GapMind for catabolism of small carbon sources

 

Aligments for a candidate for bamH in Klebsiella michiganensis M5al

Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate BWI76_RS20170 BWI76_RS20170 NADH-quinone oxidoreductase subunit F

Query= uniprot:Q39TW5
         (635 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS20170 BWI76_RS20170 NADH-quinone
           oxidoreductase subunit F
          Length = 445

 Score =  336 bits (862), Expect = 1e-96
 Identities = 167/405 (41%), Positives = 251/405 (61%), Gaps = 11/405 (2%)

Query: 151 MDDYLAIGGYSALSKVLFQMTPEDVMGEIKKSNLRGRGGGGFPAWRKW-----EESRNAP 205
           +D+Y +  GY+   K L  M P++++  +K + L+GRGG GF    KW     +ES N  
Sbjct: 26  LDEYQSKNGYAGARKALSGMAPDEIVTAVKDAGLKGRGGAGFSTGLKWSLMPKDESMN-- 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  --IRYLLCNADEMEPGTYKDRLLMEQLPHLLVEGMLISAFALKAYRGYIFLRGEYIEAAQ 141

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

Query: 326 IHTAVKGVWDHPSVLNNVETWANVTQIITKGADWFTSYGTAGSTGTKIFSLVGKITNTGL 385
              A  GVW  P+ +NNVET  NV  I+  G +W+ +  T+   GTK+    G++ N G+
Sbjct: 202 PFPASSGVWGKPTCVNNVETLCNVPAILANGVEWYQNISTSKDAGTKLMGFSGRVKNPGV 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 GTALAMAVDHEIGMVPLVRNLEEFFARESCGWCTPCRDGLPWSVKILRALERGEGQPGDI 381

Query: 506 ELLEELAE--STGAALCALGKSAPNPVLSTIRYFRDEYEAHIREK 548
           E LE+L      G   CA    A  P+ S I+YFR+E+EA I+++
Sbjct: 382 ETLEQLCRFLGPGKTFCAHAPGAVEPLQSAIKYFREEFEAGIKQQ 426


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: 722
Number of extensions: 37
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.

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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