Alignments for a candidate for dopDH in Trichormus variabilis ATCC 29413

GapMind for catabolism of small carbon sources

Alignments for a candidate for dopDH in Trichormus variabilis ATCC 29413

Align Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized)
to candidate WP_011319687.1 AVA_RS14900 L-glutamate gamma-semialdehyde dehydrogenase

Query= SwissProt::P42236
         (488 letters)



>NCBI__GCF_000204075.1:WP_011319687.1
          Length = 993

 Score =  288 bits (738), Expect = 5e-82
 Identities = 177/473 (37%), Positives = 252/473 (53%), Gaps = 22/473 (4%)

Query: 9   TYLNFINGEWVKSQSGDMVKVENPADVNDIVGYVQNSTAEDVERAVTAANEAKTAWRKLT 68
           +YL  INGE+V  Q+ +++   NP++  +++G V   + E  E+A+ AA  A   WR+  
Sbjct: 504 SYLPLINGEYV--QTAEVIDSVNPSNFGEVIGKVGLISVEQAEQAMQAAKAAFPGWRRTP 561

Query: 69  GAERGQYLYKTADIMEQRLEEIAACATREMGKTLPEAKGETARGIAILRYYAGEGMRKTG 128
             ER   L +  D++E+R  E++A    E+GK + EA  E +  I   RYYA E  R   
Sbjct: 562 VKERAAILRRAGDLLEERRAELSAWIVLEVGKPVKEADAEVSEAIDFCRYYADEMER--- 618

Query: 129 DVIPSTDKDALMFTTRV---PLGVVGVISPWNFPVAIPIWKMAPALVYGNTVVIKPATET 185
            +    + D    T R    P G+V VISPWNFP+AI       ALV GN  ++KPA  +
Sbjct: 619 -LYQGINYDVAGETNRYIYQPRGIVVVISPWNFPLAIACGMTVAALVTGNCTLLKPAETS 677

Query: 186 AVTCAKIIACFEEAGLPAGVINLVTGPGSVVGQGLAEHDGVNAVTFTGSNQVG-KIIGQA 244
           +V  AK+     EAG+P GV   V G GS VG  L  H   + + FTGS +VG +I  +A
Sbjct: 678 SVITAKLTEILLEAGIPKGVFQYVPGKGSQVGAYLVSHPDTHLIAFTGSQEVGCRIYAEA 737

Query: 245 ALARGAKYQL-----EMGGKNPVIVADDADLEAAAEAVITGAFRSTGQKCTATSRVIVQS 299
           A  +  +  +     EMGGKN +IV + ADL+ A   V+  AF  +GQKC+A SRVIV  
Sbjct: 738 ATLKPQQRHMKRVIAEMGGKNAIIVDESADLDQAVIGVVQSAFGYSGQKCSACSRVIVVE 797

Query: 300 GIYERFKEKLLQRTKDITIGDSLKEDVWMGPIASKNQLDNCLSYIEKGKQEGASLLIGGE 359
            IY+ F  +L++ TK + IG++      +GP+   N  D    YIEKGK E         
Sbjct: 798 AIYDAFIHRLVEATKSLNIGEAELPSTQVGPVIDANARDRIREYIEKGKAESQ------V 851

Query: 360 KLENGKYQNGYYVQPAIFDNVTSEMTIAQEEIFGPVIALIKVDSIEEALNIANDVKFGLS 419
            LE     +GY+V P IF  V    TIAQ+EIFGPV+A+IK     +AL IAND  + L+
Sbjct: 852 ALELSAPNHGYFVGPVIFGEVPPHGTIAQQEIFGPVLAVIKAKDFAQALAIANDTDYALT 911

Query: 420 ASIFTENIGRMLSFIDEIDAGLVRINAESAG-VELQAPFGGMKQSSSHSREQG 471
             +++     +    +E + G + IN    G +  + PFGG K S   S+  G
Sbjct: 912 GGLYSRTPSHIQQAQEEFEVGNLYINRNITGAIVARQPFGGFKLSGVGSKAGG 964


Lambda     K      H
   0.315    0.132    0.374 

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: 938
Number of extensions: 39
Number of successful extensions: 4
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: 488
Length of database: 993
Length adjustment: 39
Effective length of query: 449
Effective length of database: 954
Effective search space:   428346
Effective search space used:   428346
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 (21.5 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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