GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisD in Sulfurihydrogenibium subterraneum DSM 15120

Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate WP_028951054.1 Q385_RS0107405 histidinol dehydrogenase

Query= BRENDA::Q8G2R2
         (430 letters)



>NCBI__GCF_000619805.1:WP_028951054.1
          Length = 428

 Score =  352 bits (903), Expect = e-101
 Identities = 190/411 (46%), Positives = 271/411 (65%), Gaps = 7/411 (1%)

Query: 19  FLSGKREVSEDV-DRAVREIVDRVRREGDSALLDYSRRFDRIDLEKTGIAVTEAEIDAAF 77
           +L  + +V  D+ + AV+EI+  V+  GD AL++Y+ +FD+I +    + +   E++ A+
Sbjct: 19  YLIKRADVETDLYETAVKEIIKNVKERGDEALVEYTEKFDKIKINPEDLIIPFEELERAY 78

Query: 78  DAAPASTVEALKLARDRIEKHHARQLPKDDRYTDALGVELGSRWTAIEAVGLYVPGGTAS 137
           D        A ++A +R+ + H  Q  K   + +  G+ LG +   +E VGLYVPGG A+
Sbjct: 79  DEIEEEVRWAFEVAYERLYEFHELQKEKSF-FKEEDGMILGQKVIPLERVGLYVPGGKAA 137

Query: 138 YPSSVLMNAMPAKVAGVDRIVMVVPAPDGNLNPLVLVAARLAGVSEIYRVGGAQAIAALA 197
           YPSSVLMNA+PA+VAGV+ IV+  P P    N   L AA + G+  +YR+GGAQA+AA+A
Sbjct: 138 YPSSVLMNAVPARVAGVEEIVICSPNP----NKYTLAAAFICGIDTVYRIGGAQAVAAMA 193

Query: 198 YGTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGPSEVLIVADKDNNPDWIAADLL 257
           YGTET++ V KIVGPGN YVA AK+ VFG V IDMIAGPSE+L++AD+  N  W+AADLL
Sbjct: 194 YGTETVKKVDKIVGPGNIYVALAKKNVFGVVDIDMIAGPSEILVIADETANYKWVAADLL 253

Query: 258 AQAEHDTAAQSILMTNDEAFAHAVEEAVERQ-LHTLARTETASASWRDFGAVILVKDFED 316
           +QAEHD  A SIL+T  E  A  V++ +  + L   +R E A  S  ++G   +V+D E 
Sbjct: 254 SQAEHDELAASILITTSEELAKNVKDYLYNELLKAFSRKEIAEKSLNNYGHAFIVEDLEK 313

Query: 317 AIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTPEVIGDYVGGCNHVLPTARSA 376
           A  LAN +A EHLEI   +    + +I++AG+IF+G Y+ E +GDY+ G NHVLPT+RSA
Sbjct: 314 ACELANYLAPEHLEIVTENPFDLLNKIKHAGAIFLGHYSTEPLGDYILGPNHVLPTSRSA 373

Query: 377 RFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEGLDAHAQSVAIR 427
           RFSS L V D++KR+S++ +  E    +   AI +A +EGL+AHA SV IR
Sbjct: 374 RFSSPLGVYDFVKRSSVIYVSKEGFERVANHAINMANSEGLEAHALSVKIR 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: 429
Number of extensions: 19
Number of successful extensions: 4
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 WP_028951054.1 Q385_RS0107405 (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.665866.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.9e-170  553.2   0.2   2.2e-170  553.0   0.2    1.0  1  NCBI__GCF_000619805.1:WP_028951054.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000619805.1:WP_028951054.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  553.0   0.2  2.2e-170  2.2e-170       1     393 []      35     424 ..      35     424 .. 0.98

  Alignments for each domain:
  == domain 1  score: 553.0 bits;  conditional E-value: 2.2e-170
                             TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkv..kleslrvseeeleealeavdeelkealelaaeniekfhekqlpes 71 
                                           vkeii++v+++GdeAl+eytekfdk+  ++e+l ++ eele+a+++++ee++ a+e a+e++ +fhe q+++s
  NCBI__GCF_000619805.1:WP_028951054.1  35 VKEIIKNVKERGDEALVEYTEKFDKIkiNPEDLIIPFEELERAYDEIEEEVRWAFEVAYERLYEFHELQKEKS 107
                                           89**********************9977889**************************************9998 PP

                             TIGR00069  72 veveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpavlaaakl 144
                                            + ++e+g++lgqkv plervglYvPgGkaaypS+vlm+avpA+vAgv+eiv+++P+      n+ +laaa +
  NCBI__GCF_000619805.1:WP_028951054.1 108 -FFKEEDGMILGQKVIPLERVGLYVPGGKAAYPSSVLMNAVPARVAGVEEIVICSPN-----PNKYTLAAAFI 174
                                           .68889***************************************************.....599******** PP

                             TIGR00069 145 lgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEvlviadesanpel 217
                                           +g+d+vy++GGaqa+aa+ayGtetv+kvdkivGPGniyV+ AKk vfg v+idmiaGPsE+lviade+an ++
  NCBI__GCF_000619805.1:WP_028951054.1 175 CGIDTVYRIGGAQAVAAMAYGTETVKKVDKIVGPGNIYVALAKKNVFGVVDIDMIAGPSEILVIADETANYKW 247
                                           ************************************************************************* PP

                             TIGR00069 218 vaaDllsqaEHdedaqailvttseelaekveeeveeq.leelerkeiaekslekngaiilvddleealelsne 289
                                           vaaDllsqaEHde a++il+ttseela++v++ + ++ l++ +rkeiaeksl+++g  ++v+dle+a+el+n 
  NCBI__GCF_000619805.1:WP_028951054.1 248 VAADLLSQAEHDELAASILITTSEELAKNVKDYLYNElLKAFSRKEIAEKSLNNYGHAFIVEDLEKACELANY 320
                                           *******************************998766167789****************************** PP

                             TIGR00069 290 yApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArfasglsvedFlkrisvqel 362
                                           +ApEHLe+ t++p +ll+kik+aG++flG+y++e+lgdy+ GpnhvLPTs++Arf+s+l+v+dF+kr+sv+++
  NCBI__GCF_000619805.1:WP_028951054.1 321 LAPEHLEIVTENPFDLLNKIKHAGAIFLGHYSTEPLGDYILGPNHVLPTSRSARFSSPLGVYDFVKRSSVIYV 393
                                           ************************************************************************* PP

                             TIGR00069 363 skealeelaeaveklaeaEgLeaHaeavevR 393
                                           ske++e++a++++++a+ EgLeaHa +v++R
  NCBI__GCF_000619805.1:WP_028951054.1 394 SKEGFERVANHAINMANSEGLEAHALSVKIR 424
                                           *****************************99 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 17.72
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

Links

Downloads

Related tools

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:

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:

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:

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:

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