Alignments for a candidate for hisD in Dyella japonica UNC79MFTsu3.2

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisD in Dyella japonica UNC79MFTsu3.2

Align Histidinol dehydrogenase; HDH; EC 1.1.1.23 (characterized)
to candidate N515DRAFT_2937 N515DRAFT_2937 histidinol dehydrogenase

Query= SwissProt::P06988
         (434 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2937
          Length = 435

 Score =  475 bits (1223), Expect = e-138
 Identities = 254/432 (58%), Positives = 309/432 (71%), Gaps = 4/432 (0%)

Query: 7   IDWNSCTAEQQRQLLMRPAISASESITRTVNDILDNVKARGDEALREYSAKFDKTTVTAL 66
           +DWN+     Q Q L RPA S +E + R V  I+  V+A GD ALRE SAK+D+  + A+
Sbjct: 4   LDWNALDPAAQLQALARPAQSRAEELRRGVEAIVAKVRAEGDTALRELSAKYDRCAIDAI 63

Query: 67  KVSAEEIAAASERLSDELKQAMAVAVKNIETFHTAQKLPPVDVETQPGVRCQQVTRPVAS 126
           +V+ EE AAA   L+ ELK A+  A   I  FH      PV VET PGVR ++V RP+A 
Sbjct: 64  EVTVEEFAAAEAALAPELKAAIEEAAARIAAFHRESAPRPVAVETAPGVRVERVLRPIAK 123

Query: 127 VGLYIPGGSAPLFSTVLMLATPASIAGCKKVVLCSPPPI---ADE-ILYAAQLCGVQDVF 182
           VGLY+P GSAPL ST LML  PA +AGC++VVLCSP       DE +LYAA++ GV  VF
Sbjct: 124 VGLYVPAGSAPLPSTALMLGVPAGLAGCREVVLCSPARADGRCDEAVLYAARVTGVHRVF 183

Query: 183 NVGGAQAIAALAFGTESVPKVDKIFGPGNAFVTEAKRQVSQRLDGAAIDMPAGPSEVLVI 242
            +GGAQAIAA+A+GT SVP+ DK+FGPGNA+VTEAK QVS   DGAAIDMPAGPSEVLVI
Sbjct: 184 KLGGAQAIAAMAYGTGSVPRCDKLFGPGNAWVTEAKLQVSGDPDGAAIDMPAGPSEVLVI 243

Query: 243 ADSGATPDFVASDLLSQAEHGPDSQVILLTPAADMARRVAEAVERQLAELPRAETARQAL 302
           AD  A P+FVA+DLLSQAEHGPDSQVILL+P+  +  RVA  VERQ A LPRA  A QAL
Sbjct: 244 ADGKADPEFVAADLLSQAEHGPDSQVILLSPSDALLDRVAVEVERQCAALPRASIATQAL 303

Query: 303 NASRLIVTKDLAQCVEISNQYGPEHLIIQTRNARELVDSITSAGSVFLGDWSPESAGDYA 362
             SRLI+   LAQ V +SN+Y PEHLI+Q    R L+D I SAGS+FLG W+PES GDY 
Sbjct: 304 AQSRLILVDSLAQAVAVSNRYAPEHLILQVTEPRALLDGIDSAGSIFLGAWTPESVGDYC 363

Query: 363 SGTNHVLPTYGYTATCSSLGLADFQKRMTVQELSKEGFSALASTIETLAAAERLTAHKNA 422
           SG+NHVLPTYGY  + S + +A FQK++TVQELS +G  A+     TLA AE+L AH+ A
Sbjct: 364 SGSNHVLPTYGYARSYSGVSVASFQKQITVQELSADGLRAIGPCTATLAEAEQLEAHRRA 423

Query: 423 VTLRVNALKEQA 434
           VTLR+ AL+ +A
Sbjct: 424 VTLRLAALEARA 435


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: 511
Number of extensions: 17
Number of successful extensions: 2
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: 435
Length adjustment: 32
Effective length of query: 402
Effective length of database: 403
Effective search space:   162006
Effective search space used:   162006
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 N515DRAFT_2937 N515DRAFT_2937 (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.26043.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   4.4e-162  525.7   0.8   4.9e-162  525.5   0.8    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_2937  N515DRAFT_2937 histidinol dehydr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_2937  N515DRAFT_2937 histidinol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  525.5   0.8  4.9e-162  4.9e-162       1     393 []      33     427 ..      33     427 .. 0.99

  Alignments for each domain:
  == domain 1  score: 525.5 bits;  conditional E-value: 4.9e-162
                                    TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkvkleslrvseeeleealeavdeelkealelaaeniekfhek 66 
                                                  v++i+++vr+eGd+Al+e++ k+d++ +++++v+ ee+++a++a+ +elk+a+e+aa++i++fh++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2937  33 VEAIVAKVRAEGDTALRELSAKYDRCAIDAIEVTVEEFAAAEAALAPELKAAIEEAAARIAAFHRE 98 
                                                  799*************************************************************** PP

                                    TIGR00069  67 qlpesveveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdg 132
                                                    p+ v+vet++gv +++ +rp+ +vglYvP+G+a++pSt+lm++vpA +Ag++e+v+++P + dg
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2937  99 SAPRPVAVETAPGVRVERVLRPIAKVGLYVPAGSAPLPSTALMLGVPAGLAGCREVVLCSPARADG 164
                                                  ****************************************************************** PP

                                    TIGR00069 133 kvnpavlaaakllgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvf...gevg 195
                                                  ++++avl+aa+++gv++v+k+GGaqaiaa+ayGt +vp++dk++GPGn++Vt+AK +v+   +  +
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2937 165 RCDEAVLYAARVTGVHRVFKLGGAQAIAAMAYGTGSVPRCDKLFGPGNAWVTEAKLQVSgdpDGAA 230
                                                  ***********************************************************5444799 PP

                                    TIGR00069 196 idmiaGPsEvlviadesanpelvaaDllsqaEHdedaqailvttseelaekveeeveeqleelerk 261
                                                  idm+aGPsEvlviad +a+pe+vaaDllsqaEH++d+q+il+++s++l+++v  eve+q+++l+r+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2937 231 IDMPAGPSEVLVIADGKADPEFVAADLLSQAEHGPDSQVILLSPSDALLDRVAVEVERQCAALPRA 296
                                                  ****************************************************************** PP

                                    TIGR00069 262 eiaekslekngaiilvddleealelsneyApEHLelqtkdpeellkkiknaGsvflGeytpealgd 327
                                                  +ia+++l+ ++++ilvd+l++a+++sn+yApEHL+lq+++p++ll+ i++aGs+flG++tpe++gd
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2937 297 SIATQALA-QSRLILVDSLAQAVAVSNRYAPEHLILQVTEPRALLDGIDSAGSIFLGAWTPESVGD 361
                                                  ********.89******************************************************* PP

                                    TIGR00069 328 yvaGpnhvLPTsgtArfasglsvedFlkrisvqelskealeelaeaveklaeaEgLeaHaeavevR 393
                                                  y++G+nhvLPT+g+Ar++sg+sv++F+k+i+vqels ++l+++++ +++laeaE+LeaH++av+ R
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2937 362 YCSGSNHVLPTYGYARSYSGVSVASFQKQITVQELSADGLRAIGPCTATLAEAEQLEAHRRAVTLR 427
                                                  ***************************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (435 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: 7.39
//
[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