Aligments for a candidate for dapB in Synechococcus elongatus PCC 7942

GapMind for Amino acid biosynthesis

Aligments for a candidate for dapB in Synechococcus elongatus PCC 7942

Align 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8) (characterized)
to candidate Synpcc7942_2136 Synpcc7942_2136 dihydrodipicolinate reductase

Query= BRENDA::P9WP23
         (245 letters)



>FitnessBrowser__SynE:Synpcc7942_2136
          Length = 273

 Score =  207 bits (527), Expect = 2e-58
 Identities = 117/268 (43%), Positives = 164/268 (61%), Gaps = 29/268 (10%)

Query: 3   VGVLGAKGKVGATMVRAVAAADDLTL------SAELDAGD--------PLSLLTDGNTE- 47
           V V GA GK+G   ++A+AAADD+TL      SA++   D        PL +    + E 
Sbjct: 7   VVVNGATGKMGRETIKAIAAADDVTLVGAIARSADVQGQDIGEIVGLGPLEVPVTNDLEG 66

Query: 48  ------------VVIDFTHPDVVMGNLEFLIDNGIHAVVGTTGFTAERFQQVESWLVAKP 95
                       VV+DFTHPD +  N+   I  G+  VVGTTG   E+ Q++  +   K 
Sbjct: 67  MLCLASQEREVPVVVDFTHPDCIYDNVRKAIAYGVRPVVGTTGLNNEQLQELAEF-AEKA 125

Query: 96  NTSVLIAPNFAIGAVLSMHFAKQAARFFDSAEVIELHHPHKADAPSGTAARTAKLIAEAR 155
           +   L+ PNF+IG VL M  A QA+RF+D  E++ELHH  KADAPSGTA +TA+++AE  
Sbjct: 126 SVGCLVIPNFSIGMVLLMQAAIQASRFYDHVEILELHHDQKADAPSGTAIKTAQMLAELG 185

Query: 156 KGLPPNPDATSTSLPGARGA-DVDGIPVHAVRLAGLVAHQEVLFGTEGETLTIRHDSLDR 214
           K   P       ++PGARGA   + I +H+VRL GL+AH+EV+FG  GE LT+RHD++DR
Sbjct: 186 KTFNPPKVTEKETMPGARGAVGPENIRIHSVRLPGLIAHEEVIFGAPGEILTLRHDTMDR 245

Query: 215 TSFVPGVLLAVRRIAERPGLTVGLEPLL 242
           + ++PGVLLAVR++ +  GL  GL+ +L
Sbjct: 246 SCYMPGVLLAVRKVRQLTGLIYGLDRIL 273


Lambda     K      H
   0.319    0.135    0.389 

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: 200
Number of extensions: 12
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: 245
Length of database: 273
Length adjustment: 24
Effective length of query: 221
Effective length of database: 249
Effective search space:    55029
Effective search space used:    55029
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 (21.7 bits)
S2: 47 (22.7 bits)

Align candidate Synpcc7942_2136 Synpcc7942_2136 (dihydrodipicolinate 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.23875.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    1.6e-93  299.1   0.0    1.8e-93  299.0   0.0    1.0  1  lcl|FitnessBrowser__SynE:Synpcc7942_2136  Synpcc7942_2136 dihydrodipicolin


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SynE:Synpcc7942_2136  Synpcc7942_2136 dihydrodipicolinate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  299.0   0.0   1.8e-93   1.8e-93       2     269 ..       5     273 .]       4     273 .] 0.96

  Alignments for each domain:
  == domain 1  score: 299.0 bits;  conditional E-value: 1.8e-93
                                 TIGR00036   2 ikvavaGaaGrmGrevikavkeaedlelvaalerkgsskqgkDiGelagigkvgvpveddleavkvla. 69 
                                               i+v+v+Ga+G+mGre ika+++a+d+ lv+a+  ++ + qg+DiGe++g+g+++vpv++dle +  la 
  lcl|FitnessBrowser__SynE:Synpcc7942_2136   5 IPVVVNGATGKMGRETIKAIAAADDVTLVGAIA-RSADVQGQDIGEIVGLGPLEVPVTNDLEGMLCLAs 72 
                                               79*******************************.599**************************999988 PP

                                 TIGR00036  70 .ekkadvliDfttpeavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgvalviapNfaiGvnl 137
                                                e+++ v++Dft+p+  ++nv+ a+++gvr+VvGTTG+++e+l+el+++aek++v++++ pNf+iG++l
  lcl|FitnessBrowser__SynE:Synpcc7942_2136  73 qEREVPVVVDFTHPDCIYDNVRKAIAYGVRPVVGTTGLNNEQLQELAEFAEKASVGCLVIPNFSIGMVL 141
                                               8889999************************************************************** PP

                                 TIGR00036 138 llkllekaakvledvDiEiiElHHrhKkDaPSGTAlklaeiiakargkdlkeaaveeregltGerkk.. 204
                                               l++++ +a++  ++v  Ei+ElHH++K+DaPSGTA+k+a+++a+  + +++   v+e+e+++G+r++  
  lcl|FitnessBrowser__SynE:Synpcc7942_2136 142 LMQAAIQASRFYDHV--EILELHHDQKADAPSGTAIKTAQMLAELGK-TFNPPKVTEKETMPGARGAvg 207
                                               *******99988888..***************************999.9****************7522 PP

                                 TIGR00036 205 .eeiGiaavRggdvvgehtvlFasdGerleitHkassRaafakGvvrairwledkeekvydledvl 269
                                                e+i i++vR+++++++++v+F+  Ge l+++H++++R++++ Gv++a+r++ ++  ++y+l+ +l
  lcl|FitnessBrowser__SynE:Synpcc7942_2136 208 pENIRIHSVRLPGLIAHEEVIFGAPGEILTLRHDTMDRSCYMPGVLLAVRKVRQLTGLIYGLDRIL 273
                                               26777*********************************************************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (273 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 6.26
//
[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