Alignments for a candidate for adh in Geotalea uraniireducens Rf4

GapMind for catabolism of small carbon sources

Alignments for a candidate for adh in Geotalea uraniireducens Rf4

Align aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized)
to candidate WP_011940351.1 GURA_RS18035 aldehyde dehydrogenase family protein

Query= CharProtDB::CH_018413
         (862 letters)



>NCBI__GCF_000016745.1:WP_011940351.1
          Length = 447

 Score =  357 bits (917), Expect = e-103
 Identities = 199/445 (44%), Positives = 286/445 (64%), Gaps = 11/445 (2%)

Query: 6   VKELDEKLKVIKEAQKKFSCYSQEMVDEIFRNAAMAAIDARIELAKAAVLETGMGLVEDK 65
           V ++D+ +   ++A + F   +QE VD I      A +    +LA+ AV ETG+G VEDK
Sbjct: 5   VTQVDQMVAKARKAAEAFKGLTQEQVDRITEAMTKAGVANERKLAEMAVEETGIGNVEDK 64

Query: 66  VIKNHFAGEYIYNKYKDEKTCGIIERNEPYGITKIAEPIGVVAAIIPVTNPTSTTIFKSL 125
           VIKNHF  + +Y+  KD+++ GIIE ++  GI  IAEP GV+AAI PVTNP +TT+FKSL
Sbjct: 65  VIKNHFGTQVVYDYMKDKRSVGIIEEDD--GIISIAEPFGVIAAITPVTNPAATTLFKSL 122

Query: 126 ISLKTRNGIFFSPHPRAKKSTILAAKTILDAAVKSGAPENIIGWIDEPSIELTQYLMQKA 185
           I+LK RN I  + HP+A+K +  AA+ +LDAAV +GAP N I W++EPSIE T  LM+  
Sbjct: 123 IALKGRNVICLAFHPKAQKCSAAAARIMLDAAVAAGAPANCIQWVEEPSIEATDALMKHP 182

Query: 186 DI--TLATGGPSLVKSAYSSGKPAIGVGPGNTPVIIDESAHIKMAVSSIILSKTYDNGVI 243
            +   +ATGG ++VK+AYSSG PA+GVGPGN PV I++SA++ +A+  +I SKT+DNG I
Sbjct: 183 GVAMVIATGGGAMVKAAYSSGHPALGVGPGNVPVYIEKSANLNIAIPDVIASKTFDNGTI 242

Query: 244 CASEQSVIV-LKSIYNKVKDEFQERGAYIIKKNELDKVREVIF--KDGSVNPKIVGQSAY 300
           C+S+QSVI   K++  K    F+E GAY+    E  K+  V+F  + G  + +I+G+   
Sbjct: 243 CSSDQSVIFDDKAVAEKALKLFKENGAYLCNDEEKAKLEAVMFDKERGVPSMQIIGKKPQ 302

Query: 301 TIAAMAGIKVPKTTRILIGEVTSLGEEEPFAHEKLSPVLAMYEADNFDDALKKAVTLINL 360
            IA +AG  VP   ++L+  +T+ G E+  +HEKLSPVL  +  D+ + A+  AV+ +  
Sbjct: 303 FIAELAGFTVPADVKLLMVPLTTTGPEDWMSHEKLSPVLGWFIVDSKEKAISAAVSQLEF 362

Query: 361 GGLGHTSGIYADEIKARDKIDRFSSAMKTVRTFVNIPTSQGASGDLYNFRIPPSFTLGCG 420
           GG GH++ ++ ++         F+  +   R   N P+  G  G LYN  + PS TLGCG
Sbjct: 363 GGAGHSAVVFTED---EGVATEFALRVPANRVVWNQPSVHGTIGALYN-SLVPSLTLGCG 418

Query: 421 FWGGNSVSENVGPKHLLNIKTVAER 445
             GGN  +ENVG K+LLNIK VA R
Sbjct: 419 AMGGNITTENVGYKNLLNIKRVARR 443


Lambda     K      H
   0.317    0.134    0.378 

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: 866
Number of extensions: 41
Number of successful extensions: 7
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: 862
Length of database: 447
Length adjustment: 37
Effective length of query: 825
Effective length of database: 410
Effective search space:   338250
Effective search space used:   338250
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 Apr 09 2024. 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 2024 update 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