GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapB in Caulobacter crescentus NA1000

Align 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8) (characterized)
to candidate CCNA_03664 CCNA_03664 dihydrodipicolinate reductase

Query= BRENDA::Q2YJN7
         (268 letters)



>FitnessBrowser__Caulo:CCNA_03664
          Length = 257

 Score =  232 bits (591), Expect = 7e-66
 Identities = 135/264 (51%), Positives = 167/264 (63%), Gaps = 17/264 (6%)

Query: 3   LVVVGAGGRMGQTLIRTIQSIEGAKLVGAIERSGSPFLGKDAGEVTGIGTLGVAITDDPL 62
           + + GA GRMG+ + + ++    A +    ER G      DAGE       G+   +  L
Sbjct: 7   IAIAGANGRMGRAVAQALEGRSDAVVAARFERPG------DAGE-------GLVARETAL 53

Query: 63  PVFAKAHGVLDFTSPAASVEFAG-LAAQARIVHVIGTTGCSAEDDEKIRAAARHATIVKS 121
              A A  V+DFT P ASV  A   AA      VIG+TG S E  ++I AAA    IV+S
Sbjct: 54  ---AAAEAVIDFTLPEASVALAEEAAANGGPALVIGSTGFSDEQLDRIDAAATKIVIVRS 110

Query: 122 GNMSLGVNLLSVLVQKAAEALGPEDFDIEILEMHHRHKVDAPSGTALLLGEAAARGRDIA 181
           GN SLGVN+L  LV++AA AL  +D+DIE+ E HH+ K+DAPSGTAL+LGEAAA GR I 
Sbjct: 111 GNYSLGVNMLMGLVRQAAAALPAQDWDIEVFEAHHKRKIDAPSGTALMLGEAAAEGRGIN 170

Query: 182 LADNSVRVRDGYTGPRETGAIGFATLRGGSVIGDHSVILAGTGERVVLSHHAEDRSIFAR 241
           LA  S R RDG TGPR+ G IGF+ +RGG +IG+HSVI AG  E + LSH A DR +FAR
Sbjct: 171 LAKVSDRGRDGVTGPRKDGDIGFSVVRGGGIIGEHSVIFAGESESLTLSHSAIDRGLFAR 230

Query: 242 GAIKAALWAHGKKPGLYSMLDVLG 265
           GAI AA+W  GK PGLY M DVLG
Sbjct: 231 GAIAAAVWVKGKPPGLYDMQDVLG 254


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: 230
Number of extensions: 13
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: 268
Length of database: 257
Length adjustment: 25
Effective length of query: 243
Effective length of database: 232
Effective search space:    56376
Effective search space used:    56376
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 CCNA_03664 CCNA_03664 (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.2471127.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    7.8e-70  221.4   0.7      3e-68  216.3   0.7    2.0  1  lcl|FitnessBrowser__Caulo:CCNA_03664  CCNA_03664 dihydrodipicolinate r


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_03664  CCNA_03664 dihydrodipicolinate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  216.3   0.7     3e-68     3e-68       2     270 .]       5     254 ..       4     254 .. 0.92

  Alignments for each domain:
  == domain 1  score: 216.3 bits;  conditional E-value: 3e-68
                             TIGR00036   2 ikvavaGaaGrmGrevikavkeaedlelvaalerkgsskqgkDiGelagigkvgvpveddleavkvlaekkad 74 
                                           +k+a+aGa GrmGr v +a++   d  ++a +er        D+Ge      v    e++l         +a+
  lcl|FitnessBrowser__Caulo:CCNA_03664   5 VKIAIAGANGRMGRAVAQALEGRSDAVVAARFER------PGDAGEGL----VAR--ETAL--------AAAE 57 
                                           69***********************999999996......34767622....222..2222........3568 PP

                             TIGR00036  75 vliDfttpeavlenvkialek.gvrlVvGTTGfseedlkelkdlaekkgvalviapNfaiGvnlllkllekaa 146
                                            +iDft+pea +  ++ a+++ g  lV+G TGfs+e+l ++ ++a k  + +v + N+++Gvn+l+ l+++aa
  lcl|FitnessBrowser__Caulo:CCNA_03664  58 AVIDFTLPEASVALAEEAAANgGPALVIGSTGFSDEQLDRIDAAATK--IVIVRSGNYSLGVNMLMGLVRQAA 128
                                           99***********998777662679**********************..***********************9 PP

                             TIGR00036 147 kvl..edvDiEiiElHHrhKkDaPSGTAlklaeiiakargkdlkeaaveeregltGerkkeeiGiaavRggdv 217
                                             l  +d+DiE+ E+HH+ K DaPSGTAl l+e+ a+ rg +l ++   +r+g+tG rk+ +iG++ vRgg++
  lcl|FitnessBrowser__Caulo:CCNA_03664 129 AALpaQDWDIEVFEAHHKRKIDAPSGTALMLGEAAAEGRGINLAKVSDRGRDGVTGPRKDGDIGFSVVRGGGI 201
                                           99866899********************************99******************************* PP

                             TIGR00036 218 vgehtvlFasdGerleitHkassRaafakGvvrairwledkeekvydledvld 270
                                           +geh+v+Fa++ e l+++H a +R  fa+G++ a+ w++ k  ++yd++dvl+
  lcl|FitnessBrowser__Caulo:CCNA_03664 202 IGEHSVIFAGESESLTLSHSAIDRGLFARGAIAAAVWVKGKPPGLYDMQDVLG 254
                                           ***************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (257 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: 9.53
//
[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