Alignments for a candidate for asd in Burkholderia phytofirmans PsJN

GapMind for Amino acid biosynthesis

Alignments for a candidate for asd in Burkholderia phytofirmans PsJN

Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; Aspartate-beta-semialdehyde dehydrogenase; EC 1.2.1.11 (characterized)
to candidate BPHYT_RS33895 BPHYT_RS33895 aspartate-semialdehyde dehydrogenase

Query= SwissProt::Q51344
         (370 letters)



>FitnessBrowser__BFirm:BPHYT_RS33895
          Length = 373

 Score =  536 bits (1381), Expect = e-157
 Identities = 260/371 (70%), Positives = 306/371 (82%), Gaps = 4/371 (1%)

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

Query: 64  KTLDVILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRMEDDAVIVLDPVNRKVIDQAL 123
           K  + I++CQGGDYT+EVFPKLR AGW GYWIDAASSLRM+DDAVI+LDPVN  VI  AL
Sbjct: 63  KKCEAIISCQGGDYTNEVFPKLRAAGWNGYWIDAASSLRMKDDAVIILDPVNLDVIKNAL 122

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

Query: 184 ASVADDLANPASAILDIDRKVAETLRSEAFPTEHFGAPLGGSLIPWIDKELPNGQSREEW 243
            +  +DLA+P+SAILDIDR+V   + S+  PT++FG PL GSLIPWIDK+L NG S+EEW
Sbjct: 183 GAAKEDLADPSSAILDIDRRVLSAMNSDRMPTDNFGVPLAGSLIPWIDKDLGNGMSKEEW 242

Query: 244 KAQAETNKILAR----FKNPIPVDGICVRVGAMRCHSQALTIKLNKDVPLTDIEGLISQH 299
           K  AETNKIL +        IPVDG+CVR+GAMRCHSQALTIKLNKDVPL ++  +++  
Sbjct: 243 KGGAETNKILGKPAMGTPGSIPVDGLCVRIGAMRCHSQALTIKLNKDVPLDEVNSILASG 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: 546
Number of extensions: 12
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 BPHYT_RS33895 BPHYT_RS33895 (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.20982.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
     5e-198  643.4   0.3   5.6e-198  643.2   0.3    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS33895  BPHYT_RS33895 aspartate-semialde


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS33895  BPHYT_RS33895 aspartate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  643.2   0.3  5.6e-198  5.6e-198       1     365 [.       1     370 [.       1     371 [. 0.98

  Alignments for each domain:
  == domain 1  score: 643.2 bits;  conditional E-value: 5.6e-198
                                TIGR01745   1 kkvglvgwrgmvgsvllkrmqeekdfdaikpvffstsqlgqkapslakisailedaydidalkeldiiit 70 
                                              ++vglvgwrgmvgsvl++rmq+e dfd+i+pvffsts++g++aps+ak ++ l+da  id lk+++ ii+
  lcl|FitnessBrowser__BFirm:BPHYT_RS33895   1 MNVGLVGWRGMVGSVLMQRMQQEGDFDLIEPVFFSTSNAGGNAPSFAKNETKLKDATSIDDLKKCEAIIS 70 
                                              68******************************************************************** PP

                                TIGR01745  71 cqggdytkeiypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfvggnctvslll 140
                                              cqggdyt+e++pklr+agw+gywidaasslrmkddaviildpvnldvik+a+ kg ++f+ggnctvsl+l
  lcl|FitnessBrowser__BFirm:BPHYT_RS33895  71 CQGGDYTNEVFPKLRAAGWNGYWIDAASSLRMKDDAVIILDPVNLDVIKNALVKGQKNFIGGNCTVSLML 140
                                              ********************************************************************** PP

                                TIGR01745 141 mslgglfrdelvewvsvatyqaasgggarhmrellkqmgvlykeveeelakpssaileierkvtklsrse 210
                                              m+lgglfr++lv+w++++tyqaasg+ga+ mrell+qmg+ly+  +e+la pssail+i+r+v   + s+
  lcl|FitnessBrowser__BFirm:BPHYT_RS33895 141 MALGGLFRENLVDWMTAMTYQAASGAGAQNMRELLQQMGTLYGAAKEDLADPSSAILDIDRRVLSAMNSD 210
                                              ********************************************************************** PP

                                TIGR01745 211 elpvenfsvplagslipwidkqldngqsreewkgqaetnkilg.....tkdtilvdglcvrigalrchsq 275
                                               +p++nf+vplagslipwidk+l ng s+eewkg aetnkilg     t   i+vdglcvriga+rchsq
  lcl|FitnessBrowser__BFirm:BPHYT_RS33895 211 RMPTDNFGVPLAGSLIPWIDKDLGNGMSKEEWKGGAETNKILGkpamgTPGSIPVDGLCVRIGAMRCHSQ 280
                                              *****************************************96333337789****************** PP

                                TIGR01745 276 altiklkkdvsleeieeiirahnkwvkvvpnereitlreltpaavtgtldipvgrlrklnmgkeylsaft 345
                                              altikl+kdv+l+e+++i++++n+wvkvvpnere ++r+l+pa vtgtl++pvgr+rkl mg eylsaft
  lcl|FitnessBrowser__BFirm:BPHYT_RS33895 281 ALTIKLNKDVPLDEVNSILASGNDWVKVVPNEREASMRDLSPAVVTGTLTVPVGRVRKLAMGGEYLSAFT 350
                                              ********************************************************************** PP

                                TIGR01745 346 vgdqllwgaaeplrrmlril 365
                                              vgdqllwgaaeplrrmlri+
  lcl|FitnessBrowser__BFirm:BPHYT_RS33895 351 VGDQLLWGAAEPLRRMLRIV 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.93
//
[ok]

This GapMind analysis is from Apr 09 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