Alignments for a candidate for dapB in Kyrpidia tusciae DSM 2912

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapB in Kyrpidia tusciae DSM 2912

Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate WP_013075686.1 BTUS_RS08425 4-hydroxy-tetrahydrodipicolinate reductase

Query= BRENDA::Q3MFY8
         (278 letters)



>NCBI__GCF_000092905.1:WP_013075686.1
          Length = 267

 Score =  249 bits (635), Expect = 6e-71
 Identities = 132/275 (48%), Positives = 186/275 (67%), Gaps = 11/275 (4%)

Query: 4   QAPIPVIVNGAAGKMGREVVKAIAQAPDLNLLGAIDSSPEHQGKDAGELAGLSEPLEVPI 63
           +  I V+V+GA GKMGREV++ +     L L+GA+ S      +DAG  AG+ EPL +P+
Sbjct: 3   EGEIRVVVSGATGKMGREVIRTMVAETGLRLVGAVASRAR---EDAGVAAGM-EPLGIPV 58

Query: 64  TNQLEPMLGYVAGERQGPPGVIVDFTHPDSVYDNVRSAIAYGIRPVVGTTGLSPAQIQNL 123
           +  L   L  V+ E    P V+VDFT PD+V  +V+ A+ +G+RPVVGT+G++  Q++  
Sbjct: 59  SANLRETL--VSAE----PDVLVDFTTPDAVERHVQEALEFGVRPVVGTSGVTREQVRRW 112

Query: 124 ADFAEKASTGCLIIPNFSIGMVLLQQAAVTASQYFDHVEIIELHHNQKADAPSGTAIQTA 183
                + S G ++ PNF++G VL+ +    A++Y  HVEIIE+HH+ K DAPSGTA++TA
Sbjct: 113 DGLCRERSVGGIVAPNFAVGAVLMMRFVREAARYLPHVEIIEMHHDGKLDAPSGTAVKTA 172

Query: 184 ELLAELGKTFNSAIVEETEKIPGARGSLAGEGIRIHSVRLPGLIAHQEVIFGAPGQIYTL 243
           E LAE G   +S   +E E  PGARG+  G G+R+HSVRLPGL+AHQEVI G PGQI T+
Sbjct: 173 EELAEAGIDLSSGKPDERELFPGARGAAIG-GVRVHSVRLPGLVAHQEVILGGPGQILTV 231

Query: 244 RHDTSDRACYMPGVLLAIRKVLQLKSLVYGLEKIL 278
           RHD+ DR  +MPGV+LA+R V+    ++YGLE +L
Sbjct: 232 RHDSLDRVSFMPGVVLAVRAVMGYVGMMYGLEALL 266


Lambda     K      H
   0.317    0.136    0.386 

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: 244
Number of extensions: 10
Number of successful extensions: 3
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: 278
Length of database: 267
Length adjustment: 25
Effective length of query: 253
Effective length of database: 242
Effective search space:    61226
Effective search space used:    61226
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: 47 (22.7 bits)

Align candidate WP_013075686.1 BTUS_RS08425 (4-hydroxy-tetrahydrodipicolinate reductase)
to HMM TIGR00036 (dapB: 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR00036.hmm
# target sequence database:        /tmp/gapView.2788899.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00036  [M=270]
Accession:   TIGR00036
Description: dapB: 4-hydroxy-tetrahydrodipicolinate reductase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                             Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    2.5e-81  259.1   0.2    2.8e-81  259.0   0.2    1.0  1  NCBI__GCF_000092905.1:WP_013075686.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000092905.1:WP_013075686.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  259.0   0.2   2.8e-81   2.8e-81       2     270 .]       6     267 .]       5     267 .] 0.97

  Alignments for each domain:
  == domain 1  score: 259.0 bits;  conditional E-value: 2.8e-81
                             TIGR00036   2 ikvavaGaaGrmGrevikavkeaedlelvaalerkgsskqgkDiGelagigkvgvpveddleavkvlaekkad 74 
                                           i+v+v+Ga+G+mGrevi+++ ++ +l+lv+a+     s+  +D+G  ag+ ++g+pv+++l+ +  l+  ++d
  NCBI__GCF_000092905.1:WP_013075686.1   6 IRVVVSGATGKMGREVIRTMVAETGLRLVGAVA----SRAREDAGVAAGMEPLGIPVSANLRET--LVSAEPD 72 
                                           9*******************************9....68889******************9955..9999*** PP

                             TIGR00036  75 vliDfttpeavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgvalviapNfaiGvnlllkllekaak 147
                                           vl+Dfttp+av  +v+ ale gvr+VvGT G++ e++++   l  +++v+ ++apNfa+G++l+++++++aa+
  NCBI__GCF_000092905.1:WP_013075686.1  73 VLVDFTTPDAVERHVQEALEFGVRPVVGTSGVTREQVRRWDGLCRERSVGGIVAPNFAVGAVLMMRFVREAAR 145
                                           ************************************************************************* PP

                             TIGR00036 148 vledvDiEiiElHHrhKkDaPSGTAlklaeiiakargkdlkeaaveeregltGerkkeeiG..iaavRggdvv 218
                                           +l +v  EiiE+HH+ K DaPSGTA+k+ae +a+a   dl++   +ere ++G+r++   G  +++vR++++v
  NCBI__GCF_000092905.1:WP_013075686.1 146 YLPHV--EIIEMHHDGKLDAPSGTAVKTAEELAEAGI-DLSSGKPDERELFPGARGAAIGGvrVHSVRLPGLV 215
                                           ****9..****************************98.9****************66655599********** PP

                             TIGR00036 219 gehtvlFasdGerleitHkassRaafakGvvrairwledkeekvydledvld 270
                                           ++++v+ ++ G+ l+++H++ +R +f+ Gvv+a+r ++     +y+le +l+
  NCBI__GCF_000092905.1:WP_013075686.1 216 AHQEVILGGPGQILTVRHDSLDRVSFMPGVVLAVRAVMGYVGMMYGLEALLG 267
                                           ***********************************************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (267 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 18.63
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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
changes to Amino acid biosynthesis since the original publication.

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 Amino acid biosynthesis