Alignments for a candidate for asd in Derxia gummosa DSM 723

GapMind for Amino acid biosynthesis

Alignments for a candidate for asd in Derxia gummosa DSM 723

Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; Aspartate-beta-semialdehyde dehydrogenase; EC 1.2.1.11 (characterized)
to candidate WP_028312661.1 H566_RS0118875 aspartate-semialdehyde dehydrogenase

Query= SwissProt::Q51344
         (370 letters)



>NCBI__GCF_000482785.1:WP_028312661.1
          Length = 377

 Score =  493 bits (1268), Expect = e-144
 Identities = 248/373 (66%), Positives = 292/373 (78%), Gaps = 5/373 (1%)

Query: 2   KRVGLIGWRGMVGSVLMQRMLEERDFDLIEPVFFTTSNVGGQGPEVGKDIAPLKDAYSID 61
           K VGL+GWRGMVGSVLMQRM EE+DFD IEP+FF+TSN GG+ P   K+   L++A+ I+
Sbjct: 4   KLVGLVGWRGMVGSVLMQRMTEEKDFDHIEPLFFSTSNAGGKAPAQAKNETTLQNAFDIE 63

Query: 62  ELKTLDVILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRMEDDAVIVLDPVNRKVIDQ 121
            LK  D+ILT QGGDYT EVFPKLREAGW+G WIDAASSLRM DDA+IVLDPVN+ VI  
Sbjct: 64  ALKRCDIILTAQGGDYTKEVFPKLREAGWKGDWIDAASSLRMADDAIIVLDPVNKPVIKD 123

Query: 122 ALDAGTRNYIGGNCTVSLMLMALGGLFDAGLVEWMSAMTYQAASGAGAQNMRELLKQMGA 181
           A+  G +N+IGGNCTVS MLM +G LF A LVEWM++ TYQAASG GAQ+MRELL Q G 
Sbjct: 124 AMARGIKNWIGGNCTVSCMLMGVGALFKADLVEWMTSTTYQAASGGGAQHMRELLTQFGT 183

Query: 182 AHASVADDLANPASAILDIDRKV-AETLRSEAFPTEHFGAPLGGSLIPWIDKELPNGQSR 240
            +A V   L +PA AIL+IDRK+ A+     A  T++F  PL G+LIPWID +L +G SR
Sbjct: 184 LNAEVKSLLDDPAGAILEIDRKILAKQHALTAEETKNFLVPLAGNLIPWIDSDLGDGTSR 243

Query: 241 EEWKAQAETNKILAR----FKNPIPVDGICVRVGAMRCHSQALTIKLNKDVPLTDIEGLI 296
           EEWK  AETNKIL R         P+D ICVR+GAMRCHSQALTIKL KDVPL +IE +I
Sbjct: 244 EEWKGGAETNKILGRGAGFGSEATPIDSICVRIGAMRCHSQALTIKLKKDVPLAEIEDMI 303

Query: 297 SQHNPWVKLVPNHREVSVRELTPAAVTGTLSVPVGRLRKLNMGSQYLGAFTVGDQLLWGA 356
              N WVK+VPN +E S+R+LTPAA TGTL++PVGRLRK+ +G QYLGAFTVGDQLLWGA
Sbjct: 304 RNDNAWVKVVPNTKEASIRDLTPAATTGTLTIPVGRLRKMALGPQYLGAFTVGDQLLWGA 363

Query: 357 AEPLRRMLRILLE 369
           AEPLRRMLRIL+E
Sbjct: 364 AEPLRRMLRILIE 376


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: 530
Number of extensions: 19
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: 377
Length adjustment: 30
Effective length of query: 340
Effective length of database: 347
Effective search space:   117980
Effective search space used:   117980
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_028312661.1 H566_RS0118875 (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.30327.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.9e-185  601.4   0.1   3.3e-185  601.2   0.1    1.0  1  lcl|NCBI__GCF_000482785.1:WP_028312661.1  H566_RS0118875 aspartate-semiald


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000482785.1:WP_028312661.1  H566_RS0118875 aspartate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  601.2   0.1  3.3e-185  3.3e-185       2     366 .]       5     375 ..       4     375 .. 0.97

  Alignments for each domain:
  == domain 1  score: 601.2 bits;  conditional E-value: 3.3e-185
                                 TIGR01745   2 kvglvgwrgmvgsvllkrmqeekdfdaikpvffstsqlgqkapslakisailedaydidalkeldiiit 70 
                                                vglvgwrgmvgsvl++rm eekdfd+i+p+ffsts++g+kap+ ak +++l++a+di+alk++dii+t
  lcl|NCBI__GCF_000482785.1:WP_028312661.1   5 LVGLVGWRGMVGSVLMQRMTEEKDFDHIEPLFFSTSNAGGKAPAQAKNETTLQNAFDIEALKRCDIILT 73 
                                               69******************************************************************* PP

                                 TIGR01745  71 cqggdytkeiypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfvggnctvsll 139
                                                qggdytke++pklr+agwkg widaasslrm dda+i+ldpvn+ vikda+++gi++++ggnctvs +
  lcl|NCBI__GCF_000482785.1:WP_028312661.1  74 AQGGDYTKEVFPKLREAGWKGDWIDAASSLRMADDAIIVLDPVNKPVIKDAMARGIKNWIGGNCTVSCM 142
                                               ********************************************************************* PP

                                 TIGR01745 140 lmslgglfrdelvewvsvatyqaasgggarhmrellkqmgvlykeveeelakpssaileierkv.tkls 207
                                               lm++g lf+ +lvew++++tyqaasggga+hmrell+q+g+l  ev++ l  p+ ailei+rk+ +k  
  lcl|NCBI__GCF_000482785.1:WP_028312661.1 143 LMGVGALFKADLVEWMTSTTYQAASGGGAQHMRELLTQFGTLNAEVKSLLDDPAGAILEIDRKIlAKQH 211
                                               ***************************************************************834455 PP

                                 TIGR01745 208 rseelpvenfsvplagslipwidkqldngqsreewkgqaetnkilgt.....kdtilvdglcvrigalr 271
                                                 +   ++nf vplag+lipwid +l +g sreewkg aetnkilg      +++ ++d +cvriga+r
  lcl|NCBI__GCF_000482785.1:WP_028312661.1 212 ALTAEETKNFLVPLAGNLIPWIDSDLGDGTSREEWKGGAETNKILGRgagfgSEATPIDSICVRIGAMR 280
                                               5566789**************************************95333337899************* PP

                                 TIGR01745 272 chsqaltiklkkdvsleeieeiirahnkwvkvvpnereitlreltpaavtgtldipvgrlrklnmgkey 340
                                               chsqaltiklkkdv+l eie++ir++n wvkvvpn +e ++r+ltpaa tgtl+ipvgrlrk+ +g++y
  lcl|NCBI__GCF_000482785.1:WP_028312661.1 281 CHSQALTIKLKKDVPLAEIEDMIRNDNAWVKVVPNTKEASIRDLTPAATTGTLTIPVGRLRKMALGPQY 349
                                               ********************************************************************* PP

                                 TIGR01745 341 lsaftvgdqllwgaaeplrrmlrill 366
                                               l aftvgdqllwgaaeplrrmlril+
  lcl|NCBI__GCF_000482785.1:WP_028312661.1 350 LGAFTVGDQLLWGAAEPLRRMLRILI 375
                                               ************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (366 nodes)
Target sequences:                          1  (377 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: 7.73
//
[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