Alignments for a candidate for hisD in Caulobacter crescentus NA1000

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisD in Caulobacter crescentus NA1000

Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate CCNA_02431 CCNA_02431 histidinol dehydrogenase

Query= BRENDA::Q8G2R2
         (430 letters)



>FitnessBrowser__Caulo:CCNA_02431
          Length = 428

 Score =  478 bits (1229), Expect = e-139
 Identities = 247/421 (58%), Positives = 309/421 (73%), Gaps = 3/421 (0%)

Query: 8   TDPDFEQKFAAFLSGKREVSEDVDRAVREIVDRVRREGDSALLDYSRRFDRIDLEKTGIA 67
           +DPDF+  F AFL  +R    DVD AV  +++ VR +G  ALLDYSRRFD++DL    I 
Sbjct: 7   SDPDFQTAFKAFLDERRGSPADVDAAVAGVLEAVRTQGIEALLDYSRRFDKVDLTAETIR 66

Query: 68  VTEAEIDAAFDAAPASTVEALKLARDRIEKHHARQLPKDDRYTDALGVELGSRWTAIEAV 127
           VT  EI+A     PA   EA+  A  RI  +H+RQ P D  +TD  GVELG RWT +EAV
Sbjct: 67  VTAEEIEAGAAETPADVREAIAFAAARIRAYHSRQRPADQAWTDEAGVELGWRWTPLEAV 126

Query: 128 GLYVPGGTASYPSSVLMNAMPAKVAGVDRIVMVVPAPDGNLNPLVLVAARLAGVSEIYRV 187
           G+YVPGG A+YPS+VLMNA+PA+VAGVDRI MV P   G L P VL AA+ AGV+EI+RV
Sbjct: 127 GVYVPGGRAAYPSTVLMNAVPAQVAGVDRIAMVTPP--GKLQPAVLAAAKEAGVTEIWRV 184

Query: 188 GGAQAIAALAYGTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGPSEVLIVADKDN 247
           GGAQA+AALAYG   I+PV KIVGPGNAYV AAKR ++G VGID +AGPSE+++VAD  N
Sbjct: 185 GGAQAVAALAYGAGPIQPVDKIVGPGNAYVTAAKRRLYGVVGIDALAGPSEIVVVADNKN 244

Query: 248 NPDWIAADLLAQAEHDTAAQSILMTNDEAFAHAVEEAVERQLHTLARTETASASWRDFGA 307
           NPDWIAADLL+QAEHD AAQSIL+T+DEAFA AVE+A+  +L TLA  E A+ASWRD GA
Sbjct: 245 NPDWIAADLLSQAEHDPAAQSILITDDEAFAAAVEQAIAERLKTLATGEDAAASWRDHGA 304

Query: 308 VILVKDFEDAIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTPEVIGDYVGGCN 367
           VI +   +++  L + IA EH+E A+ + E    R+R+AG+IF+G  TPE IGDYV G N
Sbjct: 305 VI-IAPLDESPALVDAIAPEHVEFALDNPERLSDRVRHAGAIFLGRVTPEAIGDYVAGSN 363

Query: 368 HVLPTARSARFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEGLDAHAQSVAIR 427
           HVLPT+R+ARF SGLS+ D++KRTS++K        LGP  + +A+AEGL AHA S ++R
Sbjct: 364 HVLPTSRAARFQSGLSIYDFIKRTSIVKCDPASFAVLGPHTVALAKAEGLPAHALSASVR 423

Query: 428 L 428
           L
Sbjct: 424 L 424


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: 493
Number of extensions: 18
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: 428
Length adjustment: 32
Effective length of query: 398
Effective length of database: 396
Effective search space:   157608
Effective search space used:   157608
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 CCNA_02431 CCNA_02431 (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.23738.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.2e-155  502.2   2.8   7.1e-155  502.0   2.8    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_02431  CCNA_02431 histidinol dehydrogen


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_02431  CCNA_02431 histidinol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  502.0   2.8  7.1e-155  7.1e-155       1     393 []      33     423 ..      33     423 .. 0.99

  Alignments for each domain:
  == domain 1  score: 502.0 bits;  conditional E-value: 7.1e-155
                             TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkv..kleslrvseeeleealeavdeelkealelaaeniekfhekqlpes 71 
                                           v+ ++e+vr++G eAll+y+++fdkv  ++e++rv++ee+e+ +++ +++++ea++ aa++i+++h++q+p++
  lcl|FitnessBrowser__Caulo:CCNA_02431  33 VAGVLEAVRTQGIEALLDYSRRFDKVdlTAETIRVTAEEIEAGAAETPADVREAIAFAAARIRAYHSRQRPAD 105
                                           67899********************988899****************************************** PP

                             TIGR00069  72 veveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpavlaaakl 144
                                            + ++e+gv lg +++ple+vg+YvPgG+aaypStvlm+avpA+vAgv++i++vtPp   gk++pavlaaak 
  lcl|FitnessBrowser__Caulo:CCNA_02431 106 QAWTDEAGVELGWRWTPLEAVGVYVPGGRAAYPSTVLMNAVPAQVAGVDRIAMVTPP---GKLQPAVLAAAKE 175
                                           *********************************************************...79*********** PP

                             TIGR00069 145 lgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEvlviadesanpel 217
                                           +gv+e+++vGGaqa+aalayG   +++vdkivGPGn+yVtaAK+ ++g vgid +aGPsE++v+ad++ np++
  lcl|FitnessBrowser__Caulo:CCNA_02431 176 AGVTEIWRVGGAQAVAALAYGAGPIQPVDKIVGPGNAYVTAAKRRLYGVVGIDALAGPSEIVVVADNKNNPDW 248
                                           ************************************************************************* PP

                             TIGR00069 218 vaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekngaiilvddleealelsney 290
                                           +aaDllsqaEHd+ aq+il+t++e++a++ve++++e+l++l + e a +s++++ga+i+ + l+e  +l++++
  lcl|FitnessBrowser__Caulo:CCNA_02431 249 IAADLLSQAEHDPAAQSILITDDEAFAAAVEQAIAERLKTLATGEDAAASWRDHGAVII-APLDESPALVDAI 320
                                           ****************************************************9999985.679********** PP

                             TIGR00069 291 ApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArfasglsvedFlkrisvqels 363
                                           ApEH+e + ++pe+l +++++aG++flG++tpea+gdyvaG+nhvLPTs++Arf+sgls++dF+kr+s+++++
  lcl|FitnessBrowser__Caulo:CCNA_02431 321 APEHVEFALDNPERLSDRVRHAGAIFLGRVTPEAIGDYVAGSNHVLPTSRAARFQSGLSIYDFIKRTSIVKCD 393
                                           ************************************************************************* PP

                             TIGR00069 364 kealeelaeaveklaeaEgLeaHaeavevR 393
                                            ++++ l++++++la+aEgL aHa +++vR
  lcl|FitnessBrowser__Caulo:CCNA_02431 394 PASFAVLGPHTVALAKAEGLPAHALSASVR 423
                                           **************************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (428 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: 00:00:00.02
# Mc/sec: 8.12
//
[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