Alignments for a candidate for astD in Erythrobacter gangjinensis K7-2

GapMind for catabolism of small carbon sources

Alignments for a candidate for astD in Erythrobacter gangjinensis K7-2

Align N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized)
to candidate WP_047007470.1 AAW01_RS11975 succinylglutamate-semialdehyde dehydrogenase

Query= SwissProt::O50174
         (487 letters)



>NCBI__GCF_001010925.1:WP_047007470.1
          Length = 481

 Score =  431 bits (1108), Expect = e-125
 Identities = 224/463 (48%), Positives = 303/463 (65%), Gaps = 7/463 (1%)

Query: 18  LESLDPVGQGVVWSGRGADATQVDAAVCAAREAFPAWARRPLEQRIELLERFAATLKSRA 77
           L S +P     +W  R  +   VD  V  AR+A+P WA  PL +RIEL+ RF   +++  
Sbjct: 16  LISYEPATGAELWRQRHGN---VDEYVARARKAWPGWAAEPLAKRIELVRRFVNEVRAEQ 72

Query: 78  DELARVIGEETGKPLWESATEVTSMVNKVAISVQAFRERTGEKSGPLA-DATAVLRHKPH 136
           DE A++I  ETGKPLWE+ TEV +++ KV IS+ A+ ERTG++    A   +A LRHKPH
Sbjct: 73  DEFAQLISRETGKPLWEARTEVEAVMAKVDISITAYAERTGQRKLDSALQGSAALRHKPH 132

Query: 137 GVVAVFGPYNFPGHLPNGHIVPALLAGNCVVFKPSELTPKVAELTLKAWIQAGLPAGVLN 196
           GV+AV GPYNFP HLPNGHIVPAL+AGN ++ KPSE TP V E  L  + +AG+P  V+ 
Sbjct: 133 GVMAVLGPYNFPAHLPNGHIVPALIAGNAIILKPSEKTPAVGERLLSFFHKAGIPQDVVQ 192

Query: 197 LVQGGRETGVALAAHRGLDGLFFTGSSRTGNLLHSQFGGQPQKILALEMGGNNPLVVEEV 256
            + GG + G AL AH  +DG+ FTGS++ G  ++ +    P K++ALEMGGNNP+V+ + 
Sbjct: 193 CLIGGPDEGKALVAHADVDGVLFTGSAQVGIAINRKLASNPGKMVALEMGGNNPIVLWDT 252

Query: 257 ADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDALLARLVAVSATLRVGRFDEQPA 316
             L+ A   IIQSAF +AGQRCT  RRL+V    + DA L  +  ++  L V      PA
Sbjct: 253 PKLEDAAALIIQSAFTTAGQRCTAGRRLIVKSSMY-DAALEAVTKLTDRLLVDEPFADPA 311

Query: 317 PFMGAVISLSAAEHLLKAQEHLIGKGAQPLLAMTQPIDGAALLTPGILDVSAVAERPDEE 376
           PFMG VI    A+ L ++  +L+  G + +  + +P      L+P I+D + +AERPD E
Sbjct: 312 PFMGPVIDNQTADQLTESFLYLLSNGGKAIKHLRRPHGDLPFLSPSIIDTTNMAERPDVE 371

Query: 377 FFGPLLQVIRYSDFAAAIREANATQYGLAAGLLSDSRERFEQFLVESRAGIVNWNKQLTG 436
            FGP+LQV+R  DF AAI EAN T++GL+A L+    +++ +F    RAGIVNWN+   G
Sbjct: 372 LFGPILQVVRVDDFDAAIAEANNTRFGLSASLIGGDPKQYNRFWANIRAGIVNWNRPTNG 431

Query: 437 AASSAPFGGIGASGNHRPSAYYAADYCAYPVAS--LESPSVSL 477
           A+S+APFGGIG SGNHRP+A+YAADYCAYPV S  LE P  S+
Sbjct: 432 ASSAAPFGGIGLSGNHRPAAFYAADYCAYPVTSTELEQPRASV 474


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: 641
Number of extensions: 26
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: 481
Length adjustment: 34
Effective length of query: 453
Effective length of database: 447
Effective search space:   202491
Effective search space used:   202491
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: 52 (24.6 bits)

Align candidate WP_047007470.1 AAW01_RS11975 (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.4056281.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     5e-184  598.5   0.0   6.5e-184  598.1   0.0    1.0  1  NCBI__GCF_001010925.1:WP_047007470.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001010925.1:WP_047007470.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  598.1   0.0  6.5e-184  6.5e-184      13     471 ..      14     469 ..       7     476 .. 0.97

  Alignments for each domain:
  == domain 1  score: 598.1 bits;  conditional E-value: 6.5e-184
                             TIGR03240  13 eslesldpvtqevlwqgkaasaaqvekavkaarkafpawarlsleeriavvkrfaelleeekeelaeviaket 85 
                                           ++l s +p+t+++lw+ +     +v++ v+ arka+p wa+ +l++ri++v+rf + ++ e++e+a++i++et
  NCBI__GCF_001010925.1:WP_047007470.1  14 AELISYEPATGAELWRQRH---GNVDEYVARARKAWPGWAAEPLAKRIELVRRFVNEVRAEQDEFAQLISRET 83 
                                           678899*********9875...68999********************************************** PP

                             TIGR03240  86 gkplweartevasmvakvaisikayeertGekesela.dakavlrhrphGvlavfGpynfpGhlpnGhivpal 157
                                           gkplweartev++++akv+isi ay+ertG+++ + a +++a lrh+phGv+av+Gpynfp hlpnGhivpal
  NCBI__GCF_001010925.1:WP_047007470.1  84 GKPLWEARTEVEAVMAKVDISITAYAERTGQRKLDSAlQGSAALRHKPHGVMAVLGPYNFPAHLPNGHIVPAL 156
                                           *******************************997765389********************************* PP

                             TIGR03240 158 laGntvvfkpseltplvaeetvklwekaGlpaGvlnlvqGaretGkalaaeedidGllftGssntGallhrql 230
                                           +aGn++++kpse tp v+e ++  ++kaG+p+ v++ + G+ + Gkal+a+ d+dG+lftGs++ G  ++r+l
  NCBI__GCF_001010925.1:WP_047007470.1 157 IAGNAIILKPSEKTPAVGERLLSFFHKAGIPQDVVQCLIGGPDEGKALVAHADVDGVLFTGSAQVGIAINRKL 229
                                           ************************************************************************* PP

                             TIGR03240 231 agrpekilalelGGnnplvveevkdidaavhlivqsafisaGqrctcarrllvkdgaeGdallerlvevaerl 303
                                           a +p k++ale+GGnnp+v++++  ++ a++li+qsaf +aGqrct  rrl+vk++   da le+++++++rl
  NCBI__GCF_001010925.1:WP_047007470.1 230 ASNPGKMVALEMGGNNPIVLWDTPKLEDAAALIIQSAFTTAGQRCTAGRRLIVKSSM-YDAALEAVTKLTDRL 301
                                           *****************************************************9875.68999********** PP

                             TIGR03240 304 tvgkydaepqpflGavisekaakellaaqekllalggksllelkqleeeaalltpgiidvtevaevpdeeyfg 376
                                            v++  a+p+pf+G+vi +++a++l ++   ll +ggk++ +l++ + +  +l+p+iid+t++ae+pd e+fg
  NCBI__GCF_001010925.1:WP_047007470.1 302 LVDEPFADPAPFMGPVIDNQTADQLTESFLYLLSNGGKAIKHLRRPHGDLPFLSPSIIDTTNMAERPDVELFG 374
                                           ************************************************************************* PP

                             TIGR03240 377 pllkvlrykdfdealaeanntrfGlaaGllsddrelydkflleiraGivnwnkpltGassaapfGGiGasGnh 449
                                           p+l+v+r++dfd+a+aeanntrfGl+a l+  d ++y++f+ +iraGivnwn+p++GassaapfGGiG sGnh
  NCBI__GCF_001010925.1:WP_047007470.1 375 PILQVVRVDDFDAAIAEANNTRFGLSASLIGGDPKQYNRFWANIRAGIVNWNRPTNGASSAAPFGGIGLSGNH 447
                                           ************************************************************************* PP

                             TIGR03240 450 rpsayyaadycaypvasleads 471
                                           rp+a+yaadycaypv+s e ++
  NCBI__GCF_001010925.1:WP_047007470.1 448 RPAAFYAADYCAYPVTSTELEQ 469
                                           *****************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (484 nodes)
Target sequences:                          1  (481 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 23.13
//
[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 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