Alignments for a candidate for hisD in Azospirillum sp. B510

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisD in Azospirillum sp. B510

Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate WP_012977992.1 AZL_RS29225 histidinol dehydrogenase

Query= BRENDA::Q8G2R2
         (430 letters)



>NCBI__GCF_000010725.1:WP_012977992.1
          Length = 434

 Score =  512 bits (1318), Expect = e-149
 Identities = 264/421 (62%), Positives = 322/421 (76%), Gaps = 1/421 (0%)

Query: 9   DPDFEQKFAAFLSGKREVSEDVDRAVREIVDRVRREGDSALLDYSRRFDRIDLEKTGIAV 68
           D +F   F A L  KRE SEDV   V  ++D+VR  GD AL++++ R+DR+ L    + +
Sbjct: 9   DAEFAAGFEALLHAKREASEDVQTLVAGVIDQVRSRGDDALIEFTARWDRLPLTPETLRI 68

Query: 69  TEAEIDAAFDAAPASTVEALKLARDRIEKHHARQLPKDDRYTDALGVELGSRWTAIEAVG 128
              EIDAA     A T+EAL LA  RIE  H RQ+P+   Y DA GV LG+RWTA+ AVG
Sbjct: 69  GRDEIDAATAKCSAGTLEALDLAAARIEAFHRRQIPEVTDYRDAAGVRLGARWTAVGAVG 128

Query: 129 LYVPGGTASYPSSVLMNAMPAKVAGVDRIVMVVPAPDGNLNPLVLVAARLAGVSEIYRVG 188
           LYVPGGTASYPSSVLMNA+PAKVAGV+R+VMVVP PDG +NPLVL AA+  G+ EIYR+G
Sbjct: 129 LYVPGGTASYPSSVLMNALPAKVAGVERVVMVVPTPDGAINPLVLAAAKRCGIDEIYRIG 188

Query: 189 GAQAIAALAYGTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGPSEVLIVADKDNN 248
           GAQA+AALA+GT TIRPV KIVGPGNA+VAAAKR V+G VGID IAGPSE+L+VAD  N+
Sbjct: 189 GAQAVAALAHGTATIRPVDKIVGPGNAFVAAAKRQVYGLVGIDSIAGPSEILVVADGKND 248

Query: 249 PDWIAADLLAQAEHDTAAQSILMTNDEAFAHAVEEAVERQLHTLARTETASASWRDFGAV 308
           P WIA DLL+QAEHD++AQSIL+T+D AFA AV  AV+R L TL R   A  SWR+ GA+
Sbjct: 249 PAWIAMDLLSQAEHDSSAQSILITDDAAFADAVAAAVDRHLETLPRRGIAGESWREHGAI 308

Query: 309 ILVKD-FEDAIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTPEVIGDYVGGCN 367
           +LV D   DA  L +R+A EHLE+AV D +A   RIRNAG+IF+G +TPE IGDYV G N
Sbjct: 309 LLVGDLMADAPALVDRLAPEHLELAVEDPDALAARIRNAGAIFLGRHTPEAIGDYVAGPN 368

Query: 368 HVLPTARSARFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEGLDAHAQSVAIR 427
           HVLPTARSARFSSGL+VLD+MKRT+ +   ++ LRA+GPAA+ +A AEGL+AHA+SVA R
Sbjct: 369 HVLPTARSARFSSGLNVLDFMKRTTFVACDADSLRAIGPAAVTLAMAEGLEAHARSVAQR 428

Query: 428 L 428
           L
Sbjct: 429 L 429


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: 553
Number of extensions: 23
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: 430
Length of database: 434
Length adjustment: 32
Effective length of query: 398
Effective length of database: 402
Effective search space:   159996
Effective search space used:   159996
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_012977992.1 AZL_RS29225 (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.132395.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.6e-161  523.2   0.1     3e-161  523.0   0.1    1.0  1  NCBI__GCF_000010725.1:WP_012977992.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000010725.1:WP_012977992.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  523.0   0.1    3e-161    3e-161       1     393 []      34     428 ..      34     428 .. 0.99

  Alignments for each domain:
  == domain 1  score: 523.0 bits;  conditional E-value: 3e-161
                             TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkv..kleslrvseeeleealeavdeelkealelaaeniekfhekqlpes 71 
                                           v+ +i++vr++Gd+Al+e+t ++d++  ++e+lr+ ++e+++a++++++ + eal+laa++ie+fh++q+pe 
  NCBI__GCF_000010725.1:WP_012977992.1  34 VAGVIDQVRSRGDDALIEFTARWDRLplTPETLRIGRDEIDAATAKCSAGTLEALDLAAARIEAFHRRQIPEV 106
                                           6789*********************98899******************************************* PP

                             TIGR00069  72 veveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpavlaaakl 144
                                           + +++++gv lg +++++ +vglYvPgG+a+ypS+vlm+a+pAkvAgv+++v+v P+  dg +np vlaaak 
  NCBI__GCF_000010725.1:WP_012977992.1 107 TDYRDAAGVRLGARWTAVGAVGLYVPGGTASYPSSVLMNALPAKVAGVERVVMVVPTP-DGAINPLVLAAAKR 178
                                           *********************************************************6.************** PP

                             TIGR00069 145 lgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEvlviadesanpel 217
                                           +g+de+y++GGaqa+aala+Gt+t+++vdkivGPGn++V+aAK++v+g vgid+iaGPsE+lv+ad + +p++
  NCBI__GCF_000010725.1:WP_012977992.1 179 CGIDEIYRIGGAQAVAALAHGTATIRPVDKIVGPGNAFVAAAKRQVYGLVGIDSIAGPSEILVVADGKNDPAW 251
                                           ************************************************************************* PP

                             TIGR00069 218 vaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekngaiilvddl.eealelsne 289
                                           +a+DllsqaEHd++aq+il+t+++++a++v ++v+++le+l+r+ ia +s++++gai+lv dl ++a +l+++
  NCBI__GCF_000010725.1:WP_012977992.1 252 IAMDLLSQAEHDSSAQSILITDDAAFADAVAAAVDRHLETLPRRGIAGESWREHGAILLVGDLmADAPALVDR 324
                                           ************************************************************986268999**** PP

                             TIGR00069 290 yApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArfasglsvedFlkrisvqel 362
                                           +ApEHLel+++dp +l+ +i+naG++flG++tpea+gdyvaGpnhvLPT+++Arf+sgl+v dF+kr++++ +
  NCBI__GCF_000010725.1:WP_012977992.1 325 LAPEHLELAVEDPDALAARIRNAGAIFLGRHTPEAIGDYVAGPNHVLPTARSARFSSGLNVLDFMKRTTFVAC 397
                                           ************************************************************************* PP

                             TIGR00069 363 skealeelaeaveklaeaEgLeaHaeavevR 393
                                           + ++l+++++a+++la aEgLeaHa++v++R
  NCBI__GCF_000010725.1:WP_012977992.1 398 DADSLRAIGPAAVTLAMAEGLEAHARSVAQR 428
                                           ****************************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (434 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: 00:00:00.00
# Mc/sec: 20.09
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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