GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisD in Flavobacterium glycines Gm-149

Align Histidinol dehydrogenase; HDH; EC 1.1.1.23 (characterized)
to candidate WP_066326079.1 BLR17_RS14020 histidinol dehydrogenase

Query= SwissProt::P06988
         (434 letters)



>NCBI__GCF_900100165.1:WP_066326079.1
          Length = 427

 Score =  397 bits (1021), Expect = e-115
 Identities = 215/423 (50%), Positives = 282/423 (66%), Gaps = 7/423 (1%)

Query: 13  TAEQQRQLLMRPAISASESITRTVNDILDNVKARGDEALREYSAKFDKTTVTALKVSAEE 72
           T +    +L RP  + ++ I  TV +I   V+  GD A+ +Y+ +FD       +V+A E
Sbjct: 8   TPDTWASILERPTKTVND-IEATVKEIFAAVQKDGDAAVAKYTTQFDGVYFENSEVTAAE 66

Query: 73  IAAASERLSDELKQAMAVAVKNIETFHTAQKLPPVDVETQPGVRCQQVTRPVASVGLYIP 132
           I  A   +SDEL  A+++A  N+E FH AQK   V +ET  GV+C Q  RP+  VGLYIP
Sbjct: 67  IEVAINTISDELTAAISLAKANVEKFHQAQKTTRVSIETAEGVQCWQEKRPIQKVGLYIP 126

Query: 133 GGSAPLFSTVLMLATPASIAGCKKVVLCSPPP----IADEILYAAQLCGVQDVFNVGGAQ 188
           GG+APLFSTVLMLA PA IAGC ++VLCSPP     I   ILYAA LCGV  +  VGG Q
Sbjct: 127 GGTAPLFSTVLMLAVPAKIAGCSEIVLCSPPDKNGNINPAILYAANLCGVTKIIKVGGIQ 186

Query: 189 AIAALAFGTESVPKVDKIFGPGNAFVTEAKRQVSQRLDGAAIDMPAGPSEVLVIADSGAT 248
           AIA + FGT+++PKV KIFGPGN +VT AK+  +Q   G AIDMPAGPSE+LV+AD  A 
Sbjct: 187 AIAGMTFGTKAIPKVYKIFGPGNQYVTVAKQLATQF--GVAIDMPAGPSELLVVADDTAV 244

Query: 249 PDFVASDLLSQAEHGPDSQVILLTPAADMARRVAEAVERQLAELPRAETARQALNASRLI 308
           P FVASDLLSQAEHG DSQVIL++ +  M   V   ++ QL  LPR   A +A+  S+ I
Sbjct: 245 PAFVASDLLSQAEHGVDSQVILVSTSKAMIDAVESEIQAQLELLPRKTIAEKAIANSKSI 304

Query: 309 VTKDLAQCVEISNQYGPEHLIIQTRNARELVDSITSAGSVFLGDWSPESAGDYASGTNHV 368
             ++ +  +++ N+YGPEH I+ T N    VD I +AGSVF+G+++PESAGDYASGTNH 
Sbjct: 305 FVENDSIALDLINEYGPEHFIVCTANNDFYVDGIQNAGSVFIGNYTPESAGDYASGTNHT 364

Query: 369 LPTYGYTATCSSLGLADFQKRMTVQELSKEGFSALASTIETLAAAERLTAHKNAVTLRVN 428
           LPT GY    S + L  F K MT Q++S++G   + + IE +A AE L AH+NAVTLR+ 
Sbjct: 365 LPTNGYAKNYSGVNLDSFMKSMTFQKISEKGIQNIGTAIEVMAEAEGLQAHRNAVTLRLK 424

Query: 429 ALK 431
           +L+
Sbjct: 425 SLE 427


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: 446
Number of extensions: 16
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: 434
Length of database: 427
Length adjustment: 32
Effective length of query: 402
Effective length of database: 395
Effective search space:   158790
Effective search space used:   158790
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_066326079.1 BLR17_RS14020 (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.239745.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.8e-159  516.5   6.6   3.1e-159  516.3   6.6    1.0  1  NCBI__GCF_900100165.1:WP_066326079.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900100165.1:WP_066326079.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  516.3   6.6  3.1e-159  3.1e-159       1     393 []      30     422 ..      30     422 .. 0.99

  Alignments for each domain:
  == domain 1  score: 516.3 bits;  conditional E-value: 3.1e-159
                             TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkvkleslrvseeeleealeavdeelkealelaaeniekfhekqlpesve 73 
                                           vkei+++v+k Gd+A+ +yt++fd+v  e+ +v+++e+e a +++++el +a++la++n+ekfh++q++++v+
  NCBI__GCF_900100165.1:WP_066326079.1  30 VKEIFAAVQKDGDAAVAKYTTQFDGVYFENSEVTAAEIEVAINTISDELTAAISLAKANVEKFHQAQKTTRVS 102
                                           89*********************************************************************** PP

                             TIGR00069  74 veteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpavlaaakllg 146
                                           +et+egv++ q  rp+++vglY+PgG+a+++Stvlm+avpAk+Ag++eiv+++Pp+k+g++npa+l+aa+l+g
  NCBI__GCF_900100165.1:WP_066326079.1 103 IETAEGVQCWQEKRPIQKVGLYIPGGTAPLFSTVLMLAVPAKIAGCSEIVLCSPPDKNGNINPAILYAANLCG 175
                                           ************************************************************************* PP

                             TIGR00069 147 vdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfg.evgidmiaGPsEvlviadesanpelv 218
                                           v++++kvGG qaia +++Gt+ +pkv ki+GPGn+yVt AK+l ++  v+idm+aGPsE+lv+ad++a p++v
  NCBI__GCF_900100165.1:WP_066326079.1 176 VTKIIKVGGIQAIAGMTFGTKAIPKVYKIFGPGNQYVTVAKQLATQfGVAIDMPAGPSELLVVADDTAVPAFV 248
                                           *******************************************99669************************* PP

                             TIGR00069 219 aaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekngaiilvddleealelsneyA 291
                                           a+DllsqaEH+ d+q+ilv+ts++++++ve+e+++qle l+rk+iaek+++ n++ i v++ + al+l+ney+
  NCBI__GCF_900100165.1:WP_066326079.1 249 ASDLLSQAEHGVDSQVILVSTSKAMIDAVESEIQAQLELLPRKTIAEKAIA-NSKSIFVENDSIALDLINEYG 320
                                           ***************************************************.66777789999********** PP

                             TIGR00069 292 pEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArfasglsvedFlkrisvqelsk 364
                                           pEH +++t+++  +++ i+naGsvf+G+ytpe++gdy++G+nh+LPT+g+A+ +sg+++++F+k++++q++s+
  NCBI__GCF_900100165.1:WP_066326079.1 321 PEHFIVCTANNDFYVDGIQNAGSVFIGNYTPESAGDYASGTNHTLPTNGYAKNYSGVNLDSFMKSMTFQKISE 393
                                           ************************************************************************* PP

                             TIGR00069 365 ealeelaeaveklaeaEgLeaHaeavevR 393
                                           +++++++ a+e +aeaEgL+aH++av+ R
  NCBI__GCF_900100165.1:WP_066326079.1 394 KGIQNIGTAIEVMAEAEGLQAHRNAVTLR 422
                                           **************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (427 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: 00:00:00.00
# Mc/sec: 18.17
//
[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:

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