Alignments for a candidate for asd in Desulfatibacillum aliphaticivorans DSM 15576

GapMind for Amino acid biosynthesis

Alignments for a candidate for asd in Desulfatibacillum aliphaticivorans DSM 15576

Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; Aspartate-beta-semialdehyde dehydrogenase; EC 1.2.1.11 (characterized)
to candidate WP_028313608.1 G491_RS0103640 aspartate-semialdehyde dehydrogenase

Query= SwissProt::Q51344
         (370 letters)



>NCBI__GCF_000429905.1:WP_028313608.1
          Length = 373

 Score =  488 bits (1256), Expect = e-142
 Identities = 237/371 (63%), Positives = 296/371 (79%), Gaps = 3/371 (0%)

Query: 1   MKRVGLIGWRGMVGSVLMQRMLEERDFDL--IEPVFFTTSNVGGQGPEVGKDIAPLKDAY 58
           M +V  +GWRGMVGSVLM RM  E DF    ++P+FFTTS  G + P+VG   + L+DA 
Sbjct: 1   MAKVAFVGWRGMVGSVLMDRMRAEGDFKTTGLDPLFFTTSQTGQKAPDVGLGESLLQDAM 60

Query: 59  SIDELKTLDVILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRMEDDAVIVLDPVNRKV 118
             D+L  +D+I+TCQG  YT E+ PKLR  GW GYWIDAAS++RM+DD+VIVLDPVNR V
Sbjct: 61  DADKLLPMDIIVTCQGSGYTKEMHPKLRSMGWDGYWIDAASAMRMDDDSVIVLDPVNRPV 120

Query: 119 IDQALDAGTRNYIGGNCTVSLMLMALGGLFDAGLVEWMSAMTYQAASGAGAQNMRELLKQ 178
           ID+AL +G + YIGGNCTVSLMLMALGGLF+ GLVEWM++MTYQAASGAGA+NMREL+ Q
Sbjct: 121 IDKALASGVKKYIGGNCTVSLMLMALGGLFENGLVEWMTSMTYQAASGAGAKNMRELIAQ 180

Query: 179 MGAAHASVADDLANPASAILDIDRKVAETLRSEAFPTEHFGAPLGGSLIPWIDKELPNGQ 238
           M +   +    L +PASAI D+DR V ET+RS  FPT++FG PL GS+IPWID ELP+GQ
Sbjct: 181 MASISGASKALLDDPASAIQDLDRTVLETMRSGDFPTDNFGVPLAGSVIPWIDSELPSGQ 240

Query: 239 SREEWKAQAETNKILARFKNPIPVDGICVRVGAMRCHSQALTIKLNKDVPLTDIEGLISQ 298
           SREEWK   ETNKIL   K  IP+DG+CVR+G+MRCHSQALTIKL KDVP+ +IE ++++
Sbjct: 241 SREEWKGLVETNKILGTEKQ-IPIDGLCVRIGSMRCHSQALTIKLTKDVPVDEIEDMLAK 299

Query: 299 HNPWVKLVPNHREVSVRELTPAAVTGTLSVPVGRLRKLNMGSQYLGAFTVGDQLLWGAAE 358
            N WV+++PN++  S++ L+P AVTG L VPVGR+ KLNMG +YLGAFTVGDQLLWGAAE
Sbjct: 300 ANDWVRVIPNNKADSMKLLSPTAVTGGLEVPVGRIHKLNMGPEYLGAFTVGDQLLWGAAE 359

Query: 359 PLRRMLRILLE 369
           PLRR+L+I+L+
Sbjct: 360 PLRRILQIILD 370


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: 481
Number of extensions: 10
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: 373
Length adjustment: 30
Effective length of query: 340
Effective length of database: 343
Effective search space:   116620
Effective search space used:   116620
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: 49 (23.5 bits)

Align candidate WP_028313608.1 G491_RS0103640 (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.16975.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     3e-177  575.0   0.1   3.5e-177  574.8   0.1    1.0  1  lcl|NCBI__GCF_000429905.1:WP_028313608.1  G491_RS0103640 aspartate-semiald


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000429905.1:WP_028313608.1  G491_RS0103640 aspartate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  574.8   0.1  3.5e-177  3.5e-177       2     365 ..       3     368 ..       2     369 .. 0.99

  Alignments for each domain:
  == domain 1  score: 574.8 bits;  conditional E-value: 3.5e-177
                                 TIGR01745   2 kvglvgwrgmvgsvllkrmqeekdfda..ikpvffstsqlgqkapslakisailedaydidalkeldii 68 
                                               kv +vgwrgmvgsvl++rm+ e df++  ++p+ff+tsq gqkap ++  ++ l+da+d d l  +dii
  lcl|NCBI__GCF_000429905.1:WP_028313608.1   3 KVAFVGWRGMVGSVLMDRMRAEGDFKTtgLDPLFFTTSQTGQKAPDVGLGESLLQDAMDADKLLPMDII 71 
                                               799**********************864479************************************** PP

                                 TIGR01745  69 itcqggdytkeiypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfvggnctvs 137
                                               +tcqg  ytke++pklr  gw+gywidaas++rm+dd+vi+ldpvn  vi+ a++ g+++++ggnctvs
  lcl|NCBI__GCF_000429905.1:WP_028313608.1  72 VTCQGSGYTKEMHPKLRSMGWDGYWIDAASAMRMDDDSVIVLDPVNRPVIDKALASGVKKYIGGNCTVS 140
                                               ********************************************************************* PP

                                 TIGR01745 138 lllmslgglfrdelvewvsvatyqaasgggarhmrellkqmgvlykeveeelakpssaileierkvtkl 206
                                               l+lm+lgglf+++lvew++++tyqaasg+ga+ mrel+ qm  + +  +  l  p+sai +++r v ++
  lcl|NCBI__GCF_000429905.1:WP_028313608.1 141 LMLMALGGLFENGLVEWMTSMTYQAASGAGAKNMRELIAQMASISGASKALLDDPASAIQDLDRTVLET 209
                                               ********************************************************************* PP

                                 TIGR01745 207 srseelpvenfsvplagslipwidkqldngqsreewkgqaetnkilgtkdtilvdglcvrigalrchsq 275
                                               +rs+++p++nf+vplags+ipwid +l  gqsreewkg  etnkilgt++ i++dglcvrig++rchsq
  lcl|NCBI__GCF_000429905.1:WP_028313608.1 210 MRSGDFPTDNFGVPLAGSVIPWIDSELPSGQSREEWKGLVETNKILGTEKQIPIDGLCVRIGSMRCHSQ 278
                                               ********************************************************************* PP

                                 TIGR01745 276 altiklkkdvsleeieeiirahnkwvkvvpnereitlreltpaavtgtldipvgrlrklnmgkeylsaf 344
                                               altikl kdv+++eie+++++ n+wv+v+pn++ ++++ l+p+avtg+l++pvgr+ klnmg+eyl af
  lcl|NCBI__GCF_000429905.1:WP_028313608.1 279 ALTIKLTKDVPVDEIEDMLAKANDWVRVIPNNKADSMKLLSPTAVTGGLEVPVGRIHKLNMGPEYLGAF 347
                                               ********************************************************************* PP

                                 TIGR01745 345 tvgdqllwgaaeplrrmlril 365
                                               tvgdqllwgaaeplrr+l+i+
  lcl|NCBI__GCF_000429905.1:WP_028313608.1 348 TVGDQLLWGAAEPLRRILQII 368
                                               ******************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (366 nodes)
Target sequences:                          1  (373 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: 12.33
//
[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