GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bamH in Escherichia coli BW25113

Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate 16391 b2284 NADH:ubiquinone oxidoreductase, chain F (NCBI)

Query= uniprot:Q39TW5
         (635 letters)



>FitnessBrowser__Keio:16391
          Length = 445

 Score =  335 bits (858), Expect = 3e-96
 Identities = 165/404 (40%), Positives = 248/404 (61%), Gaps = 11/404 (2%)

Query: 151 MDDYLAIGGYSALSKVLFQMTPEDVMGEIKKSNLRGRGGGGFPAWRKW-----EESRNAP 205
           +D+Y +  GY    K L  ++P++++ ++K + L+GRGG GF    KW     +ES N  
Sbjct: 26  LDEYRSKNGYEGARKALTGLSPDEIVNQVKDAGLKGRGGAGFSTGLKWSLMPKDESMN-- 83

Query: 206 DPIKYVIVNADEGDPGAFMDRALIEGNPHSILEGLIIGAYAVGAHEGFIYVRQEYPLAVE 265
             I+Y++ NADE +PG + DR L+E  PH ++EG++I A+A+ A+ G+I++R EY  A  
Sbjct: 84  --IRYLLCNADEMEPGTYKDRLLMEQLPHLLVEGMLISAFALKAYRGYIFLRGEYIEAAV 141

Query: 266 NINLAIRQASERGFVGKDILGSGFDFTVKVHMGAGAFVCGESSALMTALEGRAGEPRPKY 325
           N+  AI +A+E G +GK+I+G+GFDF + VH GAG ++CGE +AL+ +LEGR   PR K 
Sbjct: 142 NLRRAIAEATEAGLLGKNIMGTGFDFELFVHTGAGRYICGEETALINSLEGRRANPRSKP 201

Query: 326 IHTAVKGVWDHPSVLNNVETWANVTQIITKGADWFTSYGTAGSTGTKIFSLVGKITNTGL 385
              A  G W  P+ +NNVET  NV  I+  G +W+ +   +   GTK+    G++ N GL
Sbjct: 202 PFPATSGAWGKPTCVNNVETLCNVPAILANGVEWYQNISKSKDAGTKLMGFSGRVKNPGL 261

Query: 386 VEVPMGVTLRDIITKVGGGIPGGKKFKAVQTGGPSGGCIPEAMLDLPVDFDELTKAGSMM 445
            E+P G T R+I+    GG+  G KFKA Q GG     + EA LDLP++F+ + KAGS +
Sbjct: 262 WELPFGTTAREILEDYAGGMRDGLKFKAWQPGGAGTDFLTEAHLDLPMEFESIGKAGSRL 321

Query: 446 GSGGMIVMDEDTCMVDIARYFIDFLKDESCGKCTPCREGIRQMLAVLTRITVGKGKEGDI 505
           G+   + +D +  MV + R   +F   ESCG CTPCR+G+   + +L  +  G+G+ GDI
Sbjct: 322 GTALAMAVDHEINMVSLVRNLEEFFARESCGWCTPCRDGLPWSVKILRALERGEGQPGDI 381

Query: 506 ELLEELAE--STGAALCALGKSAPNPVLSTIRYFRDEYEAHIRE 547
           E LE+L      G   CA    A  P+ S I+YFR+E+EA I++
Sbjct: 382 ETLEQLCRFLGPGKTFCAHAPGAVEPLQSAIKYFREEFEAGIKQ 425


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: 751
Number of extensions: 38
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: 635
Length of database: 445
Length adjustment: 35
Effective length of query: 600
Effective length of database: 410
Effective search space:   246000
Effective search space used:   246000
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.

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