Alignments for a candidate for hisD in Magnetospirillum magneticum AMB-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisD in Magnetospirillum magneticum AMB-1

Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate WP_011385702.1 AMB_RS16905 histidinol dehydrogenase

Query= BRENDA::Q8G2R2
         (430 letters)



>NCBI__GCF_000009985.1:WP_011385702.1
          Length = 433

 Score =  537 bits (1384), Expect = e-157
 Identities = 271/430 (63%), Positives = 332/430 (77%)

Query: 1   MVTTLRQTDPDFEQKFAAFLSGKREVSEDVDRAVREIVDRVRREGDSALLDYSRRFDRID 60
           MV +L   D  FE  F A L+ KREV EDVD+AV  I+  VR  GD+AL++Y+ RFDR++
Sbjct: 1   MVQSLDSRDSGFEAAFLALLAMKREVDEDVDQAVAAILAEVRSRGDAALIEYTARFDRLE 60

Query: 61  LEKTGIAVTEAEIDAAFDAAPASTVEALKLARDRIEKHHARQLPKDDRYTDALGVELGSR 120
           L    + +T  E++ A+ +     + AL+LA +RI   HARQ+P DD +TDA GV LG R
Sbjct: 61  LTPATLRITAQEVETAYASCDPELIRALELAAERIRAFHARQVPVDDSFTDAAGVRLGLR 120

Query: 121 WTAIEAVGLYVPGGTASYPSSVLMNAMPAKVAGVDRIVMVVPAPDGNLNPLVLVAARLAG 180
           W+ + A GLYVPGGTA+YPSSVLMNA+PAK AGV+R+VMVVP+P G LNPLVL AA++AG
Sbjct: 121 WSPVSAAGLYVPGGTAAYPSSVLMNAIPAKAAGVERLVMVVPSPGGVLNPLVLAAAKVAG 180

Query: 181 VSEIYRVGGAQAIAALAYGTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGPSEVL 240
           V EIYRVGGAQA+ ALAYGT TIRPV KIVGPGNA+VAAAKR VFGTVGIDMIAGPSE+L
Sbjct: 181 VDEIYRVGGAQAVGALAYGTGTIRPVDKIVGPGNAWVAAAKRRVFGTVGIDMIAGPSEIL 240

Query: 241 IVADKDNNPDWIAADLLAQAEHDTAAQSILMTNDEAFAHAVEEAVERQLHTLARTETASA 300
           +VAD+ N+P WIAADLL+QAEHDTAAQSIL+T+D  F   V  AVE  L TL R + A  
Sbjct: 241 VVADRFNDPSWIAADLLSQAEHDTAAQSILITDDAEFGQRVAAAVESHLATLPRAKIARE 300

Query: 301 SWRDFGAVILVKDFEDAIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTPEVIG 360
           SW   GA+I+V D E ++PL +RIA EHLE+AV + +A   R+RNAG+IF+G YTPE +G
Sbjct: 301 SWDSHGAIIVVPDLEASLPLIDRIAPEHLELAVENPDALAARVRNAGAIFLGRYTPEAVG 360

Query: 361 DYVGGCNHVLPTARSARFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEGLDAH 420
           DY+GG NHVLPTARSARFSSGL VLD+MKRT+LL   ++ LRA+GPAA+ +A AEGL AH
Sbjct: 361 DYIGGPNHVLPTARSARFSSGLGVLDFMKRTTLLGCDADSLRAIGPAAVRLAEAEGLGAH 420

Query: 421 AQSVAIRLNL 430
             SVA+RLNL
Sbjct: 421 GLSVALRLNL 430


Lambda     K      H
   0.318    0.134    0.375 

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: 574
Number of extensions: 22
Number of successful extensions: 1
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: 430
Length of database: 433
Length adjustment: 32
Effective length of query: 398
Effective length of database: 401
Effective search space:   159598
Effective search space used:   159598
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 WP_011385702.1 AMB_RS16905 (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.12620.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.1e-163  528.5   0.0     7e-163  528.3   0.0    1.0  1  lcl|NCBI__GCF_000009985.1:WP_011385702.1  AMB_RS16905 histidinol dehydroge


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_011385702.1  AMB_RS16905 histidinol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  528.3   0.0    7e-163    7e-163       1     393 []      34     427 ..      34     427 .. 0.99

  Alignments for each domain:
  == domain 1  score: 528.3 bits;  conditional E-value: 7e-163
                                 TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkv..kleslrvseeeleealeavdeelkealelaaeniekfhekq 67 
                                               v++i+++vr++Gd+Al+eyt +fd++  ++++lr++++e+e+a++++d+el++alelaae+i++fh++q
  lcl|NCBI__GCF_000009985.1:WP_011385702.1  34 VAAILAEVRSRGDAALIEYTARFDRLelTPATLRITAQEVETAYASCDPELIRALELAAERIRAFHARQ 102
                                               789*********************99667889************************************* PP

                                 TIGR00069  68 lpesveveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnp 136
                                               +p + + ++++gv lg ++ p++++glYvPgG+aaypS+vlm+a+pAk Agv+++v+v P    g +np
  lcl|NCBI__GCF_000009985.1:WP_011385702.1 103 VPVDDSFTDAAGVRLGLRWSPVSAAGLYVPGGTAAYPSSVLMNAIPAKAAGVERLVMVVPSP-GGVLNP 170
                                               ****9********************************************************6.999*** PP

                                 TIGR00069 137 avlaaakllgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEv 205
                                                vlaaak++gvde+y+vGGaqa++alayGt t+++vdkivGPGn++V+aAK+ vfg+vgidmiaGPsE+
  lcl|NCBI__GCF_000009985.1:WP_011385702.1 171 LVLAAAKVAGVDEIYRVGGAQAVGALAYGTGTIRPVDKIVGPGNAWVAAAKRRVFGTVGIDMIAGPSEI 239
                                               ********************************************************************* PP

                                 TIGR00069 206 lviadesanpelvaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekngai 274
                                               lv+ad+  +p+++aaDllsqaEHd+ aq+il+t+++e+ ++v ++ve++l++l+r++ia++s++++gai
  lcl|NCBI__GCF_000009985.1:WP_011385702.1 240 LVVADRFNDPSWIAADLLSQAEHDTAAQSILITDDAEFGQRVAAAVESHLATLPRAKIARESWDSHGAI 308
                                               ********************************************************************* PP

                                 TIGR00069 275 ilvddleealelsneyApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtAr 343
                                               i+v dle  l l++++ApEHLel++++p +l+ +++naG++flG+ytpea+gdy+ GpnhvLPT+++Ar
  lcl|NCBI__GCF_000009985.1:WP_011385702.1 309 IVVPDLEASLPLIDRIAPEHLELAVENPDALAARVRNAGAIFLGRYTPEAVGDYIGGPNHVLPTARSAR 377
                                               ********************************************************************* PP

                                 TIGR00069 344 fasglsvedFlkrisvqelskealeelaeaveklaeaEgLeaHaeavevR 393
                                               f+sgl+v dF+kr+++  ++ ++l+++++a+++laeaEgL aH  +v+ R
  lcl|NCBI__GCF_000009985.1:WP_011385702.1 378 FSSGLGVLDFMKRTTLLGCDADSLRAIGPAAVRLAEAEGLGAHGLSVALR 427
                                               ***********************************************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (433 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: 00:00:00.01
# Mc/sec: 10.85
//
[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