GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2432
          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.

Links

Downloads

Related tools

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