Alignments for a candidate for asd in Burkholderia vietnamiensis G4

GapMind for Amino acid biosynthesis

Alignments for a candidate for asd in Burkholderia vietnamiensis G4

Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; Aspartate-beta-semialdehyde dehydrogenase; EC 1.2.1.11 (characterized)
to candidate WP_011881757.1 aspartate-semialdehyde dehydrogenase

Query= SwissProt::Q51344
         (370 letters)



>NCBI__GCF_000016205.1:WP_011881757.1
          Length = 373

 Score =  551 bits (1421), Expect = e-162
 Identities = 271/371 (73%), Positives = 307/371 (82%), Gaps = 4/371 (1%)

Query: 4   VGLIGWRGMVGSVLMQRMLEERDFDLIEPVFFTTSNVGGQGPEVGKDIAPLKDAYSIDEL 63
           VGL+GWRGMVGSVLMQRM EE DFDLIEPVFF+TSN GG+ P   K+   LKDA ++DEL
Sbjct: 3   VGLVGWRGMVGSVLMQRMQEEGDFDLIEPVFFSTSNTGGKAPSFAKNETTLKDATNVDEL 62

Query: 64  KTLDVILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRMEDDAVIVLDPVNRKVIDQAL 123
           K  DVI+TCQGGDYT+EVFPKLR AGW GYWIDAASSLRM DDAVI+LDPVN  VI  AL
Sbjct: 63  KKCDVIITCQGGDYTNEVFPKLRAAGWNGYWIDAASSLRMNDDAVIILDPVNLDVIKDAL 122

Query: 124 DAGTRNYIGGNCTVSLMLMALGGLFDAGLVEWMSAMTYQAASGAGAQNMRELLKQMGAAH 183
             GT+N++GGNCTVSLMLMALGGLF   LV+WM+AMTYQAASGAGAQNMRELL QMGA H
Sbjct: 123 VKGTKNFVGGNCTVSLMLMALGGLFRENLVDWMTAMTYQAASGAGAQNMRELLSQMGALH 182

Query: 184 ASVADDLANPASAILDIDRKVAETLRSEAFPTEHFGAPLGGSLIPWIDKELPNGQSREEW 243
            SV   LA+PASAILDIDR+V  T+ S+A PT  FG PL GSLIPWIDK+L NG S+EEW
Sbjct: 183 GSVEQQLADPASAILDIDRRVLATMNSDAMPTSQFGVPLAGSLIPWIDKDLGNGMSKEEW 242

Query: 244 KAQAETNKILAR----FKNPIPVDGICVRVGAMRCHSQALTIKLNKDVPLTDIEGLISQH 299
           K  AETNKIL +        IPVDG+CVR+GAMRCHSQALTIKL KDVPL +I G+++  
Sbjct: 243 KGGAETNKILGKPAMGQPGSIPVDGLCVRIGAMRCHSQALTIKLKKDVPLDEINGILASA 302

Query: 300 NPWVKLVPNHREVSVRELTPAAVTGTLSVPVGRLRKLNMGSQYLGAFTVGDQLLWGAAEP 359
           N WVK+VPN RE S+R+L+PA +TGTL+VPVGRLRKL MG +YL AFTVGDQLLWGAAEP
Sbjct: 303 NDWVKVVPNEREASMRDLSPAKITGTLTVPVGRLRKLAMGGEYLSAFTVGDQLLWGAAEP 362

Query: 360 LRRMLRILLER 370
           LRRMLRILL++
Sbjct: 363 LRRMLRILLDK 373


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: 543
Number of extensions: 9
Number of successful extensions: 2
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_011881757.1 (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.2856345.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   9.6e-202  655.6   0.3   1.1e-201  655.4   0.3    1.0  1  NCBI__GCF_000016205.1:WP_011881757.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000016205.1:WP_011881757.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  655.4   0.3  1.1e-201  1.1e-201       1     366 []       1     371 [.       1     371 [. 0.98

  Alignments for each domain:
  == domain 1  score: 655.4 bits;  conditional E-value: 1.1e-201
                             TIGR01745   1 kkvglvgwrgmvgsvllkrmqeekdfdaikpvffstsqlgqkapslakisailedaydidalkeldiiitcqg 73 
                                           ++vglvgwrgmvgsvl++rmqee dfd+i+pvffsts+ g+kaps+ak +++l+da ++d lk++d+iitcqg
  NCBI__GCF_000016205.1:WP_011881757.1   1 MNVGLVGWRGMVGSVLMQRMQEEGDFDLIEPVFFSTSNTGGKAPSFAKNETTLKDATNVDELKKCDVIITCQG 73 
                                           68*********************************************************************** PP

                             TIGR01745  74 gdytkeiypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfvggnctvslllmslggl 146
                                           gdyt+e++pklr+agw+gywidaasslrm+ddaviildpvnldvikda+ kg+++fvggnctvsl+lm+lggl
  NCBI__GCF_000016205.1:WP_011881757.1  74 GDYTNEVFPKLRAAGWNGYWIDAASSLRMNDDAVIILDPVNLDVIKDALVKGTKNFVGGNCTVSLMLMALGGL 146
                                           ************************************************************************* PP

                             TIGR01745 147 frdelvewvsvatyqaasgggarhmrellkqmgvlykeveeelakpssaileierkvtklsrseelpvenfsv 219
                                           fr++lv+w++++tyqaasg+ga+ mrell+qmg l+++ve++la p+sail+i+r+v  ++ s+ +p+ +f+v
  NCBI__GCF_000016205.1:WP_011881757.1 147 FRENLVDWMTAMTYQAASGAGAQNMRELLSQMGALHGSVEQQLADPASAILDIDRRVLATMNSDAMPTSQFGV 219
                                           ************************************************************************* PP

                             TIGR01745 220 plagslipwidkqldngqsreewkgqaetnkilgtkd.....tilvdglcvrigalrchsqaltiklkkdvsl 287
                                           plagslipwidk+l ng s+eewkg aetnkilg         i+vdglcvriga+rchsqaltiklkkdv+l
  NCBI__GCF_000016205.1:WP_011881757.1 220 PLAGSLIPWIDKDLGNGMSKEEWKGGAETNKILGKPAmgqpgSIPVDGLCVRIGAMRCHSQALTIKLKKDVPL 292
                                           *********************************8654222227****************************** PP

                             TIGR01745 288 eeieeiirahnkwvkvvpnereitlreltpaavtgtldipvgrlrklnmgkeylsaftvgdqllwgaaeplrr 360
                                           +ei+ i+++ n+wvkvvpnere ++r+l+pa +tgtl++pvgrlrkl mg eylsaftvgdqllwgaaeplrr
  NCBI__GCF_000016205.1:WP_011881757.1 293 DEINGILASANDWVKVVPNEREASMRDLSPAKITGTLTVPVGRLRKLAMGGEYLSAFTVGDQLLWGAAEPLRR 365
                                           ************************************************************************* PP

                             TIGR01745 361 mlrill 366
                                           mlrill
  NCBI__GCF_000016205.1:WP_011881757.1 366 MLRILL 371
                                           ****96 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: 00:00:00.00
# Mc/sec: 26.19
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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