GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asd in Shewanella sp. ANA-3

Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate 7024285 Shewana3_1477 aspartate semialdehyde dehydrogenase (RefSeq)

Query= SwissProt::P23247
         (337 letters)



>FitnessBrowser__ANA3:7024285
          Length = 338

 Score =  481 bits (1239), Expect = e-141
 Identities = 236/338 (69%), Positives = 271/338 (80%), Gaps = 1/338 (0%)

Query: 1   MSQQFNVAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRFNGKTVRVQNVE 60
           MSQ+FNV + GA+GAVG+TM+E+L+ER FPV  L+ LAS RS G+T  F+GK V + +VE
Sbjct: 1   MSQEFNVVVLGASGAVGQTMIEILEERNFPVANLYPLASSRSAGETVSFHGKQVTILDVE 60

Query: 61  EFDWSQVHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAIAE 120
            FDWSQ  +  FSAGG++SAKWAPIAAEAG VVIDNTSHFRYD DIPLVVPEVNP AIA+
Sbjct: 61  TFDWSQAQLGFFSAGGDVSAKWAPIAAEAGCVVIDNTSHFRYDIDIPLVVPEVNPHAIAD 120

Query: 121 FRNRNIIANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKLL 180
           FRNRNIIANPNCSTIQMLVALKPIYD  GI RINV TYQSVSG GK  I+ELA Q  KLL
Sbjct: 121 FRNRNIIANPNCSTIQMLVALKPIYDTYGISRINVATYQSVSGTGKKAIEELAKQCTKLL 180

Query: 181 NGYPAETNTFSQQIAFNCIPQIDQFMDNGYTKEEMKMVWETQKIFNDPSIMVNPTCVRVP 240
            G PA+   + +QIAFN +PQID+FMDNGYTKEEMKMVWETQKIF D  I+VN T VRVP
Sbjct: 181 QGLPADAEVYPKQIAFNVLPQIDKFMDNGYTKEEMKMVWETQKIFGDDEILVNATAVRVP 240

Query: 241 VFYGHAEAVHVETRAPIDAEQVMDMLEQTDGIELFRGAD-FPTQVRDAGGKDHVLVGRVR 299
           VFYGH+EAVH+ETR P DAE +  +L   +G+ LF   D +PT V  A G D V VGRVR
Sbjct: 241 VFYGHSEAVHIETRQPADAEDIKALLRDAEGVVLFESDDEYPTAVTHAAGTDPVYVGRVR 300

Query: 300 NDISHHSGINLWVVADNVRKGAATNAVQIAELLVRDYF 337
            DISH  GINLWVV+DN+RKGAA N+VQIAE+LVRDY+
Sbjct: 301 KDISHSHGINLWVVSDNIRKGAALNSVQIAEILVRDYY 338


Lambda     K      H
   0.319    0.135    0.395 

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: 395
Number of extensions: 6
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: 337
Length of database: 338
Length adjustment: 28
Effective length of query: 309
Effective length of database: 310
Effective search space:    95790
Effective search space used:    95790
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 7024285 Shewana3_1477 (aspartate semialdehyde dehydrogenase (RefSeq))
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.15172.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   6.4e-137  442.1   0.1   7.2e-137  441.9   0.1    1.0  1  lcl|FitnessBrowser__ANA3:7024285  Shewana3_1477 aspartate semialde


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7024285  Shewana3_1477 aspartate semialdehyde dehydrogenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  441.9   0.1  7.2e-137  7.2e-137       1     338 [.       6     335 ..       6     336 .. 0.98

  Alignments for each domain:
  == domain 1  score: 441.9 bits;  conditional E-value: 7.2e-137
                         TIGR01296   1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsaGgsvskef 77 
                                       nv ++Ga+GavGq+++++Leernfp+ +l++las+rsaG+ v f+gk++++ ++e+++ ++ ++ +fsaGg vs ++
  lcl|FitnessBrowser__ANA3:7024285   6 NVVVLGASGAVGQTMIEILEERNFPVANLYPLASSRSAGETVSFHGKQVTILDVETFDWSQAQLGFFSAGGDVSAKW 82 
                                       689************************************************************************** PP

                         TIGR01296  78 apkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkplkdeaklkrvvvstYq 154
                                       ap aa+ag++viDnts fr d d+PLvvpevn + ++++++++iianPnCstiq++v+Lkp++d +++ r+ v+tYq
  lcl|FitnessBrowser__ANA3:7024285  83 APIAAEAGCVVIDNTSHFRYDIDIPLVVPEVNPHAIADFRNRNIIANPNCSTIQMLVALKPIYDTYGISRINVATYQ 159
                                       ***************************************************************************** PP

                         TIGR01296 155 avsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidklkedGytkeelkllfetrkilgied 231
                                       +vsG+Gkk++eeL++q    l+g   +       a+ ++kqiafn++p+idk++++Gytkee+k+++et+ki+g+++
  lcl|FitnessBrowser__ANA3:7024285 160 SVSGTGKKAIEELAKQCTKLLQGLPAD-------AEVYPKQIAFNVLPQIDKFMDNGYTKEEMKMVWETQKIFGDDE 229
                                       *****************9999988776.......799**************************************** PP

                         TIGR01296 232 lkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvviddpsenlyptPl.eavgkdevfvgrirkDls 307
                                       + v at+vrvPvf+ghse+v+ie+ +++++e++k lL++a+gvv+ + +  ++ypt + +a+g+d v+vgr+rkD+s
  lcl|FitnessBrowser__ANA3:7024285 230 ILVNATAVRVPVFYGHSEAVHIETRQPADAEDIKALLRDAEGVVLFESD--DEYPTAVtHAAGTDPVYVGRVRKDIS 304
                                       *********************************************9977..89**9973699*************** PP

                         TIGR01296 308 kekglalfvvaDnlrkGaalnavqiaellik 338
                                       +++g++l+vv+Dn+rkGaaln+vqiae l++
  lcl|FitnessBrowser__ANA3:7024285 305 HSHGINLWVVSDNIRKGAALNSVQIAEILVR 335
                                       ****************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (339 nodes)
Target sequences:                          1  (338 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 9.32
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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