Alignments for a candidate for hisD in Sinorhizobium meliloti 1021

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisD in Sinorhizobium meliloti 1021

Align Histidinol dehydrogenase; HDH; EC 1.1.1.23 (uncharacterized)
to candidate SMa0398 SMa0398 histidinol dehydrogenase

Query= curated2:O26327
         (426 letters)



>FitnessBrowser__Smeli:SMa0398
          Length = 456

 Score =  293 bits (750), Expect = 7e-84
 Identities = 168/427 (39%), Positives = 245/427 (57%), Gaps = 11/427 (2%)

Query: 2   LMKITEFDYRRISE-----LVERARLDVDDVLGPVADIISMVRDGGDDALRELTGRFD-- 54
           +  ++ ++Y +++      L+ R+  D+   +  VA I+  VR  GD AL       D  
Sbjct: 15  MTSVSFYEYSKLNAEEKAALLRRSETDISGFIEKVAPILEAVRTEGDKALARFGRELDKA 74

Query: 55  GVTVENFRVSREEIEEAHKNLEPGVKEALREAASNIEEFHRMQMPSG-WMSEVRPGVMAG 113
            VT  N +V+  E + A K ++  V E+++    NI +FH  Q P   W+ E+RPG  AG
Sbjct: 75  DVTEANLKVTAAEFDAAFKLVDASVLESVQFGIDNIRKFHEEQKPEAMWLKEIRPGAFAG 134

Query: 114 QLVRPIDSVGCYIPGGRAVYPSTILMTVIPARIAGVERIVCCTPPAQDGSVPDAVLVAAD 173
               PI SV  Y+P G+  +PS  +MT +PA +AGV  +   TPPA DGSV  A LVAA 
Sbjct: 135 DRFTPIQSVALYVPRGKGSFPSVTMMTSVPAVVAGVPNLAIVTPPAPDGSVDAATLVAAR 194

Query: 174 MAGASEIYRVGGAQAVAAMAYGTETIRPVDKIVGPGNIFVTAAKKLVYGEVDIDFPAGPS 233
           +AG   +Y+ GGAQAVAA+AYGTET++P  KIVGPG+ +V AAK+ + G +D   PAGPS
Sbjct: 195 LAGVETVYKAGGAQAVAAVAYGTETVKPALKIVGPGSPWVVAAKRSLSGVIDTGLPAGPS 254

Query: 234 EVLIIADETASPEYIALEILAQAEHDPQAASVLVTDSRDLALEVKEMVHENIKYM--ERA 291
           EV+I+AD+T      AL++L +AEH P +++ LVT S  +A E    + E+   M  +R 
Sbjct: 255 EVMILADDTVHGGLAALDLLIEAEHGPDSSAYLVTHSGRVAEEALAALPEHWARMTEQRT 314

Query: 292 NIIRESLE-RYGMIVLTADIDEAVDFSNAYAPEHLVIMTDSPEETLEGIRNAGSIFLGEL 350
              +  L  + G IVLT+ I+E+ +F NAYAPEHL ++++ P   L  I  A  I +G  
Sbjct: 315 AFSKTVLSGKTGGIVLTSSIEESYEFVNAYAPEHLELLSEQPFIHLGHITEASEILMGTH 374

Query: 351 SPVAAGDYGSGTNHVLPTSGCARMYSGLSTESFIKKPTVQRITKEGLRNLQGTVLKLAEY 410
           +PV+  ++  G N VLPTS  AR +  LS   F+K+ ++  +T             LA Y
Sbjct: 375 TPVSIANFSLGPNAVLPTSRWARTFGPLSVTDFVKRSSIGYVTAPAYPEFARHSHNLAIY 434

Query: 411 EGLHAHA 417
           EG  +HA
Sbjct: 435 EGFSSHA 441


Lambda     K      H
   0.317    0.135    0.382 

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: 440
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: 426
Length of database: 456
Length adjustment: 32
Effective length of query: 394
Effective length of database: 424
Effective search space:   167056
Effective search space used:   167056
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 SMa0398 SMa0398 (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.25417.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   2.2e-128  414.7   0.1   2.6e-128  414.5   0.1    1.0  1  lcl|FitnessBrowser__Smeli:SMa0398  SMa0398 histidinol dehydrogenase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMa0398  SMa0398 histidinol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  414.5   0.1  2.6e-128  2.6e-128       1     391 [.      49     445 ..      49     448 .. 0.97

  Alignments for each domain:
  == domain 1  score: 414.5 bits;  conditional E-value: 2.6e-128
                          TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkv..kleslrvseeeleealeavdeelkealelaaeniekfhekqlpes.ve 73 
                                        v++i+e+vr+eGd+Al ++ +++dk+  + ++l+v+++e+++a + vd+++ e+++  ++ni+kfhe+q+pe  + 
  lcl|FitnessBrowser__Smeli:SMa0398  49 VAPILEAVRTEGDKALARFGRELDKAdvTEANLKVTAAEFDAAFKLVDASVLESVQFGIDNIRKFHEEQKPEAmWL 124
                                        789*********************98667889**************************************99879* PP

                          TIGR00069  74 veteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpavlaaakllgvde 149
                                        +e+++g ++g++++p+++v+lYvP+Gk ++pS  +mt vpA vAgv+++++vtPp+ dg+v++a+l+aa+l+gv++
  lcl|FitnessBrowser__Smeli:SMa0398 125 KEIRPGAFAGDRFTPIQSVALYVPRGKGSFPSVTMMTSVPAVVAGVPNLAIVTPPAPDGSVDAATLVAARLAGVET 200
                                        **************************************************************************** PP

                          TIGR00069 150 vykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEvlviadesanpelvaaDllsq 225
                                        vyk+GGaqa+aa+ayGtetv+++ kivGPG+ +V aAK+ ++g ++  ++aGPsEv+++ad++ +  l a+Dll +
  lcl|FitnessBrowser__Smeli:SMa0398 201 VYKAGGAQAVAAVAYGTETVKPALKIVGPGSPWVVAAKRSLSGVIDTGLPAGPSEVMILADDTVHGGLAALDLLIE 276
                                        **************************************************************************** PP

                          TIGR00069 226 aEHdedaqailvttseelaekveeeveeqleele..rkeiaekslek.ngaiilvddleealelsneyApEHLelq 298
                                        aEH++d++a+lvt+s ++ae++ +++ e++++++  r+ + ++ l+  +g i+l++++ee  e++n+yApEHLel 
  lcl|FitnessBrowser__Smeli:SMa0398 277 AEHGPDSSAYLVTHSGRVAEEALAALPEHWARMTeqRTAFSKTVLSGkTGGIVLTSSIEESYEFVNAYAPEHLELL 352
                                        ******************************999743566667777654899************************* PP

                          TIGR00069 299 tkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArfasglsvedFlkrisvqelskealeelaeav 374
                                         ++p   l +i++a ++++G++tp++++++  Gpn vLPTs++Ar+ ++lsv+dF+kr+s+ +++  a+ e+a++ 
  lcl|FitnessBrowser__Smeli:SMa0398 353 SEQPFIHLGHITEASEILMGTHTPVSIANFSLGPNAVLPTSRWARTFGPLSVTDFVKRSSIGYVTAPAYPEFARHS 428
                                        **************************************************************************** PP

                          TIGR00069 375 eklaeaEgLeaHaeave 391
                                         +la +Eg++ Ha av+
  lcl|FitnessBrowser__Smeli:SMa0398 429 HNLAIYEGFSSHALAVS 445
                                        *************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (456 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: 00:00:00.01
# Mc/sec: 11.60
//
[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