Alignments for a candidate for hisD in Novosphingobium barchaimii LL02

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisD in Novosphingobium barchaimii LL02

Align Histidinol dehydrogenase 1; HDH 1; EC 1.1.1.23 (uncharacterized)
to candidate WP_059153352.1 V474_RS21900 histidinol dehydrogenase

Query= curated2:Q8YSM8
         (431 letters)



>NCBI__GCF_001046635.1:WP_059153352.1
          Length = 443

 Score =  281 bits (718), Expect = 4e-80
 Identities = 160/411 (38%), Positives = 234/411 (56%), Gaps = 8/411 (1%)

Query: 24  EATVDVSGTVRDI----LAHVKARGDAAVQEYTSRFDHYRPHSHHLSAAFIAEQAAKCSD 79
           EA       VRDI    LA ++ARGDAA++E ++RFD +    + LS A I       S 
Sbjct: 12  EAKATADRKVRDIVEAALADIEARGDAALREMSNRFDGWDRDDYRLSQAEIEACVNNLSP 71

Query: 80  EVKAALELAAERISSFH--QKQLPQDIGYTDTAGVKLGLNWVALSQVGIYVPGGRASYPS 137
           + +  +E A  ++ +F   Q+    D+      GV LG   + L+  G YVPGG+    +
Sbjct: 72  QERKDIEFAQTQVRNFAKIQRASMTDVEVETLPGVVLGHKNIPLNSAGCYVPGGKYPLLA 131

Query: 138 SVLMNALPAKIAGVERIVMTVPMPHGEINPAVLAAAQVAGVTEIYSIGGAQAVGALAYGT 197
           S  M+ + AK+AGV+R++   P   G+   A++AA  +AG   IY++GG QA+GA+A GT
Sbjct: 132 SAHMSVITAKVAGVKRVITCAPPFQGKPARAIVAAQAMAGADAIYALGGIQAIGAMAIGT 191

Query: 198 ETITPVDKIVGPGNAYVAEAKRQVFGTVGIDSIAGPSEILVVADRQN-NPEWIAWDLLSQ 256
           +TI PVD +VGPGNA+VAEAKRQ+FG VGID  AGP+E L++AD    +PE  A D+L Q
Sbjct: 192 QTIEPVDILVGPGNAFVAEAKRQLFGRVGIDLFAGPTETLIIADEIGCDPEMAATDILGQ 251

Query: 257 AEHDPSAQSILITDSESFAQQVIAAVEQILTTLPSQKVASSSWQNHGAVIIVRDLAESIP 316
            EH P +  +L+T+SE FA+  +A +E++L  LP+   A  +W+  G VI+     E + 
Sbjct: 252 VEHGPDSPGVLLTNSEKFARATMAEIERLLEILPTADHAGKAWETFGEVIVAESYEEMVR 311

Query: 317 LLNQLAPEHVELCVDNPQLLASQIKCAGSLFLGRYTPEAIGDYLGGPNHVLPTSRSARFA 376
           + ++LA EHV++   +P      +   G+LFLG  T  + GD + G NH LPT ++AR+ 
Sbjct: 312 IADELASEHVQVMTADPDYFLQNMTNYGALFLGNRTNVSFGDKVIGTNHTLPTKKAARYT 371

Query: 377 SGLSVYDFLKRITYLE-CNQAALQKIGQSAVTLAETEGLPAHAGSVAVRLQ 426
            GL V  FLK  TY       A   IG+    L   EG   H     +R++
Sbjct: 372 GGLWVGKFLKTCTYQRVITDEASALIGEYCSRLCALEGFAGHGEQANIRVR 422


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: 452
Number of extensions: 19
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: 431
Length of database: 443
Length adjustment: 32
Effective length of query: 399
Effective length of database: 411
Effective search space:   163989
Effective search space used:   163989
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_059153352.1 V474_RS21900 (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.3900075.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.5e-134  435.1   0.0     2e-134  434.7   0.0    1.0  1  NCBI__GCF_001046635.1:WP_059153352.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001046635.1:WP_059153352.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  434.7   0.0    2e-134    2e-134       1     393 []      25     420 ..      25     420 .. 0.97

  Alignments for each domain:
  == domain 1  score: 434.7 bits;  conditional E-value: 2e-134
                             TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkvkleslrvseeeleealeavdeelkealelaaeniekfhekqlpes.. 71 
                                           v++ ++d++++Gd+Al+e++++fd+++ ++ r+s++e+e+ +++++++ ++++e a++++++f++ q+++   
  NCBI__GCF_001046635.1:WP_059153352.1  25 VEAALADIEARGDAALREMSNRFDGWDRDDYRLSQAEIEACVNNLSPQERKDIEFAQTQVRNFAKIQRASMtd 97 
                                           567789***********************************************************99977545 PP

                             TIGR00069  72 veveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpavlaaakl 144
                                           vevet +gv+lg+k  pl+++g+YvPgGk+++++++ m +++AkvAgvk+++ ++Pp  +gk ++a++aa ++
  NCBI__GCF_001046635.1:WP_059153352.1  98 VEVETLPGVVLGHKNIPLNSAGCYVPGGKYPLLASAHMSVITAKVAGVKRVITCAPPF-QGKPARAIVAAQAM 169
                                           99*******************************************************6.9************* PP

                             TIGR00069 145 lgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEvlviades.anpe 216
                                           +g+d++y++GG qai+a+a Gt+t+++vd++vGPGn++V++AK+++fg+vgid++aGP+E l+iade  ++pe
  NCBI__GCF_001046635.1:WP_059153352.1 170 AGADAIYALGGIQAIGAMAIGTQTIEPVDILVGPGNAFVAEAKRQLFGRVGIDLFAGPTETLIIADEIgCDPE 242
                                           ******************************************************************9638*** PP

                             TIGR00069 217 lvaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekngaiilvddleealelsne 289
                                           + a+D+l q+EH++d+  +l+t+se++a+++ +e+e+ le l++++ a k++e+ g++i+++++ee++++++e
  NCBI__GCF_001046635.1:WP_059153352.1 243 MAATDILGQVEHGPDSPGVLLTNSEKFARATMAEIERLLEILPTADHAGKAWETFGEVIVAESYEEMVRIADE 315
                                           ************************************************************************* PP

                             TIGR00069 290 yApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArfasglsvedFlkrisvqel 362
                                           +A EH++++t+dp  +l++++n+G++flG+ t +++gd+v G+nh+LPT+++Ar+++gl+v +Flk++++q++
  NCBI__GCF_001046635.1:WP_059153352.1 316 LASEHVQVMTADPDYFLQNMTNYGALFLGNRTNVSFGDKVIGTNHTLPTKKAARYTGGLWVGKFLKTCTYQRV 388
                                           ***********************************************************************97 PP

                             TIGR00069 363 .skealeelaeaveklaeaEgLeaHaeavevR 393
                                            + ea + ++e +++l+++Eg++ H e +++R
  NCBI__GCF_001046635.1:WP_059153352.1 389 iTDEASALIGEYCSRLCALEGFAGHGEQANIR 420
                                           256666778999***************99988 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (443 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 31.43
//
[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:

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 2024 update 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 original 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