GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapB in Synechococcus elongatus PCC 7942

Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate Synpcc7942_2136 Synpcc7942_2136 dihydrodipicolinate reductase

Query= BRENDA::Q3MFY8
         (278 letters)



>FitnessBrowser__SynE:Synpcc7942_2136
          Length = 273

 Score =  387 bits (995), Expect = e-112
 Identities = 193/273 (70%), Positives = 229/273 (83%), Gaps = 3/273 (1%)

Query: 6   PIPVIVNGAAGKMGREVVKAIAQAPDLNLLGAIDSSPEHQGKDAGELAGLSEPLEVPITN 65
           PIPV+VNGA GKMGRE +KAIA A D+ L+GAI  S + QG+D GE+ GL  PLEVP+TN
Sbjct: 4   PIPVVVNGATGKMGRETIKAIAAADDVTLVGAIARSADVQGQDIGEIVGLG-PLEVPVTN 62

Query: 66  QLEPMLGYVAGERQGPPGVIVDFTHPDSVYDNVRSAIAYGIRPVVGTTGLSPAQIQNLAD 125
            LE ML   + ER+ P  V+VDFTHPD +YDNVR AIAYG+RPVVGTTGL+  Q+Q LA+
Sbjct: 63  DLEGMLCLASQEREVP--VVVDFTHPDCIYDNVRKAIAYGVRPVVGTTGLNNEQLQELAE 120

Query: 126 FAEKASTGCLIIPNFSIGMVLLQQAAVTASQYFDHVEIIELHHNQKADAPSGTAIQTAEL 185
           FAEKAS GCL+IPNFSIGMVLL QAA+ AS+++DHVEI+ELHH+QKADAPSGTAI+TA++
Sbjct: 121 FAEKASVGCLVIPNFSIGMVLLMQAAIQASRFYDHVEILELHHDQKADAPSGTAIKTAQM 180

Query: 186 LAELGKTFNSAIVEETEKIPGARGSLAGEGIRIHSVRLPGLIAHQEVIFGAPGQIYTLRH 245
           LAELGKTFN   V E E +PGARG++  E IRIHSVRLPGLIAH+EVIFGAPG+I TLRH
Sbjct: 181 LAELGKTFNPPKVTEKETMPGARGAVGPENIRIHSVRLPGLIAHEEVIFGAPGEILTLRH 240

Query: 246 DTSDRACYMPGVLLAIRKVLQLKSLVYGLEKIL 278
           DT DR+CYMPGVLLA+RKV QL  L+YGL++IL
Sbjct: 241 DTMDRSCYMPGVLLAVRKVRQLTGLIYGLDRIL 273


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: 314
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: 273
Length adjustment: 25
Effective length of query: 253
Effective length of database: 248
Effective search space:    62744
Effective search space used:    62744
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 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.14862.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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 9.74
//
[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:

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:

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:

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:

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