Alignments for a candidate for astD in Porphyrobacter dokdonensis DSW-74

GapMind for catabolism of small carbon sources

Alignments for a candidate for astD in Porphyrobacter dokdonensis DSW-74

Align N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized)
to candidate WP_068862716.1 I603_RS04800 succinylglutamate-semialdehyde dehydrogenase

Query= SwissProt::O50174
         (487 letters)



>NCBI__GCF_001677335.1:WP_068862716.1
          Length = 470

 Score =  456 bits (1173), Expect = e-133
 Identities = 244/469 (52%), Positives = 308/469 (65%), Gaps = 7/469 (1%)

Query: 18  LESLDPVGQGVVWSGRGADATQVDAAVCAAREAFPAWARRPLEQRIELLERFAATLKSRA 77
           L S +P     +W G   D   VDAAV  AR A+ AWA  PL  RIE L  FA  ++   
Sbjct: 6   LVSYEPASGEEIWRGNHGD---VDAAVSTARRAWGAWAALPLTNRIESLRAFANEVRREG 62

Query: 78  DELARVIGEETGKPLWESATEVTSMVNKVAISVQAFRERTGEKSGPLA-DATAVLRHKPH 136
           + LA +I  E GKPLWE+ TEV ++VNKV ISVQA+ ERTG+K      + +A +RHKPH
Sbjct: 63  EGLADLIAREAGKPLWEARTEVDAVVNKVDISVQAYAERTGKKKFDSGINGSAAVRHKPH 122

Query: 137 GVVAVFGPYNFPGHLPNGHIVPALLAGNCVVFKPSELTPKVAELTLKAWIQAGLPAGVLN 196
           GV+AV GPYNFP HLPNGHIVPAL+AGN V+FKPSE TP V E  +  + +AG+P  V+ 
Sbjct: 123 GVMAVLGPYNFPAHLPNGHIVPALIAGNAVIFKPSEKTPAVGEALVGCFHRAGVPEDVIQ 182

Query: 197 LVQGGRETGVALAAHRGLDGLFFTGSSRTGNLLHSQFGGQPQKILALEMGGNNPLVVEEV 256
           LV GG + G AL AH G+DG+ FTGS+  G  ++ +  G P KI+ALEMGGNNP+VV + 
Sbjct: 183 LVIGGPKEGKALVAHPGIDGVLFTGSADAGIAINRKLAGNPGKIVALEMGGNNPIVVIDT 242

Query: 257 ADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDALLARLVAVSATLRVGRFDEQPA 316
             L  A   I+QSAF SAGQRCT ARRL+V    + D L+A LV ++  L VG    +P 
Sbjct: 243 PKLADAATLIVQSAFTSAGQRCTAARRLIVKDSVYDD-LMAELVPLTRKLMVGNPVGEPQ 301

Query: 317 PFMGAVISLSAAEHLLKAQEHLIGKGAQPLLAMTQPIDGAALLTPGILDVSAVAERPDEE 376
           PFMG VI    A+ L+++   L+  G +PLL M + +     L+PGI+DV+ V +RPD E
Sbjct: 302 PFMGPVIDNETADRLMESFVTLMTAGGRPLLHMRRNVPDLPFLSPGIIDVTDVIDRPDLE 361

Query: 377 FFGPLLQVIRYSDFAAAIREANATQYGLAAGLLSDSRERFEQFLVESRAGIVNWNKQLTG 436
            FGPLLQVIR  D  A I EAN T++GL+A L+  + + + +F    RAGIVNWN    G
Sbjct: 362 LFGPLLQVIRVPDLDAGITEANNTRFGLSASLIGGTPDEYGRFWANIRAGIVNWNSPTNG 421

Query: 437 AASSAPFGGIGASGNHRPSAYYAADYCAYPVASLE--SPSVSLPATLTP 483
           A+S APFGGIG SGNHRP+AYYAADYCAYPVAS E   P  ++   L P
Sbjct: 422 ASSKAPFGGIGLSGNHRPAAYYAADYCAYPVASTEVDQPRATIGVGLRP 470


Lambda     K      H
   0.318    0.134    0.396 

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: 704
Number of extensions: 36
Number of successful extensions: 3
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: 487
Length of database: 470
Length adjustment: 34
Effective length of query: 453
Effective length of database: 436
Effective search space:   197508
Effective search space used:   197508
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: 51 (24.3 bits)

Align candidate WP_068862716.1 I603_RS04800 (succinylglutamate-semialdehyde dehydrogenase)
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.1624022.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.1e-188  612.3   0.0   3.8e-188  612.1   0.0    1.0  1  NCBI__GCF_001677335.1:WP_068862716.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001677335.1:WP_068862716.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  612.1   0.0  3.8e-188  3.8e-188      15     471 ..       6     459 ..       2     468 .. 0.97

  Alignments for each domain:
  == domain 1  score: 612.1 bits;  conditional E-value: 3.8e-188
                             TIGR03240  15 lesldpvtqevlwqgkaasaaqvekavkaarkafpawarlsleeriavvkrfaelleeekeelaeviaketgk 87 
                                           l s +p+++e++w+g+     +v++av +ar+a+ awa+l+l +ri+ ++ fa+ +++e e la++ia+e+gk
  NCBI__GCF_001677335.1:WP_068862716.1   6 LVSYEPASGEEIWRGNH---GDVDAAVSTARRAWGAWAALPLTNRIESLRAFANEVRREGEGLADLIAREAGK 75 
                                           67899*********985...689************************************************** PP

                             TIGR03240  88 plweartevasmvakvaisikayeertGekesela.dakavlrhrphGvlavfGpynfpGhlpnGhivpalla 159
                                           plweartev ++v+kv+is++ay+ertG+k+ + + +++a +rh+phGv+av+Gpynfp hlpnGhivpal+a
  NCBI__GCF_001677335.1:WP_068862716.1  76 PLWEARTEVDAVVNKVDISVQAYAERTGKKKFDSGiNGSAAVRHKPHGVMAVLGPYNFPAHLPNGHIVPALIA 148
                                           *****************************9987753799********************************** PP

                             TIGR03240 160 GntvvfkpseltplvaeetvklwekaGlpaGvlnlvqGaretGkalaaeedidGllftGssntGallhrqlag 232
                                           Gn+v+fkpse tp v+e++v ++++aG+p+ v++lv G+ + Gkal+a+++idG+lftGs+++G  ++r+lag
  NCBI__GCF_001677335.1:WP_068862716.1 149 GNAVIFKPSEKTPAVGEALVGCFHRAGVPEDVIQLVIGGPKEGKALVAHPGIDGVLFTGSADAGIAINRKLAG 221
                                           ************************************************************************* PP

                             TIGR03240 233 rpekilalelGGnnplvveevkdidaavhlivqsafisaGqrctcarrllvkdgaeGdallerlvevaerltv 305
                                           +p ki+ale+GGnnp+vv ++  +  a++livqsaf saGqrct arrl+vkd+   d l+++lv ++++l+v
  NCBI__GCF_001677335.1:WP_068862716.1 222 NPGKIVALEMGGNNPIVVIDTPKLADAATLIVQSAFTSAGQRCTAARRLIVKDSVY-DDLMAELVPLTRKLMV 293
                                           ***********************99999***********************98866.7799************ PP

                             TIGR03240 306 gkydaepqpflGavisekaakellaaqekllalggksllelkqleeeaalltpgiidvtevaevpdeeyfgpl 378
                                           g+   epqpf+G+vi +++a++l+++  +l+++gg+ ll++++   +  +l+pgiidvt+v ++pd e+fgpl
  NCBI__GCF_001677335.1:WP_068862716.1 294 GNPVGEPQPFMGPVIDNETADRLMESFVTLMTAGGRPLLHMRRNVPDLPFLSPGIIDVTDVIDRPDLELFGPL 366
                                           ************************************************************************* PP

                             TIGR03240 379 lkvlrykdfdealaeanntrfGlaaGllsddrelydkflleiraGivnwnkpltGassaapfGGiGasGnhrp 451
                                           l+v+r+ d+d+ ++eanntrfGl+a l+    ++y +f+ +iraGivnwn p++Gass+apfGGiG sGnhrp
  NCBI__GCF_001677335.1:WP_068862716.1 367 LQVIRVPDLDAGITEANNTRFGLSASLIGGTPDEYGRFWANIRAGIVNWNSPTNGASSKAPFGGIGLSGNHRP 439
                                           ************************************************************************* PP

                             TIGR03240 452 sayyaadycaypvasleads 471
                                           +ayyaadycaypvas e d+
  NCBI__GCF_001677335.1:WP_068862716.1 440 AAYYAADYCAYPVASTEVDQ 459
                                           *****************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (484 nodes)
Target sequences:                          1  (470 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: 00:00:00.00
# Mc/sec: 32.68
//
[ok]

This GapMind analysis is from Sep 24 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 2024 update 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