Alignments for a candidate for asd in Caulobacter crescentus NA1000

GapMind for Amino acid biosynthesis

Alignments for a candidate for asd in Caulobacter crescentus NA1000

Align aspartate-semialdehyde dehydrogenase (EC 1.2.1.11) (characterized)
to candidate CCNA_03599 CCNA_03599 aspartate-semialdehyde dehydrogenase

Query= BRENDA::P9WNX5
         (345 letters)



>FitnessBrowser__Caulo:CCNA_03599
          Length = 348

 Score =  373 bits (958), Expect = e-108
 Identities = 208/338 (61%), Positives = 242/338 (71%), Gaps = 6/338 (1%)

Query: 5   IGIVGATGQVGQVMRTLLDERDFPASAVRFFASARSQGRKLAFRGQEIEVEDAETADPSG 64
           +G+VGATG VG +MR LL ERDFP +++R FASARS G K+ F GQ+I VEDA TAD SG
Sbjct: 13  VGVVGATGLVGGMMRELLVERDFPVASLRLFASARSAGGKIDFNGQQIVVEDAATADFSG 72

Query: 65  LDIALFSAGSAMSKVQAPRFAAAGVTVIDNSSAWRKDPDVPLVVSEVNFERDAHRRPKGI 124
           LDI  FSAG + S+  AP+ AAAG  VIDNSSAWR DP+VPLVV+EVN        PKGI
Sbjct: 73  LDIVFFSAGGSTSRELAPKAAAAGAVVIDNSSAWRSDPEVPLVVAEVN-PHALQNIPKGI 131

Query: 125 IANPNCTTMAAMPVLKVLHDEARLVRLVVSSYQAVSGSGLAGVAELAEQARA-VIGGAEQ 183
           +ANPNCTTMAAMPVLK LHD+A L RL VS+YQA SG G+ G+  L+EQ RA   G  + 
Sbjct: 132 VANPNCTTMAAMPVLKPLHDKAGLKRLTVSTYQAASGGGMEGIEVLSEQLRAGAAGDLDG 191

Query: 184 LVYDGGALEFPPPNTYVAPIAFNVVPLAGSLVDDGSGETDEDQKLRFESRKILGIPDLLV 243
           L     A   P P  +  P+A+NVVPL   L +D  G T+E+ KLR ESRKIL IP L V
Sbjct: 192 LARSPDAAPLPAPRKWAVPLAYNVVPLNYVLGED--GYTEEELKLRDESRKILEIPGLPV 249

Query: 244 SGTCVRVPVFTGHSLSINAEFAQPLSPERARELLDGATGVQLVDVPTPLAAAGVDESLVG 303
           SGTCVRVPVFTGH+LSINAEF  P+S   A +LL  A GV + DVP PLAA G D   VG
Sbjct: 250 SGTCVRVPVFTGHALSINAEFDGPVSVAEALDLLAAAPGVVIDDVPNPLAATGQDPVFVG 309

Query: 304 RIRRDPGVPDGRGLALFVSGDNLRKGAALNTIQIAELL 341
           R+R DP VP   GLALFV GDNLRKGAALN +QIAE++
Sbjct: 310 RVRPDPTVP--HGLALFVVGDNLRKGAALNAVQIAEVM 345


Lambda     K      H
   0.317    0.135    0.382 

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: 441
Number of extensions: 24
Number of successful extensions: 5
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: 345
Length of database: 348
Length adjustment: 29
Effective length of query: 316
Effective length of database: 319
Effective search space:   100804
Effective search space used:   100804
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate CCNA_03599 CCNA_03599 (aspartate-semialdehyde dehydrogenase)
to HMM TIGR01296 (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/TIGR01296.hmm
# target sequence database:        /tmp/gapView.25498.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01296  [M=339]
Accession:   TIGR01296
Description: asd_B: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.7e-128  413.7   0.0   3.4e-128  413.5   0.0    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_03599  CCNA_03599 aspartate-semialdehyd


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_03599  CCNA_03599 aspartate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  413.5   0.0  3.4e-128  3.4e-128       1     336 [.      12     345 ..      12     347 .. 0.96

  Alignments for each domain:
  == domain 1  score: 413.5 bits;  conditional E-value: 3.4e-128
                             TIGR01296   1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsaGgsv 73 
                                           +v++vGatG vG  ++++L er+fp+ +l+l+as+rsaG k+ f+g+++ ve+a +++f+g+di +fsaGgs+
  lcl|FitnessBrowser__Caulo:CCNA_03599  12 HVGVVGATGLVGGMMRELLVERDFPVASLRLFASARSAGGKIDFNGQQIVVEDAATADFSGLDIVFFSAGGST 84 
                                           69*********************************************************************** PP

                             TIGR01296  74 skefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkplkdeaklk 146
                                           s+e+apkaa+ag++viDn+sa+r d++vPLvv+evn + l++ + kgi+anPnC+t+++++vLkpl+d+a+lk
  lcl|FitnessBrowser__Caulo:CCNA_03599  85 SRELAPKAAAAGAVVIDNSSAWRSDPEVPLVVAEVNPHALQNIP-KGIVANPNCTTMAAMPVLKPLHDKAGLK 156
                                           *******************************************9.**************************** PP

                             TIGR01296 147 rvvvstYqavsGaGkkgveeLknqtkav....legkekepeida.lkakkfakqiafnaiplidklkedGytk 214
                                           r+ vstYqa sG G +g+e L +q++a     l+g  ++p   + + + k+a ++a+n++pl   l edGyt+
  lcl|FitnessBrowser__Caulo:CCNA_03599 157 RLTVSTYQAASGGGMEGIEVLSEQLRAGaagdLDGLARSPDAAPlPAPRKWAVPLAYNVVPLNYVLGEDGYTE 229
                                           **************************97112244556666666458899************************ PP

                             TIGR01296 215 eelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvviddpsenlypt 287
                                           eelkl+ e+rkil+i+ l+vs+tcvrvPvftgh++s+++ef+ ++sv e+ +lL  apgvv+ d+p       
  lcl|FitnessBrowser__Caulo:CCNA_03599 230 EELKLRDESRKILEIPGLPVSGTCVRVPVFTGHALSINAEFDGPVSVAEALDLLAAAPGVVIDDVP------N 296
                                           ************************************************************999999......8 PP

                             TIGR01296 288 PleavgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaell 336
                                           Pl+a+g+d vfvgr+r D +  +glalfvv+DnlrkGaalnavqiae +
  lcl|FitnessBrowser__Caulo:CCNA_03599 297 PLAATGQDPVFVGRVRPDPTVPHGLALFVVGDNLRKGAALNAVQIAEVM 345
                                           **********************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (339 nodes)
Target sequences:                          1  (348 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: 10.22
//
[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