Alignments for a candidate for asd in Dechloromonas agitata is5

GapMind for Amino acid biosynthesis

Alignments for a candidate for asd in Dechloromonas agitata is5

Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; Aspartate-beta-semialdehyde dehydrogenase; EC 1.2.1.11 (characterized)
to candidate WP_027456320.1 K420_RS0100500 aspartate-semialdehyde dehydrogenase

Query= SwissProt::Q51344
         (370 letters)



>NCBI__GCF_000519045.1:WP_027456320.1
          Length = 377

 Score =  516 bits (1328), Expect = e-151
 Identities = 260/376 (69%), Positives = 303/376 (80%), Gaps = 7/376 (1%)

Query: 1   MKRVGLIGWRGMVGSVLMQRMLEERDFDLIEPVFFTTSNVGGQGPEVGKDIA--PLKDAY 58
           MK+VGL+GWRGMVGSVLMQRM+EE DF  I+PV+F+TS  GG+ P  G   A  PL+DA 
Sbjct: 1   MKKVGLVGWRGMVGSVLMQRMVEEGDFAHIDPVYFSTSAAGGKAPVFGGKEASLPLQDAS 60

Query: 59  SIDELKTLDVILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRMEDDAVIVLDPVNRKV 118
           SI+ LK  D+++TCQGGDYT +VFPKLR AGW G+WIDAAS+LRM DDAVI+LDPVN  V
Sbjct: 61  SIEALKACDIVITCQGGDYTKDVFPKLRAAGWNGHWIDAASALRMADDAVIILDPVNMNV 120

Query: 119 IDQALDAGTRNYIGGNCTVSLMLMALGGLFDAGLVEWMSAMTYQAASGAGAQNMRELLKQ 178
           I  +L  G +N+IGGNCTVSLMLM LGGLF   LVEW ++MTYQAASGAGAQNMREL+ Q
Sbjct: 121 IKDSLAKGGKNWIGGNCTVSLMLMGLGGLFQNDLVEWATSMTYQAASGAGAQNMRELISQ 180

Query: 179 MGAAHASVADDLANPASAILDIDRKVAETLRSEAFPTEHF-GAPLGGSLIPWIDKELPNG 237
           MG  H SV D LA+PASAILDIDRKVAET+RS+ FP ++F   PL GSLIPWID  +  G
Sbjct: 181 MGVIHDSVKDLLADPASAILDIDRKVAETIRSDGFPKKNFRNTPLAGSLIPWIDVPVEGG 240

Query: 238 QSREEWKAQAETNKILAR--FK--NPIPVDGICVRVGAMRCHSQALTIKLNKDVPLTDIE 293
           QS+EEWK  AE NKIL R  FK    IP+DG+CVR+GAMRCHSQALTIKL KDVPL +I 
Sbjct: 241 QSKEEWKGGAECNKILGRPAFKTVGSIPIDGLCVRIGAMRCHSQALTIKLKKDVPLDEIS 300

Query: 294 GLISQHNPWVKLVPNHREVSVRELTPAAVTGTLSVPVGRLRKLNMGSQYLGAFTVGDQLL 353
            ++++ N W K+VPN RE+S RELTPAAVTGTL+VPVGRL K+ MG +YL AFT GDQLL
Sbjct: 301 DMLAKANQWAKVVPNEREISERELTPAAVTGTLTVPVGRLHKMAMGPEYLAAFTCGDQLL 360

Query: 354 WGAAEPLRRMLRILLE 369
           WGAAEPLRRMLRILL+
Sbjct: 361 WGAAEPLRRMLRILLD 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: 545
Number of extensions: 11
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: 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_027456320.1 K420_RS0100500 (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.15978.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.8e-193  627.3   0.1   4.4e-193  627.1   0.1    1.0  1  lcl|NCBI__GCF_000519045.1:WP_027456320.1  K420_RS0100500 aspartate-semiald


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000519045.1:WP_027456320.1  K420_RS0100500 aspartate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  627.1   0.1  4.4e-193  4.4e-193       1     366 []       2     375 ..       2     375 .. 0.98

  Alignments for each domain:
  == domain 1  score: 627.1 bits;  conditional E-value: 4.4e-193
                                 TIGR01745   1 kkvglvgwrgmvgsvllkrmqeekdfdaikpvffstsqlgqkapslakisa..iledaydidalkeldi 67 
                                               kkvglvgwrgmvgsvl++rm+ee df +i+pv+fsts +g+kap++++ +a  +l+da  i+alk++di
  lcl|NCBI__GCF_000519045.1:WP_027456320.1   2 KKVGLVGWRGMVGSVLMQRMVEEGDFAHIDPVYFSTSAAGGKAPVFGGKEAslPLQDASSIEALKACDI 70 
                                               69********************************************988775689************** PP

                                 TIGR01745  68 iitcqggdytkeiypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfvggnctv 136
                                               +itcqggdytk+++pklr+agw+g+widaas+lrm ddaviildpvn++vikd+++kg ++++ggnctv
  lcl|NCBI__GCF_000519045.1:WP_027456320.1  71 VITCQGGDYTKDVFPKLRAAGWNGHWIDAASALRMADDAVIILDPVNMNVIKDSLAKGGKNWIGGNCTV 139
                                               ********************************************************************* PP

                                 TIGR01745 137 slllmslgglfrdelvewvsvatyqaasgggarhmrellkqmgvlykeveeelakpssaileierkvtk 205
                                               sl+lm+lgglf+++lvew +++tyqaasg+ga+ mrel++qmgv++ +v++ la p+sail+i+rkv++
  lcl|NCBI__GCF_000519045.1:WP_027456320.1 140 SLMLMGLGGLFQNDLVEWATSMTYQAASGAGAQNMRELISQMGVIHDSVKDLLADPASAILDIDRKVAE 208
                                               ********************************************************************* PP

                                 TIGR01745 206 lsrseelpvenf.svplagslipwidkqldngqsreewkgqaetnkilg.....tkdtilvdglcvrig 268
                                               ++rs+ +p +nf ++plagslipwid  ++ gqs+eewkg ae nkilg     t   i++dglcvrig
  lcl|NCBI__GCF_000519045.1:WP_027456320.1 209 TIRSDGFPKKNFrNTPLAGSLIPWIDVPVEGGQSKEEWKGGAECNKILGrpafkTVGSIPIDGLCVRIG 277
                                               ************558********************************98555446778*********** PP

                                 TIGR01745 269 alrchsqaltiklkkdvsleeieeiirahnkwvkvvpnereitlreltpaavtgtldipvgrlrklnmg 337
                                               a+rchsqaltiklkkdv+l+ei +++++ n+w+kvvpnerei++reltpaavtgtl++pvgrl k+ mg
  lcl|NCBI__GCF_000519045.1:WP_027456320.1 278 AMRCHSQALTIKLKKDVPLDEISDMLAKANQWAKVVPNEREISERELTPAAVTGTLTVPVGRLHKMAMG 346
                                               ********************************************************************* PP

                                 TIGR01745 338 keylsaftvgdqllwgaaeplrrmlrill 366
                                               +eyl+aft gdqllwgaaeplrrmlrill
  lcl|NCBI__GCF_000519045.1:WP_027456320.1 347 PEYLAAFTCGDQLLWGAAEPLRRMLRILL 375
                                               ***************************96 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 10.62
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

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