Alignments for a candidate for asd in Paraburkholderia sp. CCGE1002

GapMind for Amino acid biosynthesis

Alignments for a candidate for asd in Paraburkholderia sp. CCGE1002

Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; Aspartate-beta-semialdehyde dehydrogenase; EC 1.2.1.11 (characterized)
to candidate WP_013092939.1 BC1002_RS25770 aspartate-semialdehyde dehydrogenase

Query= SwissProt::Q51344
         (370 letters)



>NCBI__GCF_000092885.1:WP_013092939.1
          Length = 373

 Score =  543 bits (1398), Expect = e-159
 Identities = 263/371 (70%), Positives = 307/371 (82%), Gaps = 4/371 (1%)

Query: 4   VGLIGWRGMVGSVLMQRMLEERDFDLIEPVFFTTSNVGGQGPEVGKDIAPLKDAYSIDEL 63
           VGL+GWRGMVGSVLMQRM +E DFDLIEPVFF+TSN GG  P   K+   LKDA SI++L
Sbjct: 3   VGLVGWRGMVGSVLMQRMQQEGDFDLIEPVFFSTSNAGGNAPSFAKNETKLKDATSIEDL 62

Query: 64  KTLDVILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRMEDDAVIVLDPVNRKVIDQAL 123
           K  D I++CQGGDYT+EVFPKLR  GW GYWIDAASSLRM+DDAVI+LDPVN  VI  AL
Sbjct: 63  KKCDAIISCQGGDYTNEVFPKLRAVGWNGYWIDAASSLRMKDDAVIILDPVNLDVIKNAL 122

Query: 124 DAGTRNYIGGNCTVSLMLMALGGLFDAGLVEWMSAMTYQAASGAGAQNMRELLKQMGAAH 183
             G +N+IGGNCTVSLMLMALGGLF   LV+WM+AMTYQAASGAGAQNMRELL QMG  H
Sbjct: 123 VKGQKNFIGGNCTVSLMLMALGGLFRENLVDWMTAMTYQAASGAGAQNMRELLSQMGTLH 182

Query: 184 ASVADDLANPASAILDIDRKVAETLRSEAFPTEHFGAPLGGSLIPWIDKELPNGQSREEW 243
            +V ++LA+PASAILDIDR+V E + S++ PT+HFG PL GSLIPWIDK+L NG S+EEW
Sbjct: 183 GAVKNELADPASAILDIDRRVLEAMNSDSMPTDHFGVPLAGSLIPWIDKDLGNGMSKEEW 242

Query: 244 KAQAETNKILAR----FKNPIPVDGICVRVGAMRCHSQALTIKLNKDVPLTDIEGLISQH 299
           K  AETNKIL +        IPVDG+CVR+GAMRCHSQALTIKLNKDVPL ++  +++  
Sbjct: 243 KGGAETNKILGKPAMGTPGAIPVDGLCVRIGAMRCHSQALTIKLNKDVPLDEVNSILASG 302

Query: 300 NPWVKLVPNHREVSVRELTPAAVTGTLSVPVGRLRKLNMGSQYLGAFTVGDQLLWGAAEP 359
           N WVK+VPN RE S+R+L+PA VTGTL+VPVGR+RKL MG +YL AFTVGDQLLWGAAEP
Sbjct: 303 NDWVKVVPNEREASMRDLSPAVVTGTLTVPVGRVRKLAMGGEYLSAFTVGDQLLWGAAEP 362

Query: 360 LRRMLRILLER 370
           LRRMLRI+L++
Sbjct: 363 LRRMLRIVLDK 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: 537
Number of extensions: 11
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_013092939.1 BC1002_RS25770 (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.28888.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.4e-198  642.8   0.3   8.4e-198  642.6   0.3    1.0  1  lcl|NCBI__GCF_000092885.1:WP_013092939.1  BC1002_RS25770 aspartate-semiald


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000092885.1:WP_013092939.1  BC1002_RS25770 aspartate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  642.6   0.3  8.4e-198  8.4e-198       1     365 [.       1     370 [.       1     371 [. 0.98

  Alignments for each domain:
  == domain 1  score: 642.6 bits;  conditional E-value: 8.4e-198
                                 TIGR01745   1 kkvglvgwrgmvgsvllkrmqeekdfdaikpvffstsqlgqkapslakisailedaydidalkeldiii 69 
                                               ++vglvgwrgmvgsvl++rmq+e dfd+i+pvffsts++g++aps+ak ++ l+da  i+ lk++d ii
  lcl|NCBI__GCF_000092885.1:WP_013092939.1   1 MNVGLVGWRGMVGSVLMQRMQQEGDFDLIEPVFFSTSNAGGNAPSFAKNETKLKDATSIEDLKKCDAII 69 
                                               68******************************************************************* PP

                                 TIGR01745  70 tcqggdytkeiypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfvggnctvsl 138
                                               +cqggdyt+e++pklr+ gw+gywidaasslrmkddaviildpvnldvik+a+ kg ++f+ggnctvsl
  lcl|NCBI__GCF_000092885.1:WP_013092939.1  70 SCQGGDYTNEVFPKLRAVGWNGYWIDAASSLRMKDDAVIILDPVNLDVIKNALVKGQKNFIGGNCTVSL 138
                                               ********************************************************************* PP

                                 TIGR01745 139 llmslgglfrdelvewvsvatyqaasgggarhmrellkqmgvlykeveeelakpssaileierkvtkls 207
                                               +lm+lgglfr++lv+w++++tyqaasg+ga+ mrell+qmg+l++ v++ela p+sail+i+r+v + +
  lcl|NCBI__GCF_000092885.1:WP_013092939.1 139 MLMALGGLFRENLVDWMTAMTYQAASGAGAQNMRELLSQMGTLHGAVKNELADPASAILDIDRRVLEAM 207
                                               ********************************************************************* PP

                                 TIGR01745 208 rseelpvenfsvplagslipwidkqldngqsreewkgqaetnkilg.....tkdtilvdglcvrigalr 271
                                                s+ +p+++f+vplagslipwidk+l ng s+eewkg aetnkilg     t  +i+vdglcvriga+r
  lcl|NCBI__GCF_000092885.1:WP_013092939.1 208 NSDSMPTDHFGVPLAGSLIPWIDKDLGNGMSKEEWKGGAETNKILGkpamgTPGAIPVDGLCVRIGAMR 276
                                               ********************************************96333337789************** PP

                                 TIGR01745 272 chsqaltiklkkdvsleeieeiirahnkwvkvvpnereitlreltpaavtgtldipvgrlrklnmgkey 340
                                               chsqaltikl+kdv+l+e+++i++++n+wvkvvpnere ++r+l+pa vtgtl++pvgr+rkl mg ey
  lcl|NCBI__GCF_000092885.1:WP_013092939.1 277 CHSQALTIKLNKDVPLDEVNSILASGNDWVKVVPNEREASMRDLSPAVVTGTLTVPVGRVRKLAMGGEY 345
                                               ********************************************************************* PP

                                 TIGR01745 341 lsaftvgdqllwgaaeplrrmlril 365
                                               lsaftvgdqllwgaaeplrrmlri+
  lcl|NCBI__GCF_000092885.1:WP_013092939.1 346 LSAFTVGDQLLWGAAEPLRRMLRIV 370
                                               ***********************97 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 9.85
//
[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