GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bamH in Pseudomonas fluorescens FW300-N1B4

Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate Pf1N1B4_4037 NADH-ubiquinone oxidoreductase chain F (EC 1.6.5.3)

Query= uniprot:Q39TW5
         (635 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4037
          Length = 451

 Score =  312 bits (799), Expect = 2e-89
 Identities = 172/424 (40%), Positives = 244/424 (57%), Gaps = 15/424 (3%)

Query: 133 KNQQRNILSENLRLDSKS--MDDYLAIGGYSALSKVLFQMTPEDVMGEIKKSNLRGRGGG 190
           ++ + + L+  LR D ++  +D+Y A  GY+A  K    M  +D++  +K S L+GRGG 
Sbjct: 14  RSAETHPLTWRLRDDGEAVWLDEYQAKNGYAAARKAFADMAQDDIVQTVKDSGLKGRGGA 73

Query: 191 GFPAWRKW-----EESRNAPDPIKYVIVNADEGDPGAFMDRALIEGNPHSILEGLIIGAY 245
           GFP   KW     +ES N    I+Y++ NADE +P  + DR L+E  PH ++EG++I A 
Sbjct: 74  GFPTGVKWGLMPKDESIN----IRYLLCNADEMEPNTWKDRMLMEQLPHLLIEGMLISAR 129

Query: 246 AVGAHEGFIYVRQEYPLAVENINLAIRQASERGFVGKDILGSGFDFTVKVHMGAGAFVCG 305
           A+  + G+I++R EY  A +++N A+ +A   G +GK+ILGSGFDF + VH GAG ++CG
Sbjct: 130 ALKTYRGYIFLRGEYTTAAKHLNRAVEEAKAAGLLGKNILGSGFDFELFVHTGAGRYICG 189

Query: 306 ESSALMTALEGRAGEPRPKYIHTAVKGVWDHPSVLNNVETWANVTQIITKGADWFTSYGT 365
           E +AL+ +LEGR   PR K    A  GVW  P+ +NNVET  NV  II  G DW+ S   
Sbjct: 190 EETALINSLEGRRANPRSKPPFPAAVGVWGKPTCVNNVETLCNVPAIIADGVDWYKSLAR 249

Query: 366 AGS--TGTKIFSLVGKITNTGLVEVPMGVTLRDIITKVGGGIPGGKKFKAVQTGGPSGGC 423
            GS   GTK+    GK+ N GL E+P GVT R++     GG+  G K K  Q GG   G 
Sbjct: 250 EGSEDMGTKLMGFSGKVKNPGLWELPFGVTGRELFEDYAGGMRDGYKLKCWQPGGAGTGF 309

Query: 424 IPEAMLDLPVDFDELTKAGSMMGSGGMIVMDEDTCMVDIARYFIDFLKDESCGKCTPCRE 483
           +    LD  +    + K G+ MG+G  + +D+   MV + R   +F   ESCG CTPCR+
Sbjct: 310 LLPEHLDAQMYAGGIAKVGTRMGTGLAMAVDDSVNMVSLLRNMEEFFSRESCGFCTPCRD 369

Query: 484 GIRQMLAVLTRITVGKGKEGDIELLEELAE--STGAALCALGKSAPNPVLSTIRYFRDEY 541
           G+   + +L  I  G+G+ GDIE L  L      G   CA    A  P+ S I+YFR E+
Sbjct: 370 GLPWSVKLLRAIENGEGQAGDIETLLGLVGFLGPGKTFCAHAPGAVEPLGSAIKYFRPEF 429

Query: 542 EAHI 545
           EA I
Sbjct: 430 EAGI 433


Lambda     K      H
   0.319    0.138    0.420 

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: 767
Number of extensions: 46
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: 635
Length of database: 451
Length adjustment: 35
Effective length of query: 600
Effective length of database: 416
Effective search space:   249600
Effective search space used:   249600
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 (21.7 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:

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