GapMind for Amino acid biosynthesis

 

Aligments for a candidate for asd in Paraburkholderia bryophila 376MFSha3.1

Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; Aspartate-beta-semialdehyde dehydrogenase; EC 1.2.1.11 (characterized)
to candidate H281DRAFT_06071 H281DRAFT_06071 aspartate semialdehyde dehydrogenase

Query= SwissProt::Q51344
         (370 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_06071 H281DRAFT_06071
           aspartate semialdehyde dehydrogenase
          Length = 373

 Score =  535 bits (1377), Expect = e-156
 Identities = 259/371 (69%), Positives = 306/371 (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  + 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: 542
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 H281DRAFT_06071 H281DRAFT_06071 (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.14026.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   8.1e-198  642.7   0.3   9.1e-198  642.5   0.3    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_06071  H281DRAFT_06071 aspartate semial


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_06071  H281DRAFT_06071 aspartate semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  642.5   0.3  9.1e-198  9.1e-198       1     365 [.       1     370 [.       1     371 [. 0.98

  Alignments for each domain:
  == domain 1  score: 642.5 bits;  conditional E-value: 9.1e-198
                                    TIGR01745   1 kkvglvgwrgmvgsvllkrmqeekdfdaikpvffstsqlgqkapslakisailedaydidalkeld 66 
                                                  ++vglvgwrgmvgsvl++rmq+e dfd+i+pvffsts++g++aps+ak ++ l+da  i+ lk+++
  lcl|FitnessBrowser__Burk376:H281DRAFT_06071   1 MNVGLVGWRGMVGSVLMQRMQQEGDFDLIEPVFFSTSNAGGNAPSFAKNETKLKDATSIEDLKKCE 66 
                                                  68**************************************************************** PP

                                    TIGR01745  67 iiitcqggdytkeiypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfvgg 132
                                                   ii+cqggdyt+e++pklr+agw+gywidaasslrmkddaviildpvnldvik+a+ kg ++f+gg
  lcl|FitnessBrowser__Burk376:H281DRAFT_06071  67 AIISCQGGDYTNEVFPKLRAAGWNGYWIDAASSLRMKDDAVIILDPVNLDVIKNALVKGQKNFIGG 132
                                                  ****************************************************************** PP

                                    TIGR01745 133 nctvslllmslgglfrdelvewvsvatyqaasgggarhmrellkqmgvlykeveeelakpssaile 198
                                                  nctvsl+lm+lgglfr++lv+w++++tyqaasg+ga+ mrell+qmg+ly+  +e+la pssail+
  lcl|FitnessBrowser__Burk376:H281DRAFT_06071 133 NCTVSLMLMALGGLFRENLVDWMTAMTYQAASGAGAQNMRELLQQMGTLYGAAKEDLADPSSAILD 198
                                                  ****************************************************************** PP

                                    TIGR01745 199 ierkvtklsrseelpvenfsvplagslipwidkqldngqsreewkgqaetnkilg.....tkdtil 259
                                                  i+r+v   + s+ +p++nf+vplagslipwidk+l ng s+eewkg aetnkilg     t   i+
  lcl|FitnessBrowser__Burk376:H281DRAFT_06071 199 IDRRVLSAMNSDRMPTDNFGVPLAGSLIPWIDKDLGNGMSKEEWKGGAETNKILGkpamgTPGSIP 264
                                                  *****************************************************96333337789** PP

                                    TIGR01745 260 vdglcvrigalrchsqaltiklkkdvsleeieeiirahnkwvkvvpnereitlreltpaavtgtld 325
                                                  vdglcvriga+rchsqaltikl+kdv+l+e+++i++++n+wvkvvpnere ++r+l+pa vtgtl+
  lcl|FitnessBrowser__Burk376:H281DRAFT_06071 265 VDGLCVRIGAMRCHSQALTIKLNKDVPLDEVNSILASGNDWVKVVPNEREASMRDLSPAVVTGTLT 330
                                                  ****************************************************************** PP

                                    TIGR01745 326 ipvgrlrklnmgkeylsaftvgdqllwgaaeplrrmlril 365
                                                  +pvgr+rkl mg eylsaftvgdqllwgaaeplrrmlri+
  lcl|FitnessBrowser__Burk376:H281DRAFT_06071 331 VPVGRVRKLAMGGEYLSAFTVGDQLLWGAAEPLRRMLRIV 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: 9.52
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see 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