GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asd in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; Aspartate-beta-semialdehyde dehydrogenase; EC 1.2.1.11 (characterized)
to candidate WP_068173968.1 HTA01S_RS17205 aspartate-semialdehyde dehydrogenase

Query= SwissProt::Q51344
         (370 letters)



>NCBI__GCF_001592305.1:WP_068173968.1
          Length = 376

 Score =  502 bits (1293), Expect = e-147
 Identities = 247/372 (66%), Positives = 295/372 (79%), Gaps = 5/372 (1%)

Query: 2   KRVGLIGWRGMVGSVLMQRMLEERDFDLIEPVFFTTSNVGGQGPEVGKDIAPLKDAYSID 61
           K VGL+GWRGMVGSVLM RM+EE+DFDLIEP+FF+TSN GG+ P + K+   L+DA+ I 
Sbjct: 3   KLVGLVGWRGMVGSVLMDRMVEEKDFDLIEPLFFSTSNAGGKAPAMAKNETTLQDAHDIA 62

Query: 62  ELKTLDVILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRMEDDAVIVLDPVNRKVIDQ 121
            LK  D+++T QGGDYTSEVFPKLR AGW G+WIDAAS+LRME DAVI+LDPVN  VI  
Sbjct: 63  ALKRCDIVITAQGGDYTSEVFPKLRAAGWNGHWIDAASTLRMEKDAVIILDPVNMPVIKD 122

Query: 122 ALDAGTRNYIGGNCTVSLMLMALGGLFDAGLVEWMSAMTYQAASGAGAQNMRELLKQMGA 181
           AL  G +N++GGNCTVS MLM +G L+ AGLVEWMS  TYQAASG GAQ+MRELL Q G 
Sbjct: 123 ALANGGKNWVGGNCTVSCMLMGVGALYKAGLVEWMSTQTYQAASGGGAQHMRELLTQYGT 182

Query: 182 AHASVADDLANPASAILDIDRKVAETLRS-EAFPTEHFGAPLGGSLIPWIDKELPNGQSR 240
            +A V   L +P SAIL+IDRKV    R+  +  T +FG PLGGSLIPWIDK+L NG S+
Sbjct: 183 LNAEVKSLLDDPKSAILEIDRKVIAKQRALSSSETANFGVPLGGSLIPWIDKDLGNGMSK 242

Query: 241 EEWKAQAETNKILARFKN----PIPVDGICVRVGAMRCHSQALTIKLNKDVPLTDIEGLI 296
           EEWK  AETNKIL   +      IPVDG CVRVGAMRCHSQALT KL KDVP+ D+E +I
Sbjct: 243 EEWKGMAETNKILGMGEGFGSAAIPVDGFCVRVGAMRCHSQALTFKLRKDVPVADLEAMI 302

Query: 297 SQHNPWVKLVPNHREVSVRELTPAAVTGTLSVPVGRLRKLNMGSQYLGAFTVGDQLLWGA 356
           +  N WVK+VPN+RE ++++LTP AVTGT+++PVGR+RKL MG +Y+GAFT+GDQLLWGA
Sbjct: 303 AADNEWVKVVPNNREATIKDLTPVAVTGTMTIPVGRIRKLAMGPEYVGAFTIGDQLLWGA 362

Query: 357 AEPLRRMLRILL 368
           AEPLRRMLRILL
Sbjct: 363 AEPLRRMLRILL 374


Lambda     K      H
   0.319    0.136    0.409 

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: 535
Number of extensions: 20
Number of successful extensions: 3
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: 370
Length of database: 376
Length adjustment: 30
Effective length of query: 340
Effective length of database: 346
Effective search space:   117640
Effective search space used:   117640
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_068173968.1 HTA01S_RS17205 (aspartate-semialdehyde dehydrogenase)
to HMM TIGR01745 (asd: aspartate-semialdehyde dehydrogenase (EC 1.2.1.11))

# 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/TIGR01745.hmm
# target sequence database:        /tmp/gapView.2707235.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01745  [M=366]
Accession:   TIGR01745
Description: asd_gamma: aspartate-semialdehyde 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.8e-186  605.4   0.4     2e-186  605.2   0.4    1.0  1  NCBI__GCF_001592305.1:WP_068173968.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001592305.1:WP_068173968.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  605.2   0.4    2e-186    2e-186       2     366 .]       4     374 ..       3     374 .. 0.97

  Alignments for each domain:
  == domain 1  score: 605.2 bits;  conditional E-value: 2e-186
                             TIGR01745   2 kvglvgwrgmvgsvllkrmqeekdfdaikpvffstsqlgqkapslakisailedaydidalkeldiiitcqgg 74 
                                            vglvgwrgmvgsvl++rm+eekdfd+i+p+ffsts++g+kap++ak +++l+da+di alk++di+it qgg
  NCBI__GCF_001592305.1:WP_068173968.1   4 LVGLVGWRGMVGSVLMDRMVEEKDFDLIEPLFFSTSNAGGKAPAMAKNETTLQDAHDIAALKRCDIVITAQGG 76 
                                           69*********************************************************************** PP

                             TIGR01745  75 dytkeiypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfvggnctvslllmslgglf 147
                                           dyt+e++pklr+agw+g+widaas+lrm++daviildpvn+ vikda+++g +++vggnctvs +lm++g l+
  NCBI__GCF_001592305.1:WP_068173968.1  77 DYTSEVFPKLRAAGWNGHWIDAASTLRMEKDAVIILDPVNMPVIKDALANGGKNWVGGNCTVSCMLMGVGALY 149
                                           ************************************************************************* PP

                             TIGR01745 148 rdelvewvsvatyqaasgggarhmrellkqmgvlykeveeelakpssaileierkvtklsrs.eelpvenfsv 219
                                           + +lvew+s++tyqaasggga+hmrell+q g+l  ev++ l  p sailei+rkv    r+ +   + nf+v
  NCBI__GCF_001592305.1:WP_068173968.1 150 KAGLVEWMSTQTYQAASGGGAQHMRELLTQYGTLNAEVKSLLDDPKSAILEIDRKVIAKQRAlSSSETANFGV 222
                                           ********************************************************9999972456799**** PP

                             TIGR01745 220 plagslipwidkqldngqsreewkgqaetnkilgt.....kdtilvdglcvrigalrchsqaltiklkkdvsl 287
                                           pl gslipwidk+l ng s+eewkg aetnkilg      + +i+vdg cvr+ga+rchsqalt+kl+kdv++
  NCBI__GCF_001592305.1:WP_068173968.1 223 PLGGSLIPWIDKDLGNGMSKEEWKGMAETNKILGMgegfgSAAIPVDGFCVRVGAMRCHSQALTFKLRKDVPV 295
                                           *********************************9633333679****************************** PP

                             TIGR01745 288 eeieeiirahnkwvkvvpnereitlreltpaavtgtldipvgrlrklnmgkeylsaftvgdqllwgaaeplrr 360
                                            ++e +i+a+n+wvkvvpn+re t+++ltp avtgt++ipvgr+rkl mg+ey+ aft+gdqllwgaaeplrr
  NCBI__GCF_001592305.1:WP_068173968.1 296 ADLEAMIAADNEWVKVVPNNREATIKDLTPVAVTGTMTIPVGRIRKLAMGPEYVGAFTIGDQLLWGAAEPLRR 368
                                           ************************************************************************* PP

                             TIGR01745 361 mlrill 366
                                           mlrill
  NCBI__GCF_001592305.1:WP_068173968.1 369 MLRILL 374
                                           ****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (366 nodes)
Target sequences:                          1  (376 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: 18.87
//
[ok]

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

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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