GapMind for Amino acid biosynthesis

 

Aligments for a candidate for hisD in Echinicola vietnamensis KMM 6221, DSM 17526

Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate Echvi_2459 Echvi_2459 histidinol dehydrogenase

Query= BRENDA::P06988
         (434 letters)



>lcl|FitnessBrowser__Cola:Echvi_2459 Echvi_2459 histidinol
           dehydrogenase
          Length = 429

 Score =  398 bits (1022), Expect = e-115
 Identities = 211/428 (49%), Positives = 292/428 (68%), Gaps = 8/428 (1%)

Query: 10  NSCTAEQQRQLLMRPAISASESITRTVNDILDNVKARGDEALREYSAKFDKTTVTALKVS 69
           N   +E Q++L  RP +   + I + V  I+  V  +GD+AL++++ ++D   +  L VS
Sbjct: 6   NPTQSEWQKELA-RP-VQKMKDIQKIVKPIMRKVSRQGDKALKKFALEYDHVEIDNLLVS 63

Query: 70  AEEIAAASERLSDELKQAMAVAVKNIETFHTAQKLPPVDVETQPGVRCQQVTRPVASVGL 129
            +EI  A E++ + LK A+  A  NIE FH AQ+   + +E   GV C + + P+  VGL
Sbjct: 64  RDEINEAYEQVDESLKSAIQQAKVNIEKFHKAQQTEDLSMEVMEGVTCMRRSVPIQKVGL 123

Query: 130 YIPGGSAPLFSTVLMLATPASIAGCKKVVLCSPP----PIADEILYAAQLCGVQDVFNVG 185
           YIPGG+APLFSTVLML  PA+IAGC+++VLC+PP     I   ILY A L G+  +   G
Sbjct: 124 YIPGGTAPLFSTVLMLGIPANIAGCEEIVLCTPPNKEGKIHPAILYTANLIGIDKIVKAG 183

Query: 186 GAQAIAALAFGTESVPKVDKIFGPGNAFVTEAKRQVSQRLDGAAIDMPAGPSEVLVIADS 245
           GAQAIAAL +GTESVP+V KIFGPGN +VT AK+  +++  G AIDMPAGPSEVLV AD 
Sbjct: 184 GAQAIAALTYGTESVPQVAKIFGPGNQYVTAAKQLATKK--GIAIDMPAGPSEVLVYADE 241

Query: 246 GATPDFVASDLLSQAEHGPDSQVILLTPAADMARRVAEAVERQLAELPRAETARQALNAS 305
            A P FVA+DLLSQAEHG DSQVIL+  A+ +A++  + V++QLA+LPR + A++AL  S
Sbjct: 242 SAVPAFVAADLLSQAEHGIDSQVILVATASKVAKKTLKEVDKQLAKLPRKDIAKKALENS 301

Query: 306 RLIVTKDLAQCVEISNQYGPEHLIIQTRNARELVDSITSAGSVFLGDWSPESAGDYASGT 365
             +V  +  + + + N Y PEHLII   N  E+V +I +AGSVF+G+++PESAGDYASGT
Sbjct: 302 IAVVMGNQEKAIALINDYAPEHLIINVANEDEVVANIVNAGSVFIGNFTPESAGDYASGT 361

Query: 366 NHVLPTYGYTATCSSLGLADFQKRMTVQELSKEGFSALASTIETLAAAERLTAHKNAVTL 425
           NH LPTYG+    S + L  F K++T Q+++++G   L  TIE +A  E L AHKNAV++
Sbjct: 362 NHTLPTYGFARNYSGVSLDSFVKKITYQKITEKGLQNLGPTIEVMAGNELLDAHKNAVSI 421

Query: 426 RVNALKEQ 433
           R+  LKE+
Sbjct: 422 RLKYLKEK 429


Lambda     K      H
   0.315    0.128    0.356 

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: 434
Number of extensions: 11
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: 434
Length of database: 429
Length adjustment: 32
Effective length of query: 402
Effective length of database: 397
Effective search space:   159594
Effective search space used:   159594
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: 51 (24.3 bits)

Align candidate Echvi_2459 Echvi_2459 (histidinol dehydrogenase)
to HMM TIGR00069 (hisD: histidinol dehydrogenase (EC 1.1.1.23))

# 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/TIGR00069.hmm
# target sequence database:        /tmp/gapView.9366.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00069  [M=393]
Accession:   TIGR00069
Description: hisD: histidinol dehydrogenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   3.1e-162  526.2   7.3   3.6e-162  526.0   7.3    1.0  1  lcl|FitnessBrowser__Cola:Echvi_2459  Echvi_2459 histidinol dehydrogen


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_2459  Echvi_2459 histidinol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  526.0   7.3  3.6e-162  3.6e-162       1     393 []      30     422 ..      30     422 .. 0.99

  Alignments for each domain:
  == domain 1  score: 526.0 bits;  conditional E-value: 3.6e-162
                            TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkvkleslrvseeeleealeavdeelkealelaaeniekfhekqlpesvev 74 
                                          vk+i+++v ++Gd+Al++++ ++d+v++++l vs++e++ea+e+vde+lk+a+++a+ niekfh++q++e++++
  lcl|FitnessBrowser__Cola:Echvi_2459  30 VKPIMRKVSRQGDKALKKFALEYDHVEIDNLLVSRDEINEAYEQVDESLKSAIQQAKVNIEKFHKAQQTEDLSM 103
                                          899*********************************************************************** PP

                            TIGR00069  75 eteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpavlaaakllgvd 148
                                          e +egv++ ++ +p+++vglY+PgG+a+++Stvlm+++pA++Ag++eiv++tPp+k+gk++pa+l++a+l+g+d
  lcl|FitnessBrowser__Cola:Echvi_2459 104 EVMEGVTCMRRSVPIQKVGLYIPGGTAPLFSTVLMLGIPANIAGCEEIVLCTPPNKEGKIHPAILYTANLIGID 177
                                          ************************************************************************** PP

                            TIGR00069 149 evykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvf.gevgidmiaGPsEvlviadesanpelvaaD 221
                                          +++k+GGaqaiaal+yGte+vp+v ki+GPGn+yVtaAK+l + + ++idm+aGPsEvlv+adesa p++vaaD
  lcl|FitnessBrowser__Cola:Echvi_2459 178 KIVKAGGAQAIAALTYGTESVPQVAKIFGPGNQYVTAAKQLATkKGIAIDMPAGPSEVLVYADESAVPAFVAAD 251
                                          *****************************************99569**************************** PP

                            TIGR00069 222 llsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekngaiilvddleealelsneyApEHL 295
                                          llsqaEH+ d+q+ilv+t +++a+k+ +ev++ql++l+rk+ia+k+le n+  +++ + e+a++l+n+yApEHL
  lcl|FitnessBrowser__Cola:Echvi_2459 252 LLSQAEHGIDSQVILVATASKVAKKTLKEVDKQLAKLPRKDIAKKALE-NSIAVVMGNQEKAIALINDYAPEHL 324
                                          ************************************************.7888889****************** PP

                            TIGR00069 296 elqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArfasglsvedFlkrisvqelskealee 369
                                          +++++++ e++ +i naGsvf+G+ tpe++gdy++G+nh+LPT+g+Ar +sg+s+++F+k+i++q++++++l++
  lcl|FitnessBrowser__Cola:Echvi_2459 325 IINVANEDEVVANIVNAGSVFIGNFTPESAGDYASGTNHTLPTYGFARNYSGVSLDSFVKKITYQKITEKGLQN 398
                                          ************************************************************************** PP

                            TIGR00069 370 laeaveklaeaEgLeaHaeavevR 393
                                          l++++e +a  E L+aH++av++R
  lcl|FitnessBrowser__Cola:Echvi_2459 399 LGPTIEVMAGNELLDAHKNAVSIR 422
                                          **********************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (429 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: 10.08
//
[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:

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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