Alignments for a candidate for hisD in Thiomicrospira cyclica ALM1

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisD in Thiomicrospira cyclica ALM1

Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate WP_013835033.1 THICY_RS02430 histidinol dehydrogenase

Query= BRENDA::Q8G2R2
         (430 letters)



>NCBI__GCF_000214825.1:WP_013835033.1
          Length = 435

 Score =  412 bits (1060), Expect = e-120
 Identities = 220/421 (52%), Positives = 284/421 (67%), Gaps = 1/421 (0%)

Query: 9   DPDFEQKFAAFLSGKREVSEDVDRAVREIVDRVRREGDSALLDYSRRFDRIDL-EKTGIA 67
           + DF       LS +    + V++ V+E+V  VR+ G+ AL+DY+ +FD++ L +   + 
Sbjct: 13  EADFNTNMDQILSWESVSDDRVNQVVKEVVMDVRQRGNQALMDYTAKFDQLTLTDSAELE 72

Query: 68  VTEAEIDAAFDAAPASTVEALKLARDRIEKHHARQLPKDDRYTDALGVELGSRWTAIEAV 127
           +++A +  A    PA   EAL+L+  R+E +H RQ      Y +A G  LG + T ++ V
Sbjct: 73  ISQARLQQALANLPAEQREALELSAKRVEAYHLRQKSDSWSYEEADGTMLGQQVTPLDRV 132

Query: 128 GLYVPGGTASYPSSVLMNAMPAKVAGVDRIVMVVPAPDGNLNPLVLVAARLAGVSEIYRV 187
           GLYVPGG A+YPSSV+MNA+PAKVAGV  ++MVVP P G +N LVL AA + GV  ++ V
Sbjct: 133 GLYVPGGKAAYPSSVVMNAVPAKVAGVKELIMVVPTPRGEVNELVLAAAAICGVDRVFCV 192

Query: 188 GGAQAIAALAYGTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGPSEVLIVADKDN 247
           GGAQA+AALAYGTETI  V KIVGPGN YVA AKR+VFGTVGIDMIAGPSE+L+V D D 
Sbjct: 193 GGAQAVAALAYGTETIPAVDKIVGPGNIYVATAKRMVFGTVGIDMIAGPSEILVVCDGDT 252

Query: 248 NPDWIAADLLAQAEHDTAAQSILMTNDEAFAHAVEEAVERQLHTLARTETASASWRDFGA 307
           +PDWIA DL +QAEHD  AQSIL+T D AFA  V E++ R L T+ R      +    GA
Sbjct: 253 DPDWIAMDLFSQAEHDEDAQSILVTPDAAFADKVIESMTRLLETMPRKNIIRTALEARGA 312

Query: 308 VILVKDFEDAIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTPEVIGDYVGGCN 367
           VI VKD E AI + N IA EHLE++V D +A +P+IR+AG+IF+G YT E +GDY  G N
Sbjct: 313 VITVKDMEQAIEMINLIAPEHLELSVDDPKAMLPKIRHAGAIFMGRYTAEALGDYCAGPN 372

Query: 368 HVLPTARSARFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEGLDAHAQSVAIR 427
           HVLPT+R+ARFSS L V D+ KR+SL+    E    LG  A  +A  EGL AHA S   R
Sbjct: 373 HVLPTSRTARFSSPLGVYDFQKRSSLIMCSPEGADTLGRTAAILADGEGLQAHAASARYR 432

Query: 428 L 428
           L
Sbjct: 433 L 433


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: 487
Number of extensions: 20
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: 435
Length adjustment: 32
Effective length of query: 398
Effective length of database: 403
Effective search space:   160394
Effective search space used:   160394
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_013835033.1 THICY_RS02430 (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.296741.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.4e-169  549.1   0.6     4e-169  548.9   0.6    1.0  1  NCBI__GCF_000214825.1:WP_013835033.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000214825.1:WP_013835033.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  548.9   0.6    4e-169    4e-169       1     393 []      38     432 ..      38     432 .. 0.99

  Alignments for each domain:
  == domain 1  score: 548.9 bits;  conditional E-value: 4e-169
                             TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkv...kleslrvseeeleealeavdeelkealelaaeniekfhekqlpe 70 
                                           vke++ dvr++G++Al++yt kfd++   + ++l++s+++l++al+++++e +ealel+a+++e++h +q+++
  NCBI__GCF_000214825.1:WP_013835033.1  38 VKEVVMDVRQRGNQALMDYTAKFDQLtltDSAELEISQARLQQALANLPAEQREALELSAKRVEAYHLRQKSD 110
                                           899**********************96666779**************************************** PP

                             TIGR00069  71 sveveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpavlaaak 143
                                           s+++e+++g++lgq+v+pl+rvglYvPgGkaaypS+v+m+avpAkvAgvke+++v P+  +g+vn+ vlaaa+
  NCBI__GCF_000214825.1:WP_013835033.1 111 SWSYEEADGTMLGQQVTPLDRVGLYVPGGKAAYPSSVVMNAVPAKVAGVKELIMVVPTP-RGEVNELVLAAAA 182
                                           **********************************************************6.9************ PP

                             TIGR00069 144 llgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEvlviadesanpe 216
                                           ++gvd+v+ vGGaqa+aalayGtet+p+vdkivGPGniyV++AK++vfg+vgidmiaGPsE+lv++d +++p+
  NCBI__GCF_000214825.1:WP_013835033.1 183 ICGVDRVFCVGGAQAVAALAYGTETIPAVDKIVGPGNIYVATAKRMVFGTVGIDMIAGPSEILVVCDGDTDPD 255
                                           ************************************************************************* PP

                             TIGR00069 217 lvaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekngaiilvddleealelsne 289
                                           ++a+Dl+sqaEHdedaq+ilvt+++++a+kv e++++ le+++rk+i++++le +ga+i+v+d+e+a+e++n 
  NCBI__GCF_000214825.1:WP_013835033.1 256 WIAMDLFSQAEHDEDAQSILVTPDAAFADKVIESMTRLLETMPRKNIIRTALEARGAVITVKDMEQAIEMINL 328
                                           ************************************************************************* PP

                             TIGR00069 290 yApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArfasglsvedFlkrisvqel 362
                                           +ApEHLel ++dp+++l+ki++aG++f+G+yt+ealgdy+aGpnhvLPTs+tArf+s+l+v+dF+kr+s++ +
  NCBI__GCF_000214825.1:WP_013835033.1 329 IAPEHLELSVDDPKAMLPKIRHAGAIFMGRYTAEALGDYCAGPNHVLPTSRTARFSSPLGVYDFQKRSSLIMC 401
                                           ************************************************************************* PP

                             TIGR00069 363 skealeelaeaveklaeaEgLeaHaeavevR 393
                                           s e++++l+++++ la+ EgL+aHa++++ R
  NCBI__GCF_000214825.1:WP_013835033.1 402 SPEGADTLGRTAAILADGEGLQAHAASARYR 432
                                           ***************************9988 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 30.65
//
[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 2024 update 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 original 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