Alignments for a candidate for etoh-dh-c in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for etoh-dh-c in Pseudomonas stutzeri RCH2

Align alcohol dehydrogenase (cytochrome c) (EC 1.1.2.8) (characterized)
to candidate GFF1386 Psest_1423 PQQ-dependent dehydrogenase, methanol/ethanol family

Query= BRENDA::D2SZY4
         (742 letters)



>FitnessBrowser__psRCH2:GFF1386
          Length = 710

 Score =  453 bits (1166), Expect = e-131
 Identities = 276/724 (38%), Positives = 375/724 (51%), Gaps = 61/724 (8%)

Query: 21  ICAAALPYAAVPARADGQGNTGEAIIHADDHPENWLSYGRTYSEQRYSPLDQINRSNVGD 80
           I AA+L  A  P  A  +  T + +   + +  +WL+YGRT+SEQR+SPL  IN  NV  
Sbjct: 13  IMAASL-LAITPLHASDRVITDKELSD-ESNTTDWLAYGRTHSEQRFSPLKDINVENVSG 70

Query: 81  LKLAWYYTLDTNRGQEATPLVVDGIMYATTNWSKMEALDAATGKLLWQYDPKVPGNIADK 140
           LK  WY  L        TPLVVDG+MY     ++  A DA TGK+LW+YDP+V   I D 
Sbjct: 71  LKPEWYAPLPDRSDIVGTPLVVDGVMYYVGEMNRTRAFDARTGKMLWEYDPQVSKEIIDN 130

Query: 141 GCCDTV---NRGAGYWNGKVFWGTFDGRLVAADAKTGKKVWEVNTIPADASLGKQRSYTV 197
                    NRG   +  K+F  T+DGRL+A   K GK+VW+  T   D  L       +
Sbjct: 131 NMKKVFWKHNRGLSTYGDKLFIATWDGRLIAITRKDGKEVWQTRTFDHDQPLN------I 184

Query: 198 DGAVRVAKGLVLIGNGGAEFGA-RGFVSAFDAETGKLKWRFYTVPNNKNEPDHAASDNIL 256
            G  +   G V +GNGG E G  RG+V+A+D ETGK  WRFY VP N  +    A+  + 
Sbjct: 185 TGHPKAFDGKVFVGNGGTELGPMRGYVTAYDTETGKQVWRFYIVPGNPADGFEDAAQEM- 243

Query: 257 MNKAYKTWGPKGAWVRQGGGGTVWDSLVYDPVSDLIYLAVGNGSPWNYKYRSEGIGSNLF 316
              A KTW   G W   GGGG  W    YD   + +    GNG PWN K RS   G NLF
Sbjct: 244 ---AAKTW--TGRWWENGGGGNAWHGWTYDEKYNQLIFGTGNGGPWNIKVRSPDGGDNLF 298

Query: 317 LGSIVALKPETGEYVWHFQATPMDQWDYTSVQQIMTLDMPVNGEMRHVIVHAPKNGFFYV 376
           L S+VA+  +TGEY WH Q  P D WDY S   I+  D+ ++G+    ++HAPKNGFFY 
Sbjct: 299 LCSVVAVDADTGEYKWHVQTAPGDTWDYNSNMDIVLADLKIDGKDVDAVLHAPKNGFFYT 358

Query: 377 LDAKTGEFLSGKNYVYQNWANGLDPLTGRPIYNPDGLYTLNGKFWYGIPGPLGAHNFMAM 436
           +D   G+ LS + +   NW+   D    R I   D  Y    K  Y  P   GAH++ AM
Sbjct: 359 IDRSNGKVLSAEKFTDANWSTKYDLKEQRHIVAEDARYPDGEKNIY--PSAFGAHSWHAM 416

Query: 437 AYSPKTHLVYIPAHQIPFGYKNQVGGFKP--HADSWNVGLDMTKNGLPDTPEARTAYIKD 494
           +Y+P+ +L +IP + +   +K+     KP     S  + L +T   L   P        +
Sbjct: 417 SYNPELNLAFIPTNHLGNTFKDDGKDTKPGHKMASHKLYLGLTGWELTKDPH-------E 469

Query: 495 LHGWLLAWDPVKMETVWKIDHKGPWNGGILATGGDLLFQGLANGEFHAYDATNGSDLYKF 554
             G L AWDPVK + VW+++ K PW GG L T G+L+FQG  +G   AYDA  G +L+ +
Sbjct: 470 SRGSLQAWDPVKNKRVWQVNQKSPWGGGTLTTAGNLVFQGQPDGMLKAYDARTGDELWSY 529

Query: 555 DAQSGIIAPPMTYSVNGKQYVAVEVGWGGIYPISMGGVG----RTSGWT--VNHSYIAAF 608
           D   GI APP+TY ++GKQ V++ VG GG    + GG G     + GW   V+   I  F
Sbjct: 530 DVGLGISAPPITYKLDGKQMVSLLVGPGGALASNFGGSGELGFESHGWKYGVHERRIMTF 589

Query: 609 SLDGKAKLPALNNRGFLPVKPPAQYDQKVVDN-------------GYFQYQTYCQTCHGD 655
           SLDGKA          +P +P  Q  + ++D              G F  +  C  CHG 
Sbjct: 590 SLDGKA---------VIPEQPAPQLAKPIIDEKFEVDAKKAEAGAGVFA-ENLCVGCHGA 639

Query: 656 NGEGAGMLPDLRWAGAIRH--QDAFYNVVGRGALTAYGMDRFDTSMTPDEIEAIRQYLIK 713
                   PDLR +  +    + AF +VV  GAL A GM +F + +T  E+E+IR ++ +
Sbjct: 640 GAVAGMKAPDLRESPILLKGGEKAFESVVRGGALLANGMPKF-SDLTDAELESIRHFVRR 698

Query: 714 RAND 717
           +A D
Sbjct: 699 QARD 702


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: 2083
Number of extensions: 174
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: 710
Length adjustment: 40
Effective length of query: 702
Effective length of database: 670
Effective search space:   470340
Effective search space used:   470340
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