GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisD in Flavobacterium glycines Gm-149

Align Histidinol dehydrogenase; HDH; EC 1.1.1.23 (uncharacterized)
to candidate WP_066329740.1 BLR17_RS09345 histidinol dehydrogenase

Query= curated2:Q9RH05
         (430 letters)



>NCBI__GCF_900100165.1:WP_066329740.1
          Length = 431

 Score =  299 bits (766), Expect = 1e-85
 Identities = 168/412 (40%), Positives = 254/412 (61%), Gaps = 5/412 (1%)

Query: 22  ERRESEGDVSRDVSAIIADVKKRGDVAIAELTQKFDRHDLNKGGWQLTQEEIKKACDSLP 81
           E   ++  V   V  +I  VK  GD A+ EL++KFD+   +   ++L+   I++  +S+P
Sbjct: 13  EAETNDKKVREIVENLIEQVKTEGDKALFELSEKFDKW--SPESFRLSANAIEEIINSVP 70

Query: 82  SELMDALKLAATRIRYC--HENQLPESSEMTDAAGVRMGVRWQAVEAAGLYVPGGRAAYC 139
           +++++ +K A  ++R    H+       E+    GV +G +   V + G Y+PGGR    
Sbjct: 71  AQVIEDIKFAQAQVRNFAQHQKDSMRDIEVETLPGVFLGHKNVPVNSVGCYIPGGRYPMV 130

Query: 140 SSVLMNAVPAKVAGVKRLVMVTPTPDGFVNPAVIAAAVISEVDEIWKIGGAQAVAALALG 199
           +S  M+ + AKVAGVKR+V  TP  +G +  A IAA  ++  DEI+ +GG QA+AA+ALG
Sbjct: 131 ASAHMSVLTAKVAGVKRVVACTPPINGKIPAATIAAMAMAGADEIYILGGVQAIAAMALG 190

Query: 200 TEKIKPVDVVVGPGNAWVAEAKRQLYGQVGIDMVAGPSEIVVVADKDNDPEWLAADLLSQ 259
           TE I+ VD++VGPGN++VAEAKRQL+G++GID++AGP+E +V+AD+ +D E  A DLL Q
Sbjct: 191 TESIESVDMIVGPGNSYVAEAKRQLFGKIGIDLLAGPTETLVIADETSDAEICAVDLLGQ 250

Query: 260 AEHDPTSQSILISDSEDLIEKTIEAVGRRLEKLETQKVARESWDKHGATILVQSLDEAPA 319
           AEH PTS SIL+++SE L  +TI  + R+L+ L T  VA  +W  +G  ILV ++DE  A
Sbjct: 251 AEHGPTSPSILLTNSEKLAYETIAEIERQLKVLPTADVASIAWKDYGQIILVDTIDEMVA 310

Query: 320 LVDRLAPEHLELAVADPDALFANVHHSGSVFLGRYTPEAIGDYVGGPNHVLPTGRRARFS 379
             DR+A EH+++  ADP     N+ + G++FLG+YT  A GD V G NH LPT   A+++
Sbjct: 311 EADRIASEHVQVMTADPRYFLKNMTNYGALFLGKYTNVAYGDKVIGTNHTLPTKHGAKYT 370

Query: 380 SGLSVIDFMKRTTYLNC-SQEALSKIGPAAVTLAKAEGLPAHAESVISRLNK 430
            GL V  F+K  +Y    + EA + IG     L + E    H E    R+ +
Sbjct: 371 GGLWVGKFLKTCSYQEIRTPEASAMIGEYCSRLCEIENFYGHKEQADIRVRR 422


Lambda     K      H
   0.316    0.132    0.377 

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: 419
Number of extensions: 11
Number of successful extensions: 2
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: 430
Length of database: 431
Length adjustment: 32
Effective length of query: 398
Effective length of database: 399
Effective search space:   158802
Effective search space used:   158802
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 WP_066329740.1 BLR17_RS09345 (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.215927.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.3e-145  470.1   0.9     4e-145  469.9   0.9    1.0  1  NCBI__GCF_900100165.1:WP_066329740.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900100165.1:WP_066329740.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  469.9   0.9    4e-145    4e-145       1     393 []      25     419 ..      25     419 .. 0.98

  Alignments for each domain:
  == domain 1  score: 469.9 bits;  conditional E-value: 4e-145
                             TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkvkleslrvseeeleealeavdeelkealelaaeniekfhekqlpes.. 71 
                                           v+++ie+v++eGd+Al+e++ekfdk+++es+r+s++ +ee  ++v+++++e+++ a++++++f+++q+++   
  NCBI__GCF_900100165.1:WP_066329740.1  25 VENLIEQVKTEGDKALFELSEKFDKWSPESFRLSANAIEEIINSVPAQVIEDIKFAQAQVRNFAQHQKDSMrd 97 
                                           789************************************************************9999976545 PP

                             TIGR00069  72 veveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpavlaaakl 144
                                           +evet +gv+lg+k +p+++vg+Y+PgG++++++++ m +++AkvAgvk++v++tPp  +gk+ +a++aa+++
  NCBI__GCF_900100165.1:WP_066329740.1  98 IEVETLPGVFLGHKNVPVNSVGCYIPGGRYPMVASAHMSVLTAKVAGVKRVVACTPPI-NGKIPAATIAAMAM 169
                                           9********************************************************6.9************* PP

                             TIGR00069 145 lgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEvlviadesanpel 217
                                           +g+de+y +GG+qaiaa+a Gte++++vd+ivGPGn+yV++AK+++fg++gid++aGP+E lviade++++e+
  NCBI__GCF_900100165.1:WP_066329740.1 170 AGADEIYILGGVQAIAAMALGTESIESVDMIVGPGNSYVAEAKRQLFGKIGIDLLAGPTETLVIADETSDAEI 242
                                           ************************************************************************* PP

                             TIGR00069 218 vaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekngaiilvddleealelsney 290
                                           +a+Dll qaEH++++ +il+t+se+la ++ +e+e+ql+ l+++++a+ +++++g+iilvd+++e+++ ++++
  NCBI__GCF_900100165.1:WP_066329740.1 243 CAVDLLGQAEHGPTSPSILLTNSEKLAYETIAEIERQLKVLPTADVASIAWKDYGQIILVDTIDEMVAEADRI 315
                                           ************************************************************************* PP

                             TIGR00069 291 ApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArfasglsvedFlkrisvqel. 362
                                           A EH++++t+dp+ +lk+++n+G++flG+yt +a+gd+v G+nh+LPT+  A++++gl+v +Flk++s+qe+ 
  NCBI__GCF_900100165.1:WP_066329740.1 316 ASEHVQVMTADPRYFLKNMTNYGALFLGKYTNVAYGDKVIGTNHTLPTKHGAKYTGGLWVGKFLKTCSYQEIr 388
                                           ***********************************************************************93 PP

                             TIGR00069 363 skealeelaeaveklaeaEgLeaHaeavevR 393
                                           + ea + ++e +++l+e+E++  H+e +++R
  NCBI__GCF_900100165.1:WP_066329740.1 389 TPEASAMIGEYCSRLCEIENFYGHKEQADIR 419
                                           46788899******************99988 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (431 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: 15.03
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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