GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Marinobacter adhaerens HP15

Align 3-hydroxyadipyl-CoA dehydrogenase; EC 1.1.1.- (characterized)
to candidate GFF2749 HP15_2693 3-hydroxybutyryl-CoA dehydrogenase

Query= SwissProt::P76083
         (475 letters)



>FitnessBrowser__Marino:GFF2749
          Length = 506

 Score =  385 bits (988), Expect = e-111
 Identities = 224/503 (44%), Positives = 306/503 (60%), Gaps = 30/503 (5%)

Query: 3   INVQT-VAVIGSGTMGAGIAEVAASHGHQVLLYDISAEALTRAIDGIHARLNSRVTRGKL 61
           ++ QT VAV+G+G MG+GIA+VAA  GHQV L+D    A     DGI  +L  RV +GK+
Sbjct: 4   LDTQTKVAVVGAGAMGSGIAQVAAQAGHQVYLHDQREGAAEAGRDGIAKQLQRRVDKGKM 63

Query: 62  TAETCERTLKRLIPVTDIHALAAADLVIEAASERLEVKKALFAQLAEVCPPQTLLTTNTS 121
             +  +  + R+ PV  +  +A A LVIEA  E L++K+ L A L ++C    +L TNTS
Sbjct: 64  QQQELDDVIGRIHPVAKLDDVADAGLVIEAIIEDLQIKRQLLASLEDLCTADAILATNTS 123

Query: 122 SISITAIAAEIKNPERVAGLHFFNPAPVMKLVEVVSGLATAAEVVEQLCELTLSWGKQPV 181
           SIS+TA+ A++  PER+ G+HFFNPAP+M LVEVV GLAT+  V + +     +WGK+PV
Sbjct: 124 SISVTALGADMSKPERLVGMHFFNPAPLMALVEVVMGLATSKTVADTVHATATAWGKKPV 183

Query: 182 RCHSTPGFIVNRVARPYYSEAWRALEEQVAAPEVIDAALRDGAGFPMGPLELTDLIGQDV 241
              STPGFIVNRVARP+Y+E+ R L+EQ      +DA +R+   F MG  ELTDLIG DV
Sbjct: 184 YATSTPGFIVNRVARPFYAESLRLLQEQATDAATLDAIIREAGQFRMGAFELTDLIGHDV 243

Query: 242 NFAVTCSVFNAFWQERRFLPSLVQQELVIGGRLGKKSGLGVYDW--RAER---------- 289
           N+AVT SVFN+++Q+ RFLPSL+Q+ELV  GRLG+KSG G Y +   AE+          
Sbjct: 244 NYAVTSSVFNSYYQDPRFLPSLIQKELVEAGRLGRKSGQGFYPYGESAEKPQPKTEPAHQ 303

Query: 290 --EAVVGLEAVSDSFSPMKVEKKSDGVTEID----------DVLLIETQGE--TAQALAI 335
             E+V+  E      +P+    K+ G+T I+          D +L  T G   T +A   
Sbjct: 304 SDESVIIAEGNPGVAAPLLERLKAAGLTIIERDGPGQIRFGDAVLALTDGRMATERAACE 363

Query: 336 RLARPV---VVIDKMAGKVVTIAAAAVNPDSATRKAIYYLQQQGKTVLQIADYPGMLIWR 392
            +A  V   +  D      + +A A    D+A   A   LQ+ G  V  IAD PG++I R
Sbjct: 364 GVANLVLFDLAFDYSKASRLALAPADQASDAAVSCACALLQKAGIEVSLIADRPGLVIMR 423

Query: 393 TVAMIINEALDALQKGVASEQDIDTAMRLGVNYPYGPLAWGAQLGWQRILRLLENLQHHY 452
           TVAM+ NEA DA   GVA+  DID AM+ G+NYP GPL+W  +LG   + ++L N+Q  Y
Sbjct: 424 TVAMLANEAADAALHGVATVADIDLAMKAGLNYPDGPLSWSDRLGAGHVFKVLTNIQTSY 483

Query: 453 GEERYRPCSLLRQRALLESGYES 475
            E+RYRP  LLR+ A  + G+ S
Sbjct: 484 AEDRYRPALLLRKNAFAQKGFYS 506


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: 550
Number of extensions: 17
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: 475
Length of database: 506
Length adjustment: 34
Effective length of query: 441
Effective length of database: 472
Effective search space:   208152
Effective search space used:   208152
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:

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