Alignments for a candidate for astD in Escherichia coli BW25113

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.26342.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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 6.90
//
[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:

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

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 catabolism of small carbon sources