GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Escherichia coli BW25113

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate 15864 b1746 succinylglutamic semialdehyde dehydrogenase (NCBI)

Query= BRENDA::P76217
         (492 letters)



>FitnessBrowser__Keio:15864
          Length = 492

 Score =  991 bits (2563), Expect = 0.0
 Identities = 492/492 (100%), Positives = 492/492 (100%)

Query: 1   MTLWINGDWITGQGASRVKRNPVSGEVLWQGNDADAAQVEQACRAARAAFPRWARLSFAE 60
           MTLWINGDWITGQGASRVKRNPVSGEVLWQGNDADAAQVEQACRAARAAFPRWARLSFAE
Sbjct: 1   MTLWINGDWITGQGASRVKRNPVSGEVLWQGNDADAAQVEQACRAARAAFPRWARLSFAE 60

Query: 61  RHAVVERFAALLESNKAELTAIIARETGKPRWEAATEVTAMINKIAISIKAYHVRTGEQR 120
           RHAVVERFAALLESNKAELTAIIARETGKPRWEAATEVTAMINKIAISIKAYHVRTGEQR
Sbjct: 61  RHAVVERFAALLESNKAELTAIIARETGKPRWEAATEVTAMINKIAISIKAYHVRTGEQR 120

Query: 121 SEMPDGAASLRHRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNTIIFKPSELTPWSGEAV 180
           SEMPDGAASLRHRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNTIIFKPSELTPWSGEAV
Sbjct: 121 SEMPDGAASLRHRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNTIIFKPSELTPWSGEAV 180

Query: 181 MRLWQQAGLPPGVLNLVQGGRETGQALSALEDLDGLLFTGSANTGYQLHRQLSGQPEKIL 240
           MRLWQQAGLPPGVLNLVQGGRETGQALSALEDLDGLLFTGSANTGYQLHRQLSGQPEKIL
Sbjct: 181 MRLWQQAGLPPGVLNLVQGGRETGQALSALEDLDGLLFTGSANTGYQLHRQLSGQPEKIL 240

Query: 241 ALEMGGNNPLIIDEVADIDAAVHLTIQSAFVTAGQRCTCARRLLLKSGAQGDAFLARLVA 300
           ALEMGGNNPLIIDEVADIDAAVHLTIQSAFVTAGQRCTCARRLLLKSGAQGDAFLARLVA
Sbjct: 241 ALEMGGNNPLIIDEVADIDAAVHLTIQSAFVTAGQRCTCARRLLLKSGAQGDAFLARLVA 300

Query: 301 VSQRLTPGNWDDEPQPFIGGLISEQAAQQVVTAWQQLEAMGGRPLLAPRLLQAGTSLLTP 360
           VSQRLTPGNWDDEPQPFIGGLISEQAAQQVVTAWQQLEAMGGRPLLAPRLLQAGTSLLTP
Sbjct: 301 VSQRLTPGNWDDEPQPFIGGLISEQAAQQVVTAWQQLEAMGGRPLLAPRLLQAGTSLLTP 360

Query: 361 GIIEMTGVAGVPDEEVFGPLLRVWRYDTFDEAIRMANNTRFGLSCGLVSPEREKFDQLLL 420
           GIIEMTGVAGVPDEEVFGPLLRVWRYDTFDEAIRMANNTRFGLSCGLVSPEREKFDQLLL
Sbjct: 361 GIIEMTGVAGVPDEEVFGPLLRVWRYDTFDEAIRMANNTRFGLSCGLVSPEREKFDQLLL 420

Query: 421 EARAGIVNWNKPLTGAASTAPFGGIGASGNHRPSAWYAADYCAWPMASLESDSLTLPATL 480
           EARAGIVNWNKPLTGAASTAPFGGIGASGNHRPSAWYAADYCAWPMASLESDSLTLPATL
Sbjct: 421 EARAGIVNWNKPLTGAASTAPFGGIGASGNHRPSAWYAADYCAWPMASLESDSLTLPATL 480

Query: 481 NPGLDFSDEVVR 492
           NPGLDFSDEVVR
Sbjct: 481 NPGLDFSDEVVR 492


Lambda     K      H
   0.318    0.134    0.412 

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: 1050
Number of extensions: 36
Number of successful extensions: 1
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: 492
Length of database: 492
Length adjustment: 34
Effective length of query: 458
Effective length of database: 458
Effective search space:   209764
Effective search space used:   209764
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 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate 15864 b1746 (succinylglutamic semialdehyde dehydrogenase (NCBI))
to HMM TIGR03240 (astD: succinylglutamate-semialdehyde dehydrogenase (EC 1.2.1.71))

# 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.carbon/TIGR03240.hmm
# target sequence database:        /tmp/gapView.21365.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03240  [M=484]
Accession:   TIGR03240
Description: arg_catab_astD: succinylglutamate-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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
     1e-263  861.2   0.1   1.2e-263  861.0   0.1    1.0  1  lcl|FitnessBrowser__Keio:15864  b1746 succinylglutamic semialdeh


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:15864  b1746 succinylglutamic semialdehyde dehydrogenase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  861.0   0.1  1.2e-263  1.2e-263       1     484 []       3     486 ..       3     486 .. 1.00

  Alignments for each domain:
  == domain 1  score: 861.0 bits;  conditional E-value: 1.2e-263
                       TIGR03240   1 lfidGkwraGqGeslesldpvtqevlwqgkaasaaqvekavkaarkafpawarlsleeriavvkrfaelleeekeelae 79 
                                     l+i+G+w++GqG+s  +++pv++evlwqg++a+aaqve+a++aar+afp+warls++er avv+rfa+lle +k+el++
  lcl|FitnessBrowser__Keio:15864   3 LWINGDWITGQGASRVKRNPVSGEVLWQGNDADAAQVEQACRAARAAFPRWARLSFAERHAVVERFAALLESNKAELTA 81 
                                     59***************************************************************************** PP

                       TIGR03240  80 viaketgkplweartevasmvakvaisikayeertGekeseladakavlrhrphGvlavfGpynfpGhlpnGhivpall 158
                                     +ia+etgkp+wea+tev++m++k+aisikay+ rtGe++se++d++a lrhrphGvlavfGpynfpGhlpnGhivpall
  lcl|FitnessBrowser__Keio:15864  82 IIARETGKPRWEAATEVTAMINKIAISIKAYHVRTGEQRSEMPDGAASLRHRPHGVLAVFGPYNFPGHLPNGHIVPALL 160
                                     ******************************************************************************* PP

                       TIGR03240 159 aGntvvfkpseltplvaeetvklwekaGlpaGvlnlvqGaretGkalaaeedidGllftGssntGallhrqlagrpeki 237
                                     aGnt++fkpseltp+++e++++lw++aGlp GvlnlvqG+retG+al+a ed+dGllftGs+ntG++lhrql+g+peki
  lcl|FitnessBrowser__Keio:15864 161 AGNTIIFKPSELTPWSGEAVMRLWQQAGLPPGVLNLVQGGRETGQALSALEDLDGLLFTGSANTGYQLHRQLSGQPEKI 239
                                     ******************************************************************************* PP

                       TIGR03240 238 lalelGGnnplvveevkdidaavhlivqsafisaGqrctcarrllvkdgaeGdallerlvevaerltvgkydaepqpfl 316
                                     lale+GGnnpl+++ev+didaavhl++qsaf++aGqrctcarrll+k+ga+Gda+l+rlv+v++rlt g++d+epqpf+
  lcl|FitnessBrowser__Keio:15864 240 LALEMGGNNPLIIDEVADIDAAVHLTIQSAFVTAGQRCTCARRLLLKSGAQGDAFLARLVAVSQRLTPGNWDDEPQPFI 318
                                     ******************************************************************************* PP

                       TIGR03240 317 Gavisekaakellaaqekllalggksllelkqleeeaalltpgiidvtevaevpdeeyfgpllkvlrykdfdealaean 395
                                     G++ise+aa+++++a+++l+a+gg+ ll+ + l+++++lltpgii++t+va vpdee+fgpll+v+ry++fdea+++an
  lcl|FitnessBrowser__Keio:15864 319 GGLISEQAAQQVVTAWQQLEAMGGRPLLAPRLLQAGTSLLTPGIIEMTGVAGVPDEEVFGPLLRVWRYDTFDEAIRMAN 397
                                     ******************************************************************************* PP

                       TIGR03240 396 ntrfGlaaGllsddrelydkflleiraGivnwnkpltGassaapfGGiGasGnhrpsayyaadycaypvasleadslal 474
                                     ntrfGl++Gl+s++re++d++lle+raGivnwnkpltGa+s+apfGGiGasGnhrpsa+yaadyca+p+asle+dsl+l
  lcl|FitnessBrowser__Keio:15864 398 NTRFGLSCGLVSPEREKFDQLLLEARAGIVNWNKPLTGAASTAPFGGIGASGNHRPSAWYAADYCAWPMASLESDSLTL 476
                                     ******************************************************************************* PP

                       TIGR03240 475 patlspGlkl 484
                                     patl+pGl++
  lcl|FitnessBrowser__Keio:15864 477 PATLNPGLDF 486
                                     *******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (484 nodes)
Target sequences:                          1  (492 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 9.24
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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:

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