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.12866.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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 6.89
//
[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:

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:

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:

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:

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