Alignments for a candidate for hisD in Dinoroseobacter shibae DFL-12

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisD in Dinoroseobacter shibae DFL-12

Align Histidinol dehydrogenase 1; HDH 1; EC 1.1.1.23 (uncharacterized)
to candidate 3608850 Dshi_2242 Histidinol dehydrogenase (RefSeq)

Query= curated2:Q8YSM8
         (431 letters)



>FitnessBrowser__Dino:3608850
          Length = 441

 Score =  279 bits (714), Expect = 1e-79
 Identities = 158/410 (38%), Positives = 233/410 (56%), Gaps = 3/410 (0%)

Query: 20  SDRREATVDVSGTVRDILAHVKARGDAAVQEYTSRFDHYRPHSHHLSAAFIAEQAAKCSD 79
           ++R E       TV  IL  +  RGDAAV++ + +FD Y P +  LS + I     K + 
Sbjct: 12  TERAEDDARTQATVTGILQDISTRGDAAVRDLSEKFDGYTPQAFRLSPSEIEAAMQKVTT 71

Query: 80  EVKAALELAAERISSFHQKQLPQ--DIGYTDTAGVKLGLNWVALSQVGIYVPGGRASYPS 137
                +  A ++I +F Q Q     D+      GV LG   + ++ VG YVPGG+    +
Sbjct: 72  REMGDIRFAQDQIRNFAQVQRASMTDVEVETIPGVILGHKNIPVNSVGCYVPGGKFPMVA 131

Query: 138 SVLMNALPAKIAGVERIVMTVPMPHGEINPAVLAAAQVAGVTEIYSIGGAQAVGALAYGT 197
           S  M+ + AK+AGV+R+V + P   G  +PA++AA    G  EI  +GG QAVGA+A GT
Sbjct: 132 SAHMSVITAKVAGVKRVVASAPPVKGAPHPAIVAAMHEGGADEILVLGGVQAVGAMALGT 191

Query: 198 ETITPVDKIVGPGNAYVAEAKRQVFGTVGIDSIAGPSEILVVADRQNNPEWIAWDLLSQA 257
           E+I PVD +VGPGNA+VAEAKRQ+FG VGID  AGP+E  V+AD   + E +A DLL QA
Sbjct: 192 ESIAPVDMLVGPGNAFVAEAKRQLFGRVGIDLFAGPTETCVIADDTVDGEMVATDLLGQA 251

Query: 258 EHDPSAQSILITDSESFAQQVIAAVEQILTTLPSQKVASSSWQNHGAVIIVRDLAESIPL 317
           EH  ++ ++LIT S   A+  ++ ++++L  LP+ + A  SW+++G VI+  D  E + +
Sbjct: 252 EHGYNSPAVLITCSRKLAEDTLSEIDRLLAILPTAETARVSWEDYGEVILCTDYDEMLRV 311

Query: 318 LNQLAPEHVELCVDNPQLLASQIKCAGSLFLGRYTPEAIGDYLGGPNHVLPTSRSARFAS 377
            + +A EHV++  D        +   G+LFLG  T  A GD + G NH LPT ++ R+  
Sbjct: 312 ADDVASEHVQVMTDRDDWFLDNMTNYGALFLGPRTNVANGDKVIGTNHTLPTKKAGRYTG 371

Query: 378 GLSVYDFLKRITYLE-CNQAALQKIGQSAVTLAETEGLPAHAGSVAVRLQ 426
           GL V  FLK  +Y +     A + +G+    L   EG   HA    VR++
Sbjct: 372 GLWVGKFLKTHSYQKVLTDEAAKLVGEYGSRLCMLEGFVGHAEQCNVRVR 421


Lambda     K      H
   0.316    0.131    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: 475
Number of extensions: 22
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: 431
Length of database: 441
Length adjustment: 32
Effective length of query: 399
Effective length of database: 409
Effective search space:   163191
Effective search space used:   163191
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 3608850 Dshi_2242 (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.24126.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   3.4e-133  430.6   0.0   4.2e-133  430.3   0.0    1.0  1  lcl|FitnessBrowser__Dino:3608850  Dshi_2242 Histidinol dehydrogena


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3608850  Dshi_2242 Histidinol dehydrogenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  430.3   0.0  4.2e-133  4.2e-133       1     393 []      25     419 ..      25     419 .. 0.97

  Alignments for each domain:
  == domain 1  score: 430.3 bits;  conditional E-value: 4.2e-133
                         TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkvkleslrvseeeleealeavdeelkealelaaeniekfhekqlpes..veve 75 
                                       v+ i++d+ ++Gd+A+++++ekfd+++++++r+s +e+e+a+++v+ +   +++ a+++i++f++ q+++   veve
  lcl|FitnessBrowser__Dino:3608850  25 VTGILQDISTRGDAAVRDLSEKFDGYTPQAFRLSPSEIEAAMQKVTTREMGDIRFAQDQIRNFAQVQRASMtdVEVE 101
                                       678***************************************************************997754599** PP

                         TIGR00069  76 teegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpavlaaakllgvdevyk 152
                                       t +gv+lg+k  p+++vg+YvPgGk ++++++ m +++AkvAgvk++v+ +Pp  +g  +pa++aa++  g+de++ 
  lcl|FitnessBrowser__Dino:3608850 102 TIPGVILGHKNIPVNSVGCYVPGGKFPMVASAHMSVITAKVAGVKRVVASAPPV-KGAPHPAIVAAMHEGGADEILV 177
                                       *****************************************************6.9********************* PP

                         TIGR00069 153 vGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEvlviadesanpelvaaDllsqaEHd 229
                                       +GG+qa++a+a Gte++ +vd++vGPGn++V++AK+++fg+vgid++aGP+E +viad++ + e+va+Dll qaEH+
  lcl|FitnessBrowser__Dino:3608850 178 LGGVQAVGAMALGTESIAPVDMLVGPGNAFVAEAKRQLFGRVGIDLFAGPTETCVIADDTVDGEMVATDLLGQAEHG 254
                                       ***************************************************************************** PP

                         TIGR00069 230 edaqailvttseelaekveeeveeqleelerkeiaekslekngaiilvddleealelsneyApEHLelqtkdpeell 306
                                        ++ a+l+t s++lae++ +e+++ l+ l+++e+a+ s+e++g++il+ d++e+l++++++A EH++++t+    +l
  lcl|FitnessBrowser__Dino:3608850 255 YNSPAVLITCSRKLAEDTLSEIDRLLAILPTAETARVSWEDYGEVILCTDYDEMLRVADDVASEHVQVMTDRDDWFL 331
                                       ***************************************************************************** PP

                         TIGR00069 307 kkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArfasglsvedFlkrisvqel.skealeelaeaveklaeaEg 382
                                       ++++n+G++flG+ t +a gd+v G+nh+LPT+++ r+++gl+v +Flk+ s+q++ + ea++ ++e  ++l+ +Eg
  lcl|FitnessBrowser__Dino:3608850 332 DNMTNYGALFLGPRTNVANGDKVIGTNHTLPTKKAGRYTGGLWVGKFLKTHSYQKVlTDEAAKLVGEYGSRLCMLEG 408
                                       ******************************************************9725566666788899******* PP

                         TIGR00069 383 LeaHaeavevR 393
                                       +  Hae  +vR
  lcl|FitnessBrowser__Dino:3608850 409 FVGHAEQCNVR 419
                                       ******99988 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (441 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.69
//
[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