Alignments for a candidate for hisD in Shewanella amazonensis SB2B

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisD in Shewanella amazonensis SB2B

Align Histidinol dehydrogenase; HDH; EC 1.1.1.23 (characterized)
to candidate 6937801 Sama_1942 histidinol dehydrogenase (RefSeq)

Query= SwissProt::P06988
         (434 letters)



>FitnessBrowser__SB2B:6937801
          Length = 435

 Score =  503 bits (1294), Expect = e-147
 Identities = 261/426 (61%), Positives = 315/426 (73%), Gaps = 1/426 (0%)

Query: 9   WNSCTAEQQRQLLMRPAISASESITRTVNDILDNVKARGDEALREYSAKFDKTTVTALKV 68
           WN+ + + +RQ L R  +   +S+  +V+DIL NVK RGD  L EY+A+FDK  +  L +
Sbjct: 6   WNTLSEDAKRQALSRSPLVGDDSLATSVSDILCNVKRRGDSTLIEYAARFDKAEIDTLAL 65

Query: 69  SAEEIAAASERLSDELKQAMAVAVKNIETFHTAQKLPPVDVETQPGVRCQQVTRPVASVG 128
           SA+EIAAA ER+S ELK A+  A  NI  FH+AQ+   + +ETQPGVRC+  +  +  VG
Sbjct: 66  SADEIAAACERVSPELKDAINAARTNIARFHSAQQFSEISLETQPGVRCELKSEAIEKVG 125

Query: 129 LYIPGGSAPLFSTVLMLATPASIAGCKKVVLCSPPPIADEILYAAQLCGVQDVFNVGGAQ 188
           LYIPGGSAPL STVLMLA PA+IAGC K VL SPPPI D ILYAA +CG+ DVF +GGAQ
Sbjct: 126 LYIPGGSAPLISTVLMLAVPAAIAGCTKRVLVSPPPIDDAILYAASVCGITDVFQIGGAQ 185

Query: 189 AIAALAFGTESVPKVDKIFGPGNAFVTEAKRQVSQRLDGA-AIDMPAGPSEVLVIADSGA 247
           AIAALA+GTESVPKVDKIFGPGN +VTEAK QV++    A  IDMPAGPSEVLVIAD  A
Sbjct: 186 AIAALAYGTESVPKVDKIFGPGNRYVTEAKAQVARDTQAAVTIDMPAGPSEVLVIADDAA 245

Query: 248 TPDFVASDLLSQAEHGPDSQVILLTPAADMARRVAEAVERQLAELPRAETARQALNASRL 307
            P+F+A+DLLSQAEHG DSQVI +T +   A  V  A+ERQL  LPR ETA  AL+ SR+
Sbjct: 246 NPEFIAADLLSQAEHGSDSQVIFVTDSRTQANAVEAALERQLTLLPRRETAEGALSCSRI 305

Query: 308 IVTKDLAQCVEISNQYGPEHLIIQTRNARELVDSITSAGSVFLGDWSPESAGDYASGTNH 367
           I+T  L +   +SN Y PEHLIIQTR  R L+  I +AGSVFLG ++PES GDYASGTNH
Sbjct: 306 IITATLDEAAIVSNLYAPEHLIIQTREPRALLPRIRAAGSVFLGAYTPESVGDYASGTNH 365

Query: 368 VLPTYGYTATCSSLGLADFQKRMTVQELSKEGFSALASTIETLAAAERLTAHKNAVTLRV 427
           VLPTYGY+ T SSL LADF +R TVQELS EG   L  T+ TLAAAE L AHKNAV +R+
Sbjct: 366 VLPTYGYSKTVSSLSLADFCRRFTVQELSAEGLKGLGQTVMTLAAAESLDAHKNAVKVRL 425

Query: 428 NALKEQ 433
           +A+  +
Sbjct: 426 DAIARE 431


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: 483
Number of extensions: 13
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 6937801 Sama_1942 (histidinol dehydrogenase (RefSeq))
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.12846.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   3.6e-160  519.4   1.8   4.1e-160  519.2   1.8    1.0  1  lcl|FitnessBrowser__SB2B:6937801  Sama_1942 histidinol dehydrogena


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6937801  Sama_1942 histidinol dehydrogenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  519.2   1.8  4.1e-160  4.1e-160       1     393 []      33     424 ..      33     424 .. 0.99

  Alignments for each domain:
  == domain 1  score: 519.2 bits;  conditional E-value: 4.1e-160
                         TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkvkleslrvseeeleealeavdeelkealelaaeniekfhekqlpesvevete 77 
                                       v++i+ +v+++Gd+ l+ey+ +fdk+++++l++s++e+++a e+v++elk+a+++a +ni++fh++q+ +++++et+
  lcl|FitnessBrowser__SB2B:6937801  33 VSDILCNVKRRGDSTLIEYAARFDKAEIDTLALSADEIAAACERVSPELKDAINAARTNIARFHSAQQFSEISLETQ 109
                                       789************************************************************************** PP

                         TIGR00069  78 egvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpavlaaakllgvdevykvG 154
                                       +gv ++ k +++e+vglY+PgG+a+++Stvlm+avpA +Ag+++ v+v+Pp     +++a+l+aa+++g+++v+++G
  lcl|FitnessBrowser__SB2B:6937801 110 PGVRCELKSEAIEKVGLYIPGGSAPLISTVLMLAVPAAIAGCTKRVLVSPPP----IDDAILYAASVCGITDVFQIG 182
                                       ***************************************************6....********************* PP

                         TIGR00069 155 GaqaiaalayGtetvpkvdkivGPGniyVtaAKklvf....gevgidmiaGPsEvlviadesanpelvaaDllsqaE 227
                                       GaqaiaalayGte+vpkvdki+GPGn yVt+AK +v+      v idm+aGPsEvlviad+ anpe++aaDllsqaE
  lcl|FitnessBrowser__SB2B:6937801 183 GAQAIAALAYGTESVPKVDKIFGPGNRYVTEAKAQVArdtqAAVTIDMPAGPSEVLVIADDAANPEFIAADLLSQAE 259
                                       ************************************97765589********************************* PP

                         TIGR00069 228 HdedaqailvttseelaekveeeveeqleelerkeiaekslekngaiilvddleealelsneyApEHLelqtkdpee 304
                                       H++d+q+i+vt+s++ a++ve+++e+ql+ l+r+e+ae +l+  ++ii++++l+ea+ +sn yApEHL++qt++p++
  lcl|FitnessBrowser__SB2B:6937801 260 HGSDSQVIFVTDSRTQANAVEAALERQLTLLPRRETAEGALS-CSRIIITATLDEAAIVSNLYAPEHLIIQTREPRA 335
                                       ******************************************.9********************************* PP

                         TIGR00069 305 llkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArfasglsvedFlkrisvqelskealeelaeaveklaeaE 381
                                       ll++i++aGsvflG+ytpe++gdy++G+nhvLPT+g++++ s+ls++dF++r++vqels e+l+ l+++v++la+aE
  lcl|FitnessBrowser__SB2B:6937801 336 LLPRIRAAGSVFLGAYTPESVGDYASGTNHVLPTYGYSKTVSSLSLADFCRRFTVQELSAEGLKGLGQTVMTLAAAE 412
                                       ***************************************************************************** PP

                         TIGR00069 382 gLeaHaeavevR 393
                                        L+aH++av+vR
  lcl|FitnessBrowser__SB2B:6937801 413 SLDAHKNAVKVR 424
                                       **********99 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.85
//
[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