Alignments for a candidate for dapB in Sphingomonas koreensis DSMZ 15582

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapB in Sphingomonas koreensis DSMZ 15582

Align 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8) (characterized)
to candidate Ga0059261_2545 Ga0059261_2545 dihydrodipicolinate reductase (EC 1.3.1.26)

Query= BRENDA::Q2YJN7
         (268 letters)



>FitnessBrowser__Korea:Ga0059261_2545
          Length = 242

 Score =  221 bits (563), Expect = 1e-62
 Identities = 133/262 (50%), Positives = 165/262 (62%), Gaps = 25/262 (9%)

Query: 5   VVGAGGRMGQTLIRTIQSIEGAKLVGAIERSGSPFLGKDAGEVTGIGTLGVAITDDPLPV 64
           + G+ GRMG   IR I + +G K  G          G DAG             DDP  +
Sbjct: 6   IYGSLGRMG-VAIRDILAEQGVKFAG----------GADAG-------------DDPAVL 41

Query: 65  FAKAHGVLDFTSPAASVEFAGLAAQARIVHVIGTTGCSAEDDEKIRAAARHATIVKSGNM 124
            A A  ++DF++PAA       A  A    VIGTTG +A+    I  AAR   ++++GN 
Sbjct: 42  AAAADALVDFSTPAALESHLAAARAAGTPIVIGTTGLTAQHHALIDDAAREIAVLQTGNT 101

Query: 125 SLGVNLLSVLVQKAAEALGPEDFDIEILEMHHRHKVDAPSGTALLLGEAAARGRDIALAD 184
           SLGV LL+ LV++AA  LGP D+DIEI EMHHR KVDAPSGTAL+LGEAAA GR ++L +
Sbjct: 102 SLGVVLLARLVREAATRLGP-DWDIEIAEMHHRQKVDAPSGTALMLGEAAAAGRAVSLGE 160

Query: 185 NSVRVRDGYTGPRETGAIGFATLRGGSVIGDHSVILAGTGERVVLSHHAEDRSIFARGAI 244
             V  R G TG R  G IGFA+LRGG+VIGDH V+LAG GER+ L+H AEDR+IFARGA+
Sbjct: 161 VRVADRAGLTGARAEGTIGFASLRGGTVIGDHLVVLAGAGERIELAHRAEDRAIFARGAV 220

Query: 245 KAALWAHGKKPGLYSMLDVLGL 266
           +AALW   K  G Y+M  VLGL
Sbjct: 221 RAALWLADKPAGRYTMDAVLGL 242


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: 242
Number of extensions: 11
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: 242
Length adjustment: 24
Effective length of query: 244
Effective length of database: 218
Effective search space:    53192
Effective search space used:    53192
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 Ga0059261_2545 Ga0059261_2545 (dihydrodipicolinate reductase (EC 1.3.1.26))
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.30909.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    7.9e-67  211.6   2.5    2.7e-65  206.5   0.2    2.0  2  lcl|FitnessBrowser__Korea:Ga0059261_2545  Ga0059261_2545 dihydrodipicolina


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_2545  Ga0059261_2545 dihydrodipicolinate reductase (EC 1.3.1.26)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.8   0.2   0.00046   0.00046       4      34 ..       4      33 ..       1      40 [. 0.82
   2 !  206.5   0.2   2.7e-65   2.7e-65      70     270 .]      42     241 ..      32     241 .. 0.97

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.00046
                                 TIGR00036  4 vavaGaaGrmGrevikavkeaedlelvaale 34
                                              ++++G+ GrmG  +i+ + ++++++ ++  +
  lcl|FitnessBrowser__Korea:Ga0059261_2545  4 IGIYGSLGRMGV-AIRDILAEQGVKFAGGAD 33
                                              89*********7.579999999999887665 PP

  == domain 2  score: 206.5 bits;  conditional E-value: 2.7e-65
                                 TIGR00036  70 ekkadvliDfttpeavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgvalviapNfaiGvnll 138
                                                 +ad l+Df+tp a  +++++a ++g  +V+GTTG++ ++ + + d+a +  +a++ + N ++Gv+ll
  lcl|FitnessBrowser__Korea:Ga0059261_2545  42 AAAADALVDFSTPAALESHLAAARAAGTPIVIGTTGLTAQHHALIDDAARE--IAVLQTGNTSLGVVLL 108
                                               5689***********************************************..**************** PP

                                 TIGR00036 139 lkllekaakvle.dvDiEiiElHHrhKkDaPSGTAlklaeiiakargkdlkeaaveeregltGerkkee 206
                                                +l+++aa  l+ d+DiEi E+HHr+K+DaPSGTAl l+e+ a+ r   l e+ v  r gltG+r + +
  lcl|FitnessBrowser__Korea:Ga0059261_2545 109 ARLVREAATRLGpDWDIEIAEMHHRQKVDAPSGTALMLGEAAAAGRAVSLGEVRVADRAGLTGARAEGT 177
                                               **********97699****************************************************** PP

                                 TIGR00036 207 iGiaavRggdvvgehtvlFasdGerleitHkassRaafakGvvrairwledkeekvydledvld 270
                                               iG+a++Rgg v+g+h v+ a+ Ger+e+ H+a +Ra+fa+G+vra+ wl+dk ++ y+++ vl+
  lcl|FitnessBrowser__Korea:Ga0059261_2545 178 IGFASLRGGTVIGDHLVVLAGAGERIELAHRAEDRAIFARGAVRAALWLADKPAGRYTMDAVLG 241
                                               ************************************************************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (242 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: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 1.91
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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 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 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