Alignments for a candidate for hisD in Escherichia coli BW25113

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisD in Escherichia coli BW25113

Align Histidinol dehydrogenase; HDH; EC 1.1.1.23 (characterized)
to candidate 16128 b2020 histidinol dehydrogenase (NCBI)

Query= SwissProt::P06988
         (434 letters)



>FitnessBrowser__Keio:16128
          Length = 434

 Score =  836 bits (2160), Expect = 0.0
 Identities = 434/434 (100%), Positives = 434/434 (100%)

Query: 1   MSFNTIIDWNSCTAEQQRQLLMRPAISASESITRTVNDILDNVKARGDEALREYSAKFDK 60
           MSFNTIIDWNSCTAEQQRQLLMRPAISASESITRTVNDILDNVKARGDEALREYSAKFDK
Sbjct: 1   MSFNTIIDWNSCTAEQQRQLLMRPAISASESITRTVNDILDNVKARGDEALREYSAKFDK 60

Query: 61  TTVTALKVSAEEIAAASERLSDELKQAMAVAVKNIETFHTAQKLPPVDVETQPGVRCQQV 120
           TTVTALKVSAEEIAAASERLSDELKQAMAVAVKNIETFHTAQKLPPVDVETQPGVRCQQV
Sbjct: 61  TTVTALKVSAEEIAAASERLSDELKQAMAVAVKNIETFHTAQKLPPVDVETQPGVRCQQV 120

Query: 121 TRPVASVGLYIPGGSAPLFSTVLMLATPASIAGCKKVVLCSPPPIADEILYAAQLCGVQD 180
           TRPVASVGLYIPGGSAPLFSTVLMLATPASIAGCKKVVLCSPPPIADEILYAAQLCGVQD
Sbjct: 121 TRPVASVGLYIPGGSAPLFSTVLMLATPASIAGCKKVVLCSPPPIADEILYAAQLCGVQD 180

Query: 181 VFNVGGAQAIAALAFGTESVPKVDKIFGPGNAFVTEAKRQVSQRLDGAAIDMPAGPSEVL 240
           VFNVGGAQAIAALAFGTESVPKVDKIFGPGNAFVTEAKRQVSQRLDGAAIDMPAGPSEVL
Sbjct: 181 VFNVGGAQAIAALAFGTESVPKVDKIFGPGNAFVTEAKRQVSQRLDGAAIDMPAGPSEVL 240

Query: 241 VIADSGATPDFVASDLLSQAEHGPDSQVILLTPAADMARRVAEAVERQLAELPRAETARQ 300
           VIADSGATPDFVASDLLSQAEHGPDSQVILLTPAADMARRVAEAVERQLAELPRAETARQ
Sbjct: 241 VIADSGATPDFVASDLLSQAEHGPDSQVILLTPAADMARRVAEAVERQLAELPRAETARQ 300

Query: 301 ALNASRLIVTKDLAQCVEISNQYGPEHLIIQTRNARELVDSITSAGSVFLGDWSPESAGD 360
           ALNASRLIVTKDLAQCVEISNQYGPEHLIIQTRNARELVDSITSAGSVFLGDWSPESAGD
Sbjct: 301 ALNASRLIVTKDLAQCVEISNQYGPEHLIIQTRNARELVDSITSAGSVFLGDWSPESAGD 360

Query: 361 YASGTNHVLPTYGYTATCSSLGLADFQKRMTVQELSKEGFSALASTIETLAAAERLTAHK 420
           YASGTNHVLPTYGYTATCSSLGLADFQKRMTVQELSKEGFSALASTIETLAAAERLTAHK
Sbjct: 361 YASGTNHVLPTYGYTATCSSLGLADFQKRMTVQELSKEGFSALASTIETLAAAERLTAHK 420

Query: 421 NAVTLRVNALKEQA 434
           NAVTLRVNALKEQA
Sbjct: 421 NAVTLRVNALKEQA 434


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: 750
Number of extensions: 15
Number of successful extensions: 1
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: 434
Length adjustment: 32
Effective length of query: 402
Effective length of database: 402
Effective search space:   161604
Effective search space used:   161604
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 16128 b2020 (histidinol dehydrogenase (NCBI))
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.30543.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   1.7e-165  537.0   1.6   1.9e-165  536.8   1.6    1.0  1  lcl|FitnessBrowser__Keio:16128  b2020 histidinol dehydrogenase (


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:16128  b2020 histidinol dehydrogenase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  536.8   1.6  1.9e-165  1.9e-165       1     393 []      36     426 ..      36     426 .. 0.99

  Alignments for each domain:
  == domain 1  score: 536.8 bits;  conditional E-value: 1.9e-165
                       TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkvkleslrvseeeleealeavdeelkealelaaeniekfhekqlpesveveteeg 79 
                                     v++i+++v+++GdeAl+ey+ kfdk+++++l+vs+ee+++a+e++++elk+a++ a++nie+fh++q+   v vet++g
  lcl|FitnessBrowser__Keio:16128  36 VNDILDNVKARGDEALREYSAKFDKTTVTALKVSAEEIAAASERLSDELKQAMAVAVKNIETFHTAQKLPPVDVETQPG 114
                                     899*****************************************************************999******** PP

                       TIGR00069  80 vllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpavlaaakllgvdevykvGGaqa 158
                                     v ++q +rp+ +vglY+PgG+a+++Stvlm+a pA +Ag+k++v+++Pp     +++++l+aa+l+gv++v++vGGaqa
  lcl|FitnessBrowser__Keio:16128 115 VRCQQVTRPVASVGLYIPGGSAPLFSTVLMLATPASIAGCKKVVLCSPPP----IADEILYAAQLCGVQDVFNVGGAQA 189
                                     *************************************************6....************************* PP

                       TIGR00069 159 iaalayGtetvpkvdkivGPGniyVtaAKklvf...gevgidmiaGPsEvlviadesanpelvaaDllsqaEHdedaqa 234
                                     iaala+Gte+vpkvdki+GPGn++Vt+AK++v+   +  +idm+aGPsEvlviad+ a p++va+DllsqaEH++d+q+
  lcl|FitnessBrowser__Keio:16128 190 IAALAFGTESVPKVDKIFGPGNAFVTEAKRQVSqrlDGAAIDMPAGPSEVLVIADSGATPDFVASDLLSQAEHGPDSQV 268
                                     *********************************5444789*************************************** PP

                       TIGR00069 235 ilvttseelaekveeeveeqleelerkeiaekslekngaiilvddleealelsneyApEHLelqtkdpeellkkiknaG 313
                                     il+t+ +++a++v e+ve+ql+el+r+e+a+++l+  +++i+++dl++++e+sn+y+pEHL++qt++++el+++i++aG
  lcl|FitnessBrowser__Keio:16128 269 ILLTPAADMARRVAEAVERQLAELPRAETARQALN-ASRLIVTKDLAQCVEISNQYGPEHLIIQTRNARELVDSITSAG 346
                                     ***********************************.89***************************************** PP

                       TIGR00069 314 svflGeytpealgdyvaGpnhvLPTsgtArfasglsvedFlkrisvqelskealeelaeaveklaeaEgLeaHaeavev 392
                                     svflG+++pe++gdy++G+nhvLPT+g++ + s+l+++dF+kr++vqelske++++la+++e+la+aE L+aH++av+ 
  lcl|FitnessBrowser__Keio:16128 347 SVFLGDWSPESAGDYASGTNHVLPTYGYTATCSSLGLADFQKRMTVQELSKEGFSALASTIETLAAAERLTAHKNAVTL 425
                                     *****************************************************************************99 PP

                       TIGR00069 393 R 393
                                     R
  lcl|FitnessBrowser__Keio:16128 426 R 426
                                     8 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.44
//
[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