Alignments for a candidate for asd in Hydrogenophaga taeniospiralis NBRC 102512

GapMind for Amino acid biosynthesis

Alignments for a candidate for asd in Hydrogenophaga taeniospiralis 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.9544.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  lcl|NCBI__GCF_001592305.1:WP_068173968.1  HTA01S_RS17205 aspartate-semiald


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001592305.1:WP_068173968.1  HTA01S_RS17205 aspartate-semialdehyde dehydrogenase
   #    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 kvglvgwrgmvgsvllkrmqeekdfdaikpvffstsqlgqkapslakisailedaydidalkeldiiit 70 
                                                vglvgwrgmvgsvl++rm+eekdfd+i+p+ffsts++g+kap++ak +++l+da+di alk++di+it
  lcl|NCBI__GCF_001592305.1:WP_068173968.1   4 LVGLVGWRGMVGSVLMDRMVEEKDFDLIEPLFFSTSNAGGKAPAMAKNETTLQDAHDIAALKRCDIVIT 72 
                                               69******************************************************************* PP

                                 TIGR01745  71 cqggdytkeiypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfvggnctvsll 139
                                                qggdyt+e++pklr+agw+g+widaas+lrm++daviildpvn+ vikda+++g +++vggnctvs +
  lcl|NCBI__GCF_001592305.1:WP_068173968.1  73 AQGGDYTSEVFPKLRAAGWNGHWIDAASTLRMEKDAVIILDPVNMPVIKDALANGGKNWVGGNCTVSCM 141
                                               ********************************************************************* PP

                                 TIGR01745 140 lmslgglfrdelvewvsvatyqaasgggarhmrellkqmgvlykeveeelakpssaileierkvtklsr 208
                                               lm++g l++ +lvew+s++tyqaasggga+hmrell+q g+l  ev++ l  p sailei+rkv    r
  lcl|NCBI__GCF_001592305.1:WP_068173968.1 142 LMGVGALYKAGLVEWMSTQTYQAASGGGAQHMRELLTQYGTLNAEVKSLLDDPKSAILEIDRKVIAKQR 210
                                               ****************************************************************99999 PP

                                 TIGR01745 209 s.eelpvenfsvplagslipwidkqldngqsreewkgqaetnkilgt.....kdtilvdglcvrigalr 271
                                               + +   + nf+vpl gslipwidk+l ng s+eewkg aetnkilg      + +i+vdg cvr+ga+r
  lcl|NCBI__GCF_001592305.1:WP_068173968.1 211 AlSSSETANFGVPLGGSLIPWIDKDLGNGMSKEEWKGMAETNKILGMgegfgSAAIPVDGFCVRVGAMR 279
                                               72456799*************************************9633333679************** PP

                                 TIGR01745 272 chsqaltiklkkdvsleeieeiirahnkwvkvvpnereitlreltpaavtgtldipvgrlrklnmgkey 340
                                               chsqalt+kl+kdv++ ++e +i+a+n+wvkvvpn+re t+++ltp avtgt++ipvgr+rkl mg+ey
  lcl|NCBI__GCF_001592305.1:WP_068173968.1 280 CHSQALTFKLRKDVPVADLEAMIAADNEWVKVVPNNREATIKDLTPVAVTGTMTIPVGRIRKLAMGPEY 348
                                               ********************************************************************* PP

                                 TIGR01745 341 lsaftvgdqllwgaaeplrrmlrill 366
                                               + aft+gdqllwgaaeplrrmlrill
  lcl|NCBI__GCF_001592305.1:WP_068173968.1 349 VGAFTIGDQLLWGAAEPLRRMLRILL 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.02
# Mc/sec: 6.68
//
[ok]

This GapMind analysis is from Apr 10 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