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

GapMind for catabolism of small carbon sources

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

Align alcohol dehydrogenase (cytochrome c) (EC 1.1.2.8) (characterized)
to candidate Pf6N2E2_1752 Quino(hemo)protein alcohol dehydrogenase, PQQ-dependent (EC 1.1.99.8)

Query= BRENDA::D2SZY4
         (742 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1752
          Length = 726

 Score =  594 bits (1532), Expect = e-174
 Identities = 319/709 (44%), Positives = 424/709 (59%), Gaps = 20/709 (2%)

Query: 10  RSLLGILAAGTICAAALPYAAVPARADGQGNTGEAIIHADDHPENWLSYGRTYSEQRYSP 69
           +SL G L      A+AL  +  PA  D Q      +I AD  P NW+S GRTY EQRYSP
Sbjct: 22  KSLAGALLLSLATASALA-SETPANVDSQ-----RLIAADKEPGNWMSTGRTYDEQRYSP 75

Query: 70  LDQINRSNVGDLKLAWYYTLDTNRGQEATPLVVDGIMYATTNWSKMEALDAATGKLLWQY 129
           L +I+  NVG L LAW Y LD +RG EATP+VVDG+MY T  +S + ALDA  GKL+W+Y
Sbjct: 76  LKRISDQNVGQLGLAWSYKLDLDRGVEATPIVVDGVMYTTGPFSVVYALDARNGKLIWKY 135

Query: 130 DPKVPGNIADKGCCDTVNRGAGYWNGKVFWGTFDGRLVAADAKTGKKVWEVNTIPADASL 189
           DP+   N A + CCD VNRG   W GKV+ G  DGRL A DAKTG++ W V+T       
Sbjct: 136 DPQSDRNRAGEACCDAVNRGVAVWKGKVYVGVLDGRLEAIDAKTGQRAWSVDT-----RA 190

Query: 190 GKQRSYTVDGAVRVAKGLVLIGNGGAEFGARGFVSAFDAETGKLKWRFYTVPNNKNEPDH 249
             +RSYT+ GA RV  G V+IGNGGAEFG RG+V+A+DAETGK  WRFYTVP +   P  
Sbjct: 191 DHKRSYTITGAPRVVNGKVVIGNGGAEFGVRGYVTAYDAETGKQAWRFYTVPGDPKLPPE 250

Query: 250 AASDNILMNKAYKTWGPKGAWVRQGGGGTVWDSLVYDPVSDLIYLAVGNGSPWNYKYRSE 309
                  M  A KTW    A+V QGGGGT WDS  +DP  +L+Y+ VGNGS W+ K+RS+
Sbjct: 251 DKG----MAIAAKTWHGD-AFVEQGGGGTAWDSFAFDPDLNLLYIGVGNGSLWDPKWRSQ 305

Query: 310 GIGSNLFLGSIVALKPETGEYVWHFQATPMDQWDYTSVQQIMTLDMPVNGEMRHVIVHAP 369
             G NLFL SIVA+  +TGEYVWH+Q TP D WDYT+ Q ++  ++P++G+ R V++ AP
Sbjct: 306 AKGDNLFLSSIVAVNADTGEYVWHYQTTPGDAWDYTATQHMILAELPIDGKPRKVLMQAP 365

Query: 370 KNGFFYVLDAKTGEFLSGKNYVYQNWANGLDPLTGRPIYNPD-GLYTLNGKFWYGIPGPL 428
           KNGFFYV+D  TG+ LS K  V Q+W  G+D  TGRPI + +   Y  +GK     P   
Sbjct: 366 KNGFFYVIDRATGQLLSAKGIVPQSWTKGMDMKTGRPIVDDENAAYWKDGKRKLVTPAFW 425

Query: 429 GAHNFMAMAYSPKTHLVYIPAHQIPFGYKNQVGGFKPHADSWNVGLDMTKNGLPDTPEAR 488
           GAH++  M+Y+P T LVYIPAH +   Y++     K +       L +    +P+  +  
Sbjct: 426 GAHDWQPMSYNPNTGLVYIPAHIMSAYYEHIPEAPKRNPFKSMYQLGLRTGMMPENVDGL 485

Query: 489 TAYIKDLHGWLLAWDPVKMETVWKIDHKGPWNGGILATGGDLLFQGLANGEFHAYDATNG 548
               K   G L+AWDPVK +  W++ +   +NGG L+T G+L+F+G A+G   AY A  G
Sbjct: 486 LEMAKGWSGKLIAWDPVKQQPAWEVPYVTIFNGGTLSTAGNLVFEGSADGRVIAYAADTG 545

Query: 549 SDLYKFDAQSGIIAPPMTYSVNGKQYVAVEVGWGGIYPISMGGVGRTSGWTVNHSYIAAF 608
             L++  A SG++A P+TYSV+G+QYV    GWGG +    G +   +G     S +  +
Sbjct: 546 KKLWEQPAASGVMAAPITYSVDGEQYVTFMAGWGGAFSTFAGALSLRAG-VQPFSQVLTY 604

Query: 609 SLDGKAKLPALNNRGFLPVKPPAQYDQKVVDNGYFQYQTYCQTCHGDNGEGAGMLPDLRW 668
            + G AKL     R   P  P    D   ++ G   Y  YC  CHG +    G+LPDLR 
Sbjct: 605 KIGGTAKLQEPAPRPDTPKPPALSTDTAAIEAGGKLYDGYCSQCHGIHAVSGGVLPDLRK 664

Query: 669 AGAIRHQDAFYNVVGRGALTAYGMDRFDTSMTPDEIEAIRQYLIKRAND 717
               +HQ  F  ++  G +   GM  F  + TP++++ I QYLIKRA+D
Sbjct: 665 LTPEKHQ-MFLGILFGGRVPD-GMPSFADAFTPEQVDQIHQYLIKRAHD 711


Lambda     K      H
   0.318    0.137    0.441 

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: 2136
Number of extensions: 168
Number of successful extensions: 19
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: 742
Length of database: 726
Length adjustment: 40
Effective length of query: 702
Effective length of database: 686
Effective search space:   481572
Effective search space used:   481572
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 (21.7 bits)
S2: 55 (25.8 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources