTLDALMREAGGFAMGAFELTDLIGHDVNYAVTC 249

Query: 248 SVFNAFWQERRFLPSLVQQELVIGGRLGKKSGLGVYDWR--AER---------------- 289
           SVF+A++Q+ RFLPSL+Q+ELV GGRLG+KSG G Y +   AER                
Sbjct: 250 SVFDAYYQDTRFLPSLIQKELVDGGRLGRKSGQGFYCYAQGAERPQAGEISSSASVETCI 309

Query: 290 -EAVVGL-EAVSDSFSPMKVE---KKSDGVTEIDDVLLIETQGETA-QALAIRLARPVVV 343
            E  +G+ + +    S   VE   +   G+  + D +L  + G  A Q       R +++
Sbjct: 310 AEGDLGIAQGLLARLSEQGVEVIRRDGRGLLRVGDAVLALSDGRMACQRAREDGLRNLIL 369

Query: 344 IDKM-----AGKVVTIAAAAVNPDSATRKAIYYLQQQGKTVLQIADYPGMLIWRTVAMII 398
           +D       A ++    AA ++P  A  + +  LQ+ G  V  ++D P + + RTVAM+ 
Sbjct: 370 LDLAFDYGNAKRIAISHAAGIDP-LALEQGVALLQRAGLMVSLLSDSPALAVLRTVAMLA 428

Query: 399 NEALDALQKGVASEQDIDTAMRLGVNYPYGPLAWGAQLGWQRILRLLENLQHHYGEERYR 458
           NEA DAL +GVAS  DID AMR GVNYP GPLAW   +G   IL  LENLQ  YGEERYR
Sbjct: 429 NEAADALLQGVASAADIDLAMRAGVNYPQGPLAWADAIGLSHILETLENLQASYGEERYR 488

Query: 459 PCSLLRQR 466
           P  LLR+R
Sbjct: 489 PSLLLRRR 496


Lambda     K      H
   0.319    0.134    0.386 

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: 533
Number of extensions: 20
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: 475
Length of database: 505
Length adjustment: 34
Effective length of query: 441
Effective length of database: 471
Effective search space:   207711
Effective search space used:   207711
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: 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