Alignments for a candidate for hisD in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisD in Echinicola vietnamensis KMM 6221, DSM 17526

Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate Echvi_2459 Echvi_2459 histidinol dehydrogenase

Query= BRENDA::G7IKX3
         (478 letters)



>FitnessBrowser__Cola:Echvi_2459
          Length = 429

 Score =  400 bits (1028), Expect = e-116
 Identities = 216/429 (50%), Positives = 294/429 (68%), Gaps = 5/429 (1%)

Query: 48  LSNLTQTELLSLKSRPRIDFSSVFDIVNPIVDDVHAHGDAAVKQYTSKFDKVDLENIVEL 107
           ++N TQ+E     +RP      +  IV PI+  V   GD A+K++  ++D V+++N++  
Sbjct: 4   ITNPTQSEWQKELARPVQKMKDIQKIVKPIMRKVSRQGDKALKKFALEYDHVEIDNLLVS 63

Query: 108 VSDLPDPV--LDPAIKEAFDVAYSNIYAFHAAQKSPEKSVENMKGVQCKRVARSINSVGL 165
             ++ +    +D ++K A   A  NI  FH AQ++ + S+E M+GV C R +  I  VGL
Sbjct: 64  RDEINEAYEQVDESLKSAIQQAKVNIEKFHKAQQTEDLSMEVMEGVTCMRRSVPIQKVGL 123

Query: 166 YVPGGTAVLPSTALMLAVPAQIAGCKTIVLANPPTRDGTTCKEVLYCAKKAGVTHLLKAG 225
           Y+PGGTA L ST LML +PA IAGC+ IVL  PP ++G     +LY A   G+  ++KAG
Sbjct: 124 YIPGGTAPLFSTVLMLGIPANIAGCEEIVLCTPPNKEGKIHPAILYTANLIGIDKIVKAG 183

Query: 226 GAQAISAMAWGTETCPKVEKIFGPGNQYVTAAKMILQNSEAMVSIDMPAGPSEVLVIADK 285
           GAQAI+A+ +GTE+ P+V KIFGPGNQYVTAAK +   ++  ++IDMPAGPSEVLV AD+
Sbjct: 184 GAQAIAALTYGTESVPQVAKIFGPGNQYVTAAKQLA--TKKGIAIDMPAGPSEVLVYADE 241

Query: 286 HAIPSHVAADLLSQAEHGPDSQVVLVIAGDGVDQNAIQEEVSKQCQSLPRGEFAAKALSH 345
            A+P+ VAADLLSQAEHG DSQV+LV     V +  ++E V KQ   LPR + A KAL +
Sbjct: 242 SAVPAFVAADLLSQAEHGIDSQVILVATASKVAKKTLKE-VDKQLAKLPRKDIAKKALEN 300

Query: 346 SFIVHARDMLEAITFSNMYAPEHLIINVKDAEKWESFIENAGSVFLGSWTPESVGDYASG 405
           S  V   +  +AI   N YAPEHLIINV + ++  + I NAGSVF+G++TPES GDYASG
Sbjct: 301 SIAVVMGNQEKAIALINDYAPEHLIINVANEDEVVANIVNAGSVFIGNFTPESAGDYASG 360

Query: 406 TNHVLPTYGYARMYSGVSLDSFLKYITVQSLTEEGLRKLGPYVETMAEVEGLEAHKRAVT 465
           TNH LPTYG+AR YSGVSLDSF+K IT Q +TE+GL+ LGP +E MA  E L+AHK AV+
Sbjct: 361 TNHTLPTYGFARNYSGVSLDSFVKKITYQKITEKGLQNLGPTIEVMAGNELLDAHKNAVS 420

Query: 466 LRLQDIEAR 474
           +RL+ ++ +
Sbjct: 421 IRLKYLKEK 429


Lambda     K      H
   0.316    0.130    0.378 

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: 507
Number of extensions: 24
Number of successful extensions: 4
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: 478
Length of database: 429
Length adjustment: 33
Effective length of query: 445
Effective length of database: 396
Effective search space:   176220
Effective search space used:   176220
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 Echvi_2459 Echvi_2459 (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.19707.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   3.1e-162  526.2   7.3   3.6e-162  526.0   7.3    1.0  1  lcl|FitnessBrowser__Cola:Echvi_2459  Echvi_2459 histidinol dehydrogen


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_2459  Echvi_2459 histidinol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  526.0   7.3  3.6e-162  3.6e-162       1     393 []      30     422 ..      30     422 .. 0.99

  Alignments for each domain:
  == domain 1  score: 526.0 bits;  conditional E-value: 3.6e-162
                            TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkvkleslrvseeeleealeavdeelkealelaaeniekfhekqlpesvev 74 
                                          vk+i+++v ++Gd+Al++++ ++d+v++++l vs++e++ea+e+vde+lk+a+++a+ niekfh++q++e++++
  lcl|FitnessBrowser__Cola:Echvi_2459  30 VKPIMRKVSRQGDKALKKFALEYDHVEIDNLLVSRDEINEAYEQVDESLKSAIQQAKVNIEKFHKAQQTEDLSM 103
                                          899*********************************************************************** PP

                            TIGR00069  75 eteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpavlaaakllgvd 148
                                          e +egv++ ++ +p+++vglY+PgG+a+++Stvlm+++pA++Ag++eiv++tPp+k+gk++pa+l++a+l+g+d
  lcl|FitnessBrowser__Cola:Echvi_2459 104 EVMEGVTCMRRSVPIQKVGLYIPGGTAPLFSTVLMLGIPANIAGCEEIVLCTPPNKEGKIHPAILYTANLIGID 177
                                          ************************************************************************** PP

                            TIGR00069 149 evykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvf.gevgidmiaGPsEvlviadesanpelvaaD 221
                                          +++k+GGaqaiaal+yGte+vp+v ki+GPGn+yVtaAK+l + + ++idm+aGPsEvlv+adesa p++vaaD
  lcl|FitnessBrowser__Cola:Echvi_2459 178 KIVKAGGAQAIAALTYGTESVPQVAKIFGPGNQYVTAAKQLATkKGIAIDMPAGPSEVLVYADESAVPAFVAAD 251
                                          *****************************************99569**************************** PP

                            TIGR00069 222 llsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekngaiilvddleealelsneyApEHL 295
                                          llsqaEH+ d+q+ilv+t +++a+k+ +ev++ql++l+rk+ia+k+le n+  +++ + e+a++l+n+yApEHL
  lcl|FitnessBrowser__Cola:Echvi_2459 252 LLSQAEHGIDSQVILVATASKVAKKTLKEVDKQLAKLPRKDIAKKALE-NSIAVVMGNQEKAIALINDYAPEHL 324
                                          ************************************************.7888889****************** PP

                            TIGR00069 296 elqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArfasglsvedFlkrisvqelskealee 369
                                          +++++++ e++ +i naGsvf+G+ tpe++gdy++G+nh+LPT+g+Ar +sg+s+++F+k+i++q++++++l++
  lcl|FitnessBrowser__Cola:Echvi_2459 325 IINVANEDEVVANIVNAGSVFIGNFTPESAGDYASGTNHTLPTYGFARNYSGVSLDSFVKKITYQKITEKGLQN 398
                                          ************************************************************************** PP

                            TIGR00069 370 laeaveklaeaEgLeaHaeavevR 393
                                          l++++e +a  E L+aH++av++R
  lcl|FitnessBrowser__Cola:Echvi_2459 399 LGPTIEVMAGNELLDAHKNAVSIR 422
                                          **********************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (429 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: 12.92
//
[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