GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-c in Pseudomonas fluorescens FW300-N2E2

Align quinoprotein decanol dehydrogenase; EC 1.1.-.- (characterized)
to candidate Pf6N2E2_1382 Quino(hemo)protein alcohol dehydrogenase, PQQ-dependent (EC 1.1.99.8)

Query= CharProtDB::CH_107432
         (595 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1382
          Length = 591

 Score = 1167 bits (3020), Expect = 0.0
 Identities = 549/587 (93%), Positives = 576/587 (98%)

Query: 1   MTRSPRRPMFAVSLVLSAMLLAGAAHAAVSNEEILQDPKNPQQIVTNGLGVQGQRYSPLD 60
           M++  RR  FAVSL+LSAMLL+G+A AAV+++EILQDPKNP+QIVTNGLGVQGQRYSPLD
Sbjct: 1   MSQPARRQPFAVSLLLSAMLLSGSALAAVTDQEILQDPKNPEQIVTNGLGVQGQRYSPLD 60

Query: 61  LLNANNVKELRPVWAFSFGGEKQRGQQAQPLIKDGVMYLTGSYSRVFAVDARTGKKLWQY 120
            LN +NVK+LRPVWAFSFGGEKQRGQQAQP+IKDGVMYLTGSYSRVFAVDARTGKKLWQY
Sbjct: 61  TLNTDNVKDLRPVWAFSFGGEKQRGQQAQPMIKDGVMYLTGSYSRVFAVDARTGKKLWQY 120

Query: 121 DARLPDDIRPCCDVINRGVALYGDLVFFGTLDAKLVALNKDTGKVVWSKKVADHKEGYSI 180
           DARLPDDIRPCCDVINRGVALYGDLVFFGTLDAKLVALNKDTGKVVWSKKVADHKEGYSI
Sbjct: 121 DARLPDDIRPCCDVINRGVALYGDLVFFGTLDAKLVALNKDTGKVVWSKKVADHKEGYSI 180

Query: 181 SAAPMIVNGKLITGVAGGEFGVVGKIQAYNPENGELLWMRPTVEGHMGYVYKDGKAIENG 240
           SAAP+IVNGKLITGVAGGEFGVVG+I AY+P+NGELLW RPTVEGHMGYVYKDGKA+ENG
Sbjct: 181 SAAPLIVNGKLITGVAGGEFGVVGQISAYDPKNGELLWTRPTVEGHMGYVYKDGKAVENG 240

Query: 241 ISGGEAGKTWPGDLWKTGGAAPWLGGYYDPETNLILFGTGNPAPWNSHLRPGDNLYSSSR 300
           ISGGEAGKTWPGDLWKTGGAAPWLGGYYDPETNL+LFGTGNPAPWNSHLRPGDNLYSSSR
Sbjct: 241 ISGGEAGKTWPGDLWKTGGAAPWLGGYYDPETNLLLFGTGNPAPWNSHLRPGDNLYSSSR 300

Query: 301 LALNPDDGTIKWHFQSTPHDGWDFDGVNELISFNYKDGGKEVKAAATADRNGFFYVLDRT 360
           LALNPDDGTIKWHFQSTPHDGWD+DGVNELISFNYK+GGK++KAAATADRNGFFYVLDRT
Sbjct: 301 LALNPDDGTIKWHFQSTPHDGWDYDGVNELISFNYKEGGKDIKAAATADRNGFFYVLDRT 360

Query: 361 NGKFIRGFPFVDKITWATGLDKDGRPIYNDASRPGAPGSEAKGSSVFVAPAFLGAKNWMP 420
           NGKFIRGFPFVDKITWATGLDKDGRPIYN+ASRPGAPGSEAKGSSVFVAPAFLGAKNWMP
Sbjct: 361 NGKFIRGFPFVDKITWATGLDKDGRPIYNEASRPGAPGSEAKGSSVFVAPAFLGAKNWMP 420

Query: 421 MAYNKDTGLFYVPSNEWGMDIWNEGIAYKKGAAFLGAGFTIKPLNEDYIGVLRAIDPISG 480
           MAYN+DTGLFYVPSNEWGMDIWNEGIAYKKGAAFLGAGFTIKPLNEDYIGVLRAIDP +G
Sbjct: 421 MAYNQDTGLFYVPSNEWGMDIWNEGIAYKKGAAFLGAGFTIKPLNEDYIGVLRAIDPKTG 480

Query: 481 KEVWRHKNYAPLWGGVLTTKGNLVFTGTPEGFLQAFNAKTGDKVWEFQTGSGVLGSPVTW 540
           KEVWRHKNYAPLWGGVLTTKGNLVFTGTPEGFLQAFNAKTG+KVWEFQTGSGVLGSP+TW
Sbjct: 481 KEVWRHKNYAPLWGGVLTTKGNLVFTGTPEGFLQAFNAKTGEKVWEFQTGSGVLGSPITW 540

Query: 541 EMDGEQYVSVVSGWGGAVPLWGGEVAKRVKDFNQGGMLWTFKLPKQL 587
           EMDGEQYVSVVSGWGGAVPLWGGEVAKRVKDFNQGGMLWTFKLPK L
Sbjct: 541 EMDGEQYVSVVSGWGGAVPLWGGEVAKRVKDFNQGGMLWTFKLPKAL 587


Lambda     K      H
   0.317    0.137    0.438 

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: 2004
Number of extensions: 135
Number of successful extensions: 13
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: 595
Length of database: 591
Length adjustment: 37
Effective length of query: 558
Effective length of database: 554
Effective search space:   309132
Effective search space used:   309132
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: 53 (25.0 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