Alignments for a candidate for hisD in Desulfovibrio vulgaris Miyazaki F

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisD in Desulfovibrio vulgaris Miyazaki F

Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate 8502101 DvMF_2814 histidinol dehydrogenase (RefSeq)

Query= BRENDA::Q8G2R2
         (430 letters)



>FitnessBrowser__Miya:8502101
          Length = 434

 Score =  336 bits (862), Expect = 7e-97
 Identities = 190/428 (44%), Positives = 257/428 (60%), Gaps = 4/428 (0%)

Query: 4   TLRQTDPDFEQKFAAFLSGKREVSEDVDRAVREIVDRVRREGDSALLDYSRRFDRIDLEK 63
           TL     D  ++  A L+G+    + V+ AVREI+D VR  GD+AL DY+ RFD    + 
Sbjct: 5   TLFLRSVDDWKELQALLAGRDNPGDTVEPAVREILDTVRAGGDAALADYTSRFDCPGFDA 64

Query: 64  TGIAVTEAEIDAAFDAAPASTVEALKLARDRIEKHHARQLPKDDRYTDALGVELGSRWTA 123
             I V E EI AA +         +  A   I   H  Q  +    T   G  LG   T 
Sbjct: 65  ARIRVGEDEIAAALEEVGPDDRAIIAEAAANIRAFHEAQKEQSWFTTRPDGSVLGQMVTP 124

Query: 124 IEAVGLYVPGGTASYP---SSVLMNAMPAKVAGVDRIVMVVPA-PDGNLNPLVLVAARLA 179
           ++  GLYVPGG        SS+LMNA+PA+VAGV  I ++ P   DG LNP +L AA   
Sbjct: 125 VDRAGLYVPGGQGGNTPLISSLLMNAIPAQVAGVPEIAVISPPRKDGTLNPFILAAAHHL 184

Query: 180 GVSEIYRVGGAQAIAALAYGTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGPSEV 239
           G++E++R G A AIAALA+GTET+RPV  I GPGN +V  AKR++ G VGIDMIAGPSE+
Sbjct: 185 GITEVHRAGSAWAIAALAFGTETVRPVDVIAGPGNIWVTTAKRLLIGRVGIDMIAGPSEI 244

Query: 240 LIVADKDNNPDWIAADLLAQAEHDTAAQSILMTNDEAFAHAVEEAVERQLHTLARTETAS 299
           LI+AD     DW+AAD+L+QAEHD  A SI +T+  A   A++  +  Q  TL R + A 
Sbjct: 245 LILADHTARADWVAADMLSQAEHDPLASSICITDSPALVDALKLELAAQCDTLPRADIAR 304

Query: 300 ASWRDFGAVILVKDFEDAIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTPEVI 359
            +  D+GA+++V D    I + N++A EHLE+   D  A +  IR+AG++F+GG++PE +
Sbjct: 305 KALADWGAIVVVPDMATGIGITNKVAPEHLEVLTKDPWALLGTIRHAGAVFLGGWSPEPV 364

Query: 360 GDYVGGCNHVLPTARSARFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEGLDA 419
           GDY  G NHVLPT  +ARFSS LSV  + KRTS++   +   R    +   +AR EGL+A
Sbjct: 365 GDYYAGPNHVLPTMGTARFSSALSVQTFCKRTSVISATAAFTRGHAASIARLARLEGLEA 424

Query: 420 HAQSVAIR 427
           HA+S   R
Sbjct: 425 HARSAESR 432


Lambda     K      H
   0.318    0.134    0.375 

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: 489
Number of extensions: 27
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: 430
Length of database: 434
Length adjustment: 32
Effective length of query: 398
Effective length of database: 402
Effective search space:   159996
Effective search space used:   159996
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: 51 (24.3 bits)

Align candidate 8502101 DvMF_2814 (histidinol dehydrogenase (RefSeq))
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.19757.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   9.6e-158  511.4   0.0   1.1e-157  511.2   0.0    1.0  1  lcl|FitnessBrowser__Miya:8502101  DvMF_2814 histidinol dehydrogena


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8502101  DvMF_2814 histidinol dehydrogenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  511.2   0.0  1.1e-157  1.1e-157       1     393 []      35     432 ..      35     432 .. 0.99

  Alignments for each domain:
  == domain 1  score: 511.2 bits;  conditional E-value: 1.1e-157
                         TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkv..kleslrvseeeleealeavdeelkealelaaeniekfhekqlpesveve 75 
                                       v+ei++ vr+ Gd+Al +yt++fd    +++++rv e+e+++ale+v ++ ++ +++aa+ni++fhe+q+++s++++
  lcl|FitnessBrowser__Miya:8502101  35 VREILDTVRAGGDAALADYTSRFDCPgfDAARIRVGEDEIAAALEEVGPDDRAIIAEAAANIRAFHEAQKEQSWFTT 111
                                       89**********************8766999********************************************** PP

                         TIGR00069  76 teegvllgqkvrplervglYvPgGk...aaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpavlaaakllgvde 149
                                       + +g++lgq+v+p++r+glYvPgG+   ++++S++lm+a+pA+vAgv+ei+v++Pp+kdg++np +laaa+ lg++e
  lcl|FitnessBrowser__Miya:8502101 112 RPDGSVLGQMVTPVDRAGLYVPGGQggnTPLISSLLMNAIPAQVAGVPEIAVISPPRKDGTLNPFILAAAHHLGITE 188
                                       **********************9765559************************************************ PP

                         TIGR00069 150 vykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEvlviadesanpelvaaDllsqa 226
                                       v ++G a aiaala+Gtetv++vd+i+GPGni+Vt+AK+l+ g+vgidmiaGPsE+l++ad++a +++vaaD+lsqa
  lcl|FitnessBrowser__Miya:8502101 189 VHRAGSAWAIAALAFGTETVRPVDVIAGPGNIWVTTAKRLLIGRVGIDMIAGPSEILILADHTARADWVAADMLSQA 265
                                       ***************************************************************************** PP

                         TIGR00069 227 EHdedaqailvttseelaekveeeveeqleelerkeiaekslekngaiilvddleealelsneyApEHLelqtkdpe 303
                                       EHd+ a++i++t+s +l+++++ e+++q+++l+r++ia+k+l++ gai++v d++  + ++n++ApEHLe+ tkdp+
  lcl|FitnessBrowser__Miya:8502101 266 EHDPLASSICITDSPALVDALKLELAAQCDTLPRADIARKALADWGAIVVVPDMATGIGITNKVAPEHLEVLTKDPW 342
                                       ***************************************************************************** PP

                         TIGR00069 304 ellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArfasglsvedFlkrisvqelskealeelaeaveklaea 380
                                       +ll +i++aG+vflG ++pe++gdy aGpnhvLPT+gtArf+s+lsv++F+kr+sv++++ + ++  a ++++la++
  lcl|FitnessBrowser__Miya:8502101 343 ALLGTIRHAGAVFLGGWSPEPVGDYYAGPNHVLPTMGTARFSSALSVQTFCKRTSVISATAAFTRGHAASIARLARL 419
                                       ***************************************************************************** PP

                         TIGR00069 381 EgLeaHaeavevR 393
                                       EgLeaHa+++e R
  lcl|FitnessBrowser__Miya:8502101 420 EGLEAHARSAESR 432
                                       *********9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (434 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: 9.08
//
[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:

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
the source code
instructions for running GapMind on your computer
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