GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hcs in Azoarcus olearius BH72

Align Homocitrate synthase; EC 2.3.3.14 (characterized)
to candidate WP_011764286.1 AZO_RS02775 homocitrate synthase

Query= SwissProt::P05342
         (385 letters)



>NCBI__GCF_000061505.1:WP_011764286.1
          Length = 396

 Score =  393 bits (1010), Expect = e-114
 Identities = 214/374 (57%), Positives = 258/374 (68%), Gaps = 5/374 (1%)

Query: 2   ASVIIDDTTLRDGEQSAGVAFNADEKIAIARALAELGVPELEIGIPSMGEEE----REVM 57
           A V IDDTTLRDGEQSAGVAF   EK  IAR LAE+GVPELEIGIP+MG EE    R + 
Sbjct: 3   APVTIDDTTLRDGEQSAGVAFTRAEKCGIARILAEIGVPELEIGIPAMGSEECGDIRAIA 62

Query: 58  HAIAGLGLSSRLLAWCRLCDVDLAAARSTGVTMVDLSLPVSDLMLHHKLNRDRDWALREV 117
             +A  G  +RL+ W RL   D+ A RS  V M++LS+PVSD  + HKL   RD  L  +
Sbjct: 63  DTLADGGHDTRLIVWGRLTSADIDACRSLPVQMLELSVPVSDQQIRHKLGATRDEVLARI 122

Query: 118 ARLVGEARMAGLEVCLGCEDASRADLEFVVQVGEVAQAAGARRLRFADTVGVMEPFGMLD 177
           AR V  AR AG +V +G EDASRAD  F+ +V + A+AAGARR RFADT+G+++PF   +
Sbjct: 123 ARWVPVAREAGFDVGVGGEDASRADPAFLAEVIQAAEAAGARRFRFADTLGILDPFATFE 182

Query: 178 RFRFLSRRLDMELEVHAHDDFGLATANTLAAVMGGATHINTTVNGLGERAGNAALEECVL 237
             R L     +E+E+HAHDD GLATANTLAAV  GA+H+NTTVNGLGERAGNAALEE  L
Sbjct: 183 AIRALRAASKLEIEMHAHDDLGLATANTLAAVRAGASHVNTTVNGLGERAGNAALEEVAL 242

Query: 238 ALKNLHGIDTGIDTRGIPAISALVERASGRQVAWQKSVVGAGVFTHEAGIHVDGLLKHRR 297
            L+  HG+   ID   +   S  V RASGR V W KSVVG GVFTHEAGIHVDGLLK   
Sbjct: 243 GLRQFHGMGEIIDFTRLLDTSEAVARASGRPVGWHKSVVGEGVFTHEAGIHVDGLLKDPA 302

Query: 298 NYEGLNPDELGRSHSLVLGKHSGAHMVRNTYRDLGIELADWQSQALLGRIRAFSTRTKRR 357
           NY+G++P  LGRSH ++LGKHSG   V   Y  LGIEL   ++  LL RIR F++RTK R
Sbjct: 303 NYQGIDPALLGRSHRMLLGKHSGGRGVAAAYAGLGIELDAARTACLLARIREFTSRTK-R 361

Query: 358 SPQPAELQDFYRQL 371
           +PQ  +L  F+ +L
Sbjct: 362 TPQREDLLAFWEEL 375


Lambda     K      H
   0.320    0.135    0.396 

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: 511
Number of extensions: 22
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: 385
Length of database: 396
Length adjustment: 31
Effective length of query: 354
Effective length of database: 365
Effective search space:   129210
Effective search space used:   129210
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate WP_011764286.1 AZO_RS02775 (homocitrate synthase)
to HMM TIGR02660 (nifV: homocitrate synthase (EC 2.3.3.14))

# 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/TIGR02660.hmm
# target sequence database:        /tmp/gapView.3960842.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02660  [M=365]
Accession:   TIGR02660
Description: nifV_homocitr: homocitrate synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     2e-156  506.8   1.5   2.2e-156  506.6   1.5    1.0  1  NCBI__GCF_000061505.1:WP_011764286.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000061505.1:WP_011764286.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  506.6   1.5  2.2e-156  2.2e-156       2     364 ..       5     371 ..       4     372 .. 0.98

  Alignments for each domain:
  == domain 1  score: 506.6 bits;  conditional E-value: 2.2e-156
                             TIGR02660   2 vlinDttLRDGEqaagvaFsaeEKlaiAkaLdeaGvdelEvGipamgeeEraairaiaal....glkarllaW 70 
                                           v+i+DttLRDGEq+agvaF+++EK+ iA++L+e+Gv+elE+Gipamg+eE+ +iraia++    g+++rl++W
  NCBI__GCF_000061505.1:WP_011764286.1   5 VTIDDTTLRDGEQSAGVAFTRAEKCGIARILAEIGVPELEIGIPAMGSEECGDIRAIADTladgGHDTRLIVW 77 
                                           89*******************************************************98722225689***** PP

                             TIGR02660  71 cRlraedieaaaevGvkavdlsvpvsdlqleaklkkdrawvleelkelvslakeeglkvsvgaeDasRadeef 143
                                            Rl+++di+a +++ v++++lsvpvsd+q+++kl  +r+ vl+++++ v +a+e+g +v vg+eDasRad++f
  NCBI__GCF_000061505.1:WP_011764286.1  78 GRLTSADIDACRSLPVQMLELSVPVSDQQIRHKLGATRDEVLARIARWVPVAREAGFDVGVGGEDASRADPAF 150
                                           ************************************************************************* PP

                             TIGR02660 144 lvelaevakeagakRlRfaDtvgvldPfstyelvkalraalelelElHaHnDlGlAtAntlaavkaGassvsv 216
                                           l+e+++ a++aga+R+RfaDt+g+ldPf+t+e+++alraa++le+E+HaH+DlGlAtAntlaav+aGas+v++
  NCBI__GCF_000061505.1:WP_011764286.1 151 LAEVIQAAEAAGARRFRFADTLGILDPFATFEAIRALRAASKLEIEMHAHDDLGLATANTLAAVRAGASHVNT 223
                                           ************************************************************************* PP

                             TIGR02660 217 tvlGlGERAGnAaleevalalkellgldtgidlselkelsqlvakasgraleaqkavvGesvFaHEsGiHvdg 289
                                           tv+GlGERAGnAaleeval+l++ +g+   id+++l   s++va+asgr++ ++k+vvGe vF+HE+GiHvdg
  NCBI__GCF_000061505.1:WP_011764286.1 224 TVNGLGERAGNAALEEVALGLRQFHGMGEIIDFTRLLDTSEAVARASGRPVGWHKSVVGEGVFTHEAGIHVDG 296
                                           ************************************************************************* PP

                             TIGR02660 290 llkdeatYesldPeevGrerelviGKHsgraaviealkelgleleeeeaeelleavravaerlKrsleeeela 362
                                           llkd+a+Y+++dP+++Gr++++ +GKHsg ++v++a++ lg+el++++++ ll+++r++++r+Kr++++e+l 
  NCBI__GCF_000061505.1:WP_011764286.1 297 LLKDPANYQGIDPALLGRSHRMLLGKHSGGRGVAAAYAGLGIELDAARTACLLARIREFTSRTKRTPQREDLL 369
                                           ***********************************************************************98 PP

                             TIGR02660 363 al 364
                                           a+
  NCBI__GCF_000061505.1:WP_011764286.1 370 AF 371
                                           76 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (396 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: 00:00:00.00
# Mc/sec: 20.93
//
[ok]

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

Links

Downloads

Related tools

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:

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:

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:

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:

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