Alignments for a candidate for dapB in Phyllobacterium endophyticum PEPV15

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapB in Phyllobacterium endophyticum PEPV15

Align 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8) (characterized)
to candidate WP_106714899.1 CU100_RS02115 4-hydroxy-tetrahydrodipicolinate reductase

Query= BRENDA::Q2YJN7
         (268 letters)



>NCBI__GCF_003010935.1:WP_106714899.1
          Length = 277

 Score =  400 bits (1027), Expect = e-116
 Identities = 200/268 (74%), Positives = 226/268 (84%)

Query: 1   MGLVVVGAGGRMGQTLIRTIQSIEGAKLVGAIERSGSPFLGKDAGEVTGIGTLGVAITDD 60
           M L VVGA GRMGQTLIR I S  GA L GAIER GSP +G DAG + G+G LGV I+DD
Sbjct: 10  MKLAVVGAAGRMGQTLIRIIHSTPGAMLSGAIERVGSPHIGSDAGVLAGVGKLGVPISDD 69

Query: 61  PLPVFAKAHGVLDFTSPAASVEFAGLAAQARIVHVIGTTGCSAEDDEKIRAAARHATIVK 120
            L  FA   GVLDFT+PAASVEFAGLAAQ  IVHV+GTTGC + DD KI  AARHA ++K
Sbjct: 70  ALAAFAGVEGVLDFTTPAASVEFAGLAAQTGIVHVVGTTGCDSTDDAKIALAARHAVVIK 129

Query: 121 SGNMSLGVNLLSVLVQKAAEALGPEDFDIEILEMHHRHKVDAPSGTALLLGEAAARGRDI 180
           SGNMSLGVNLL+VLV++AA+ALG +DFD+EILEMHH+HKVDAPSGTALLLGEAAA GR+I
Sbjct: 130 SGNMSLGVNLLAVLVKQAAKALGADDFDVEILEMHHKHKVDAPSGTALLLGEAAAEGRNI 189

Query: 181 ALADNSVRVRDGYTGPRETGAIGFATLRGGSVIGDHSVILAGTGERVVLSHHAEDRSIFA 240
            L  +SVRVRDG+TG RE G IGFA+LRGGSV+GDHSVILAG GER+ LSHHAEDRSIFA
Sbjct: 190 GLGQHSVRVRDGHTGAREAGTIGFASLRGGSVVGDHSVILAGQGERITLSHHAEDRSIFA 249

Query: 241 RGAIKAALWAHGKKPGLYSMLDVLGLNT 268
           RGA+KAALW  G+KPGLY+MLDVLGL+T
Sbjct: 250 RGAVKAALWGRGRKPGLYTMLDVLGLDT 277


Lambda     K      H
   0.318    0.136    0.387 

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: 335
Number of extensions: 18
Number of successful extensions: 2
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: 268
Length of database: 277
Length adjustment: 25
Effective length of query: 243
Effective length of database: 252
Effective search space:    61236
Effective search space used:    61236
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: 47 (22.7 bits)

Align candidate WP_106714899.1 CU100_RS02115 (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.127896.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    3.3e-80  255.5   4.0    3.8e-80  255.3   4.0    1.0  1  NCBI__GCF_003010935.1:WP_106714899.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003010935.1:WP_106714899.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  255.3   4.0   3.8e-80   3.8e-80       2     270 .]      10     274 ..       9     274 .. 0.97

  Alignments for each domain:
  == domain 1  score: 255.3 bits;  conditional E-value: 3.8e-80
                             TIGR00036   2 ikvavaGaaGrmGrevikavkeaedlelvaalerkgsskqgkDiGelagigkvgvpveddleavkvlaekkad 74 
                                           +k+av GaaGrmG+ +i+ ++++++  l++a+er gs++ g+D+G lag+gk+gvp++dd  a+       ++
  NCBI__GCF_003010935.1:WP_106714899.1  10 MKLAVVGAAGRMGQTLIRIIHSTPGAMLSGAIERVGSPHIGSDAGVLAGVGKLGVPISDDALAA----FAGVE 78 
                                           89********************************************************998876....67888 PP

                             TIGR00036  75 vliDfttpeavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgvalviapNfaiGvnlllkllekaak 147
                                            ++Dfttp a +e + +a+++g+  VvGTTG +  d ++++ +a +  + ++ + N+++Gvnll  l+++aak
  NCBI__GCF_003010935.1:WP_106714899.1  79 GVLDFTTPAASVEFAGLAAQTGIVHVVGTTGCDSTDDAKIALAARH--AVVIKSGNMSLGVNLLAVLVKQAAK 149
                                           999**************************************99999..88999******************** PP

                             TIGR00036 148 vl..edvDiEiiElHHrhKkDaPSGTAlklaeiiakargkdlkeaaveeregltGerkkeeiGiaavRggdvv 218
                                            l  +d+D+Ei+E+HH+hK+DaPSGTAl l+e+ a+ r+  l ++ v  r+g+tG+r++ +iG+a++Rgg vv
  NCBI__GCF_003010935.1:WP_106714899.1 150 ALgaDDFDVEILEMHHKHKVDAPSGTALLLGEAAAEGRNIGLGQHSVRVRDGHTGAREAGTIGFASLRGGSVV 222
                                           *944588****************************************************************** PP

                             TIGR00036 219 gehtvlFasdGerleitHkassRaafakGvvrairwledkeekvydledvld 270
                                           g+h+v+ a++Ger++++H+a +R++fa+G+v+a+ w    + ++y++ dvl+
  NCBI__GCF_003010935.1:WP_106714899.1 223 GDHSVILAGQGERITLSHHAEDRSIFARGAVKAALWGRGRKPGLYTMLDVLG 274
                                           **************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (277 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 8.53
//
[ok]

This GapMind analysis is from Jul 26 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