Alignments for a candidate for hisD in Shewanella oneidensis MR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisD in Shewanella oneidensis MR-1

Align Histidinol dehydrogenase; HDH; EC 1.1.1.23 (characterized)
to candidate 201230 SO2073 histidinol dehydrogenase (NCBI ptt file)

Query= SwissProt::P06988
         (434 letters)



>FitnessBrowser__MR1:201230
          Length = 438

 Score =  479 bits (1234), Expect = e-140
 Identities = 249/437 (56%), Positives = 322/437 (73%), Gaps = 13/437 (2%)

Query: 6   IIDWNSCTAEQQRQLLMRPAISASESITRTVNDILDNVKARGDEALREYSAKFDKTTVTA 65
           ++ W + +A++Q+  L R  +     + ++V  I+D V +RGD A++E++ KFD   +  
Sbjct: 3   MLTWAALSADEQKTALQRSPLIGDSGLEQSVRAIVDAVASRGDAAIKEFNQKFDGARLAN 62

Query: 66  --------LKVSAEEIAAASERLSDELKQAMAVAVKNIETFHTAQKLPPVDVETQPGVRC 117
                   L++S  EI AAS R+S ELK A+A A+ NI+ FH+AQ+  P+D+ETQ GVRC
Sbjct: 63  ISSANSDNLRLSEHEIEAASARVSPELKAAIAQAMANIDVFHSAQQFRPIDIETQAGVRC 122

Query: 118 QQVTRPVASVGLYIPGGSAPLFSTVLMLATPASIAGCKKVVLCSPPPIADEILYAAQLCG 177
           +  + P+  VGLYIPGGSAPL STVLMLA PA+IAGC++ VL SPPPI D I+YAA +CG
Sbjct: 123 ELRSEPIEKVGLYIPGGSAPLISTVLMLALPATIAGCEQRVLVSPPPINDAIVYAANVCG 182

Query: 178 VQDVFNVGGAQAIAALAFGTESVPKVDKIFGPGNAFVTEAKRQVSQRLDG---AAIDMPA 234
           + +++ VGGAQAIAALAFGTE++P VDKIFGPGN +VTEAKR VSQ  DG    +IDMPA
Sbjct: 183 ITEIYQVGGAQAIAALAFGTETIPSVDKIFGPGNRYVTEAKRLVSQ--DGRCTVSIDMPA 240

Query: 235 GPSEVLVIADSGATPDFVASDLLSQAEHGPDSQVILLTPAADMARRVAEAVERQLAELPR 294
           GPSEVLVIADS A   F+A+DLLSQAEHGPDSQVIL+T +  +A+ V +A++ QLA LPR
Sbjct: 241 GPSEVLVIADSDANAQFIAADLLSQAEHGPDSQVILVTDSLPLAQAVNQALKSQLAALPR 300

Query: 295 AETARQALNASRLIVTKDLAQCVEISNQYGPEHLIIQTRNARELVDSITSAGSVFLGDWS 354
            E A  AL  SR I+ KD+ +   +SN+YGPEHLIIQTR  RE++++I +AGSVFLG ++
Sbjct: 301 QEIAATALKGSRTILVKDMQEAALVSNRYGPEHLIIQTRFPREVLNNIRAAGSVFLGAYT 360

Query: 355 PESAGDYASGTNHVLPTYGYTATCSSLGLADFQKRMTVQELSKEGFSALASTIETLAAAE 414
           PES GDYASGTNHVLPTYGY+   SSL LADF +R TVQELS +G   L   + TLA+ E
Sbjct: 361 PESVGDYASGTNHVLPTYGYSRAVSSLSLADFSRRFTVQELSAKGLLGLGQAVMTLASNE 420

Query: 415 RLTAHKNAVTLRVNALK 431
            L AHKNAV +R+ +LK
Sbjct: 421 LLDAHKNAVAVRLASLK 437


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: 467
Number of extensions: 14
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: 438
Length adjustment: 32
Effective length of query: 402
Effective length of database: 406
Effective search space:   163212
Effective search space used:   163212
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 201230 SO2073 (histidinol dehydrogenase (NCBI ptt file))
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.22135.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   8.3e-157  508.3   2.0   9.4e-157  508.2   2.0    1.0  1  lcl|FitnessBrowser__MR1:201230  SO2073 histidinol dehydrogenase 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:201230  SO2073 histidinol dehydrogenase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  508.2   2.0  9.4e-157  9.4e-157       1     393 []      33     432 ..      33     432 .. 0.98

  Alignments for each domain:
  == domain 1  score: 508.2 bits;  conditional E-value: 9.4e-157
                       TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkv........kleslrvseeeleealeavdeelkealelaaeniekfhekqlpes 71 
                                     v++i+++v ++Gd+A++e+++kfd++        + ++lr+se+e+e+a+++v++elk+a+++a++ni+ fh++q+ + 
  lcl|FitnessBrowser__MR1:201230  33 VRAIVDAVASRGDAAIKEFNQKFDGArlanissaNSDNLRLSEHEIEAASARVSPELKAAIAQAMANIDVFHSAQQFRP 111
                                     789*********************98778777777789***************************************** PP

                       TIGR00069  72 veveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpavlaaakllgvdev 150
                                     + +et++gv ++ + +p+e+vglY+PgG+a+++Stvlm+a+pA +Ag+++ v+v+Pp     +n+a+++aa+++g++e+
  lcl|FitnessBrowser__MR1:201230 112 IDIETQAGVRCELRSEPIEKVGLYIPGGSAPLISTVLMLALPATIAGCEQRVLVSPPP----INDAIVYAANVCGITEI 186
                                     *********************************************************6....***************** PP

                       TIGR00069 151 ykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvf..g..evgidmiaGPsEvlviadesanpelvaaDllsq 225
                                     y+vGGaqaiaala+Gtet+p+vdki+GPGn yVt+AK+lv+  g  +v+idm+aGPsEvlviad++an++++aaDllsq
  lcl|FitnessBrowser__MR1:201230 187 YQVGGAQAIAALAFGTETIPSVDKIFGPGNRYVTEAKRLVSqdGrcTVSIDMPAGPSEVLVIADSDANAQFIAADLLSQ 265
                                     *****************************************662568******************************** PP

                       TIGR00069 226 aEHdedaqailvttseelaekveeeveeqleelerkeiaekslekngaiilvddleealelsneyApEHLelqtkdpee 304
                                     aEH++d+q+ilvt+s  la++v++++++ql++l+r+eia ++l+  ++ ilv+d++ea+ +sn+y+pEHL++qt+ p+e
  lcl|FitnessBrowser__MR1:201230 266 AEHGPDSQVILVTDSLPLAQAVNQALKSQLAALPRQEIAATALK-GSRTILVKDMQEAALVSNRYGPEHLIIQTRFPRE 343
                                     ********************************************.788899**************************** PP

                       TIGR00069 305 llkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArfasglsvedFlkrisvqelskealeelaeaveklaeaEgL 383
                                     +l++i++aGsvflG+ytpe++gdy++G+nhvLPT+g++r+ s+ls++dF +r++vqels ++l  l++av++la+ E L
  lcl|FitnessBrowser__MR1:201230 344 VLNNIRAAGSVFLGAYTPESVGDYASGTNHVLPTYGYSRAVSSLSLADFSRRFTVQELSAKGLLGLGQAVMTLASNELL 422
                                     ******************************************************************************* PP

                       TIGR00069 384 eaHaeavevR 393
                                     +aH++av+vR
  lcl|FitnessBrowser__MR1:201230 423 DAHKNAVAVR 432
                                     *******998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (438 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: 8.27
//
[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