GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adhBqn in Burkholderia phytofirmans PsJN

Align Alcohol dehydrogenase (quinone), cytochrome c subunit; ADH; Alcohol dehydrogenase (quinone), subunit II; Cytochrome c-553; Cytochrome c553; Ethanol:Q2 reductase; G3-ADH subunit II; Quinohemoprotein-cytochrome c complex; Ubiquinol oxidase; EC 1.1.5.5 (characterized)
to candidate BPHYT_RS23020 BPHYT_RS23020 alcohol dehydrogenase

Query= SwissProt::P0A388
         (468 letters)



>FitnessBrowser__BFirm:BPHYT_RS23020
          Length = 451

 Score =  460 bits (1183), Expect = e-134
 Identities = 225/410 (54%), Positives = 279/410 (68%), Gaps = 2/410 (0%)

Query: 17  LAGTALAQTPDADSALVQKGAYVARLGDCVACHTALHGQSYAGGLEIKSPIGTIYSTNIT 76
           LA  A A     D+ L+  G Y+AR GDC+ACH+A  G+ +AGGL+  +PIG IYSTNIT
Sbjct: 28  LAAHAAAPQSRNDTTLIAHGEYLARAGDCIACHSAPSGKPFAGGLKFDTPIGAIYSTNIT 87

Query: 77  PDPTYGIGRYTFAEFDEAVRHGIRKDGSTLYPAMPYPSFSRMTKEDMQALYAYFMHGVKP 136
           PD + GIG +TFA+FD AVR G++ +G TLYPAMP+PS++R++++DM ALYAYF HGV P
Sbjct: 88  PDRSTGIGSWTFAQFDRAVRAGVKPNGDTLYPAMPFPSYARLSQDDMHALYAYFTHGVAP 147

Query: 137 VAQPDKQPDISWPLSMRWPLGIWRMMFSPSPKDFTPAPGTDPEIARGDYLVTGPGHCGAC 196
           V Q +K  DI WPLSMRWPLGIWR +F+P P  F      DP IARG YLV G GHCGAC
Sbjct: 148 VNQKNKPVDIVWPLSMRWPLGIWRHLFAPEPVSFDAKRYADPVIARGAYLVQGLGHCGAC 207

Query: 197 HTPRGFAMQEKALDAAGGPDFLSGGAPIDNWVAPSLRNDPVVGLGRWSEDDIYTFLKSGR 256
           HTPR   MQE+AL    GP FL+GGA ID W+  SLR +P  G+G WSE D+  FLK+GR
Sbjct: 208 HTPRAATMQERALSEFDGPAFLAGGAAIDGWIPSSLRGNPRTGIGAWSEADLVQFLKTGR 267

Query: 257 IDHSAVFGGMGDVVAWSTQYFTDDDLHAIAKYLKSLPPVPPSQGNYTYDPSTANMLASGN 316
             HSA FGGM DVV  S Q+  D DL AIA+YLK+LP   P +  Y YD + A  L  G+
Sbjct: 268 TQHSAAFGGMTDVVQHSMQHMNDADLTAIARYLKTLPSTDPQETPYAYDDTAARALRMGD 327

Query: 317 TASVPGADTYVKECAICHRNDGGGVARMFPPLAGNPVVVTENPTSLVNVIAHGGVLPPSN 376
            AS PGA  Y   C  CHR+DG G  R+FP L GNPVV  ++ TSL++V+  G  L  + 
Sbjct: 328 -ASAPGAAVYRDNCTACHRSDGRGYNRVFPALGGNPVVQGKDATSLIHVLLTGSTLEGTK 386

Query: 377 WAPSAVAMPGYSKSLSAQQIADVVNFIRTSWGNKAPGTVTAADVTKLRDT 426
            APS+  MP +   L+ Q++ADV NF+RTSWGN    TV+A DV K+R T
Sbjct: 387 TAPSSFTMPAFGWRLNDQEVADVTNFVRTSWGNSG-STVSATDVAKVRKT 435


Lambda     K      H
   0.317    0.134    0.425 

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: 763
Number of extensions: 46
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: 468
Length of database: 451
Length adjustment: 33
Effective length of query: 435
Effective length of database: 418
Effective search space:   181830
Effective search space used:   181830
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 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