Aligments for a candidate for dapB in Sphingomonas koreensis DSMZ 15582

GapMind for Amino acid biosynthesis

Aligments for a candidate for dapB in Sphingomonas koreensis DSMZ 15582

Align dihydrodipicolinate reductase; EC 1.3.1.26 (characterized)
to candidate Ga0059261_2545 Ga0059261_2545 dihydrodipicolinate reductase (EC 1.3.1.26)

Query= CharProtDB::CH_002128
         (273 letters)



>lcl|FitnessBrowser__Korea:Ga0059261_2545 Ga0059261_2545
           dihydrodipicolinate reductase (EC 1.3.1.26)
          Length = 242

 Score =  177 bits (450), Expect = 1e-49
 Identities = 109/263 (41%), Positives = 144/263 (54%), Gaps = 24/263 (9%)

Query: 8   VAIAGAGGRMGRQLIQAALALEGVQLGAALEREGSSLLGSDAGELAGAGKTGVTVQSSLD 67
           + I G+ GRMG   I+  LA +GV+        G +  G D   LA A            
Sbjct: 4   IGIYGSLGRMG-VAIRDILAEQGVKFA------GGADAGDDPAVLAAAA----------- 45

Query: 68  AVKDDFDVFIDFTRPEGTLNHLAFCRQHGKGMVIGTTGFDEAGKQAIRDAAADIAIVFAA 127
                 D  +DF+ P    +HLA  R  G  +VIGTTG        I DAA +IA++   
Sbjct: 46  ------DALVDFSTPAALESHLAAARAAGTPIVIGTTGLTAQHHALIDDAAREIAVLQTG 99

Query: 128 NFSVGVNVMLKLLEKAAKVMGDYTDIEIIEAHHRHKVDAPSGTALAMGEAIAHALDKDLK 187
           N S+GV ++ +L+ +AA  +G   DIEI E HHR KVDAPSGTAL +GEA A      L 
Sbjct: 100 NTSLGVVLLARLVREAATRLGPDWDIEIAEMHHRQKVDAPSGTALMLGEAAAAGRAVSLG 159

Query: 188 DCAVYSREGHTGERVPGTIGFATVRAGDIVGEHTAMFADIGERLEITHKASSRMTFANGA 247
           +  V  R G TG R  GTIGFA++R G ++G+H  + A  GER+E+ H+A  R  FA GA
Sbjct: 160 EVRVADRAGLTGARAEGTIGFASLRGGTVIGDHLVVLAGAGERIELAHRAEDRAIFARGA 219

Query: 248 VRSALWLSGKESGLFDMRDVLDL 270
           VR+ALWL+ K +G + M  VL L
Sbjct: 220 VRAALWLADKPAGRYTMDAVLGL 242


Lambda     K      H
   0.319    0.135    0.383 

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: 217
Number of extensions: 8
Number of successful extensions: 1
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: 273
Length of database: 242
Length adjustment: 24
Effective length of query: 249
Effective length of database: 218
Effective search space:    54282
Effective search space used:    54282
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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.7222.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 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 1.83
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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 paper from 2022 on GapMind for carbon sources, or view the source code, or see 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