Alignments for a candidate for asd in Malonomonas rubra DSM 5091

GapMind for Amino acid biosynthesis

Alignments for a candidate for asd in Malonomonas rubra DSM 5091

Align aspartate-semialdehyde dehydrogenase (EC 1.2.1.11) (characterized)
to candidate WP_072909625.1 BUB13_RS15225 aspartate-semialdehyde dehydrogenase

Query= BRENDA::P44801
         (371 letters)



>NCBI__GCF_900142125.1:WP_072909625.1
          Length = 369

 Score =  499 bits (1284), Expect = e-146
 Identities = 240/366 (65%), Positives = 297/366 (81%), Gaps = 2/366 (0%)

Query: 4   VGFIGWRGMVGSVLMDRMSQENDFENLNPVFFTTSQAGQKAPVFGGKDAGDLKSAFDIEE 63
           VG +GWRGMVGSVLM RM +END   ++  FF+TSQAGQ AP FG      L+ A DI +
Sbjct: 3   VGLVGWRGMVGSVLMQRMVEENDLVGVDATFFSTSQAGQTAPDFGQTGGTTLEDASDITK 62

Query: 64  LKKLDIIVTCQGGDYTNEVYPKLKATGWDGYWVDAASALRMKDDAIIVLDPVNQHVISEG 123
           L + D+I+TCQGGDYT EV+PKL++ GW+GYW+DAAS+LRM+D+A+I+LDP N  VI E 
Sbjct: 63  LAEQDVIITCQGGDYTKEVHPKLRSGGWNGYWIDAASSLRMEDNAVIILDPTNLDVIEEA 122

Query: 124 LKKGIKTFVGGNCTVSLMLMAIGGLFEKDLVEWISVATYQAASGAGAKNMRELLSQMGLL 183
           LK G+K F+GGNCTVSLMLMAIGGLF+  LVEW+S  TYQAASGAGA NMRELLSQMG L
Sbjct: 123 LKNGVKDFIGGNCTVSLMLMAIGGLFKAGLVEWVSSMTYQAASGAGAPNMRELLSQMGYL 182

Query: 184 EQAVSSELKDPASSILDIERKVTAKMRADNFPTDNFGAALGGSLIPWIDKLLPETGQTKE 243
            ++V+ ELK P S+IL+I++KVTA +R+D  PT  FG  L GS++PWID+ + E GQ++E
Sbjct: 183 NESVAEELKTPGSAILEIDQKVTAALRSDGIPTAEFGFPLAGSVLPWIDREV-EDGQSRE 241

Query: 244 EWKGYAETNKILGLSDNPIPVDGLCVRIGALRCHSQAFTIKLKKDLPLEEIEQIIASHNE 303
           EWKG+ ETNKILG +  PIPVDG+CVRIGA+RCHSQA TIKL KDLP++EIEQII   N+
Sbjct: 242 EWKGFVETNKILG-NKTPIPVDGVCVRIGAMRCHSQALTIKLNKDLPIKEIEQIIDGDNQ 300

Query: 304 WVKVIPNDKEITLRELTPAKVTGTLSVPVGRLRKLAMGPEYLAAFTVGDQLLWGAAEPVR 363
           WVK++PN K  TL +LTP  V+GTLSVPVGR+RK+ MGP+YL+AFT GDQLLWGAAEP+R
Sbjct: 301 WVKLVPNKKAETLEQLTPTAVSGTLSVPVGRVRKMKMGPQYLSAFTCGDQLLWGAAEPLR 360

Query: 364 RILKQL 369
           R+L+ L
Sbjct: 361 RMLRIL 366


Lambda     K      H
   0.317    0.136    0.402 

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: 482
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: 371
Length of database: 369
Length adjustment: 30
Effective length of query: 341
Effective length of database: 339
Effective search space:   115599
Effective search space used:   115599
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate WP_072909625.1 BUB13_RS15225 (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.8102.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.5e-190  618.0   0.2   2.8e-190  617.9   0.2    1.0  1  lcl|NCBI__GCF_900142125.1:WP_072909625.1  BUB13_RS15225 aspartate-semialde


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900142125.1:WP_072909625.1  BUB13_RS15225 aspartate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  617.9   0.2  2.8e-190  2.8e-190       1     365 [.       1     366 [.       1     367 [. 0.99

  Alignments for each domain:
  == domain 1  score: 617.9 bits;  conditional E-value: 2.8e-190
                                 TIGR01745   1 kkvglvgwrgmvgsvllkrmqeekdfdaikpvffstsqlgqkapslakisa.iledaydidalkeldii 68 
                                               +kvglvgwrgmvgsvl++rm+ee+d+  +++ ffstsq+gq ap ++++ + +leda di  l e d+i
  lcl|NCBI__GCF_900142125.1:WP_072909625.1   1 MKVGLVGWRGMVGSVLMQRMVEENDLVGVDATFFSTSQAGQTAPDFGQTGGtTLEDASDITKLAEQDVI 69 
                                               69***********************************************9879**************** PP

                                 TIGR01745  69 itcqggdytkeiypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfvggnctvs 137
                                               itcqggdytke++pklr  gw+gywidaasslrm+d+aviildp nldvi++a+++g+++f+ggnctvs
  lcl|NCBI__GCF_900142125.1:WP_072909625.1  70 ITCQGGDYTKEVHPKLRSGGWNGYWIDAASSLRMEDNAVIILDPTNLDVIEEALKNGVKDFIGGNCTVS 138
                                               ********************************************************************* PP

                                 TIGR01745 138 lllmslgglfrdelvewvsvatyqaasgggarhmrellkqmgvlykeveeelakpssaileierkvtkl 206
                                               l+lm++gglf+ +lvewvs++tyqaasg+ga  mrell+qmg l ++v+eel +p sailei++kvt  
  lcl|NCBI__GCF_900142125.1:WP_072909625.1 139 LMLMAIGGLFKAGLVEWVSSMTYQAASGAGAPNMRELLSQMGYLNESVAEELKTPGSAILEIDQKVTAA 207
                                               ********************************************************************* PP

                                 TIGR01745 207 srseelpvenfsvplagslipwidkqldngqsreewkgqaetnkilgtkdtilvdglcvrigalrchsq 275
                                                rs+ +p+ +f+ plags++pwid+++++gqsreewkg  etnkilg k+ i+vdg+cvriga+rchsq
  lcl|NCBI__GCF_900142125.1:WP_072909625.1 208 LRSDGIPTAEFGFPLAGSVLPWIDREVEDGQSREEWKGFVETNKILGNKTPIPVDGVCVRIGAMRCHSQ 276
                                               ********************************************************************* PP

                                 TIGR01745 276 altiklkkdvsleeieeiirahnkwvkvvpnereitlreltpaavtgtldipvgrlrklnmgkeylsaf 344
                                               altikl+kd++++eie+ii  +n+wvk+vpn++  tl++ltp+av+gtl++pvgr+rk++mg++ylsaf
  lcl|NCBI__GCF_900142125.1:WP_072909625.1 277 ALTIKLNKDLPIKEIEQIIDGDNQWVKLVPNKKAETLEQLTPTAVSGTLSVPVGRVRKMKMGPQYLSAF 345
                                               ********************************************************************* PP

                                 TIGR01745 345 tvgdqllwgaaeplrrmlril 365
                                               t gdqllwgaaeplrrmlril
  lcl|NCBI__GCF_900142125.1:WP_072909625.1 346 TCGDQLLWGAAEPLRRMLRIL 366
                                               *******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (366 nodes)
Target sequences:                          1  (369 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.85
//
[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