Alignments for a candidate for astD in Sphingomonas indica Dd16

GapMind for catabolism of small carbon sources

Alignments for a candidate for astD in Sphingomonas indica Dd16

Align N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized)
to candidate WP_085219240.1 B9N75_RS13395 succinylglutamate-semialdehyde dehydrogenase

Query= SwissProt::O50174
         (487 letters)



>NCBI__GCF_900177405.1:WP_085219240.1
          Length = 477

 Score =  470 bits (1210), Expect = e-137
 Identities = 245/459 (53%), Positives = 312/459 (67%), Gaps = 7/459 (1%)

Query: 16  ETLESLDPVGQGVVWSGRGADATQVDAAVCAAREAFPAWARRPLEQRIELLERFAATLKS 75
           E+L S +P     +W G   DA   DA V  AR A+ +WA +PL  R+E L RFA  +++
Sbjct: 3   ESLISTEPATGAELWRGAIGDA---DAEVRTARAAWGSWASKPLAVRVETLRRFANVVRA 59

Query: 76  RADELARVIGEETGKPLWESATEVTSMVNKVAISVQAFRERTGEK--SGPLADATAVLRH 133
             D+ A +I  ETGKPLWE+ TEV ++V KV ISV A+ ERT ++   G +    AV RH
Sbjct: 60  AKDDFADLIARETGKPLWEAGTEVDAVVGKVDISVSAYSERTSQRRMEGAMGARVAV-RH 118

Query: 134 KPHGVVAVFGPYNFPGHLPNGHIVPALLAGNCVVFKPSELTPKVAELTLKAWIQAGLPAG 193
           KPHGV+ V GPYNFP HLPNGHIVPALLAGN VVFKPSE TP V E  ++ + +AG+P G
Sbjct: 119 KPHGVLGVLGPYNFPAHLPNGHIVPALLAGNAVVFKPSEKTPAVGERLVRYFHEAGVPEG 178

Query: 194 VLNLVQGGRETGVALAAHRGLDGLFFTGSSRTGNLLHSQFGGQPQKILALEMGGNNPLVV 253
           V+  + GG E G +LA H GLDGL FTGS+R G  LH QF   P KILALE+GGNNPLVV
Sbjct: 179 VVRCLIGGPEQGKSLAGHPGLDGLLFTGSARAGMALHRQFAETPHKILALELGGNNPLVV 238

Query: 254 EEVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDALLARLVAVSATLRVGRFDE 313
            +  D+ AA    +QSAF+SAGQRCT ARRL+V  G   + L+  ++ ++  + V     
Sbjct: 239 WQAPDIHAAAVIAVQSAFLSAGQRCTAARRLIVEDGK-HEQLVETILKLTDRIIVDHPHA 297

Query: 314 QPAPFMGAVISLSAAEHLLKAQEHLIGKGAQPLLAMTQPIDGAALLTPGILDVSAVAERP 373
            PAPFMG V+   AA+ L  A   L+ KG +PL  + +P DG   LTP ILDV+ V++RP
Sbjct: 298 NPAPFMGPVVDNGAADQLQAAYLDLVLKGGKPLKHLERPDDGKPFLTPSILDVTGVSDRP 357

Query: 374 DEEFFGPLLQVIRYSDFAAAIREANATQYGLAAGLLSDSRERFEQFLVESRAGIVNWNKQ 433
           D E FGP+LQ++R +DF AA+ EAN T++GLAA L+  S + +++F    RAG+VNWNK 
Sbjct: 358 DAELFGPVLQIVRVADFDAALAEANNTRFGLAASLIGGSPQLYDRFWANVRAGVVNWNKP 417

Query: 434 LTGAASSAPFGGIGASGNHRPSAYYAADYCAYPVASLES 472
             GA SSAPFGG+G SGNHRPSA+YAADYCAYPV S E+
Sbjct: 418 TNGAPSSAPFGGVGISGNHRPSAFYAADYCAYPVTSSEA 456


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: 39
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: 477
Length adjustment: 34
Effective length of query: 453
Effective length of database: 443
Effective search space:   200679
Effective search space used:   200679
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_085219240.1 B9N75_RS13395 (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.2766318.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.8e-190  618.0   0.2   7.1e-190  617.7   0.2    1.0  1  NCBI__GCF_900177405.1:WP_085219240.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900177405.1:WP_085219240.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  617.7   0.2  7.1e-190  7.1e-190      13     473 ..       3     460 ..       1     466 [. 0.97

  Alignments for each domain:
  == domain 1  score: 617.7 bits;  conditional E-value: 7.1e-190
                             TIGR03240  13 eslesldpvtqevlwqgkaasaaqvekavkaarkafpawarlsleeriavvkrfaelleeekeelaeviaket 85 
                                           esl s++p+t+++lw+g+  +a   ++ v++ar+a+ +wa+ +l+ r++ ++rfa++++  k+++a++ia+et
  NCBI__GCF_900177405.1:WP_085219240.1   3 ESLISTEPATGAELWRGAIGDA---DAEVRTARAAWGSWASKPLAVRVETLRRFANVVRAAKDDFADLIARET 72 
                                           57889************98876...5689******************************************** PP

                             TIGR03240  86 gkplweartevasmvakvaisikayeertGekeselad.akavlrhrphGvlavfGpynfpGhlpnGhivpal 157
                                           gkplwea tev ++v+kv+is+ ay+ert +++ e a  a+  +rh+phGvl v+Gpynfp hlpnGhivpal
  NCBI__GCF_900177405.1:WP_085219240.1  73 GKPLWEAGTEVDAVVGKVDISVSAYSERTSQRRMEGAMgARVAVRHKPHGVLGVLGPYNFPAHLPNGHIVPAL 145
                                           ******************************99988665156779***************************** PP

                             TIGR03240 158 laGntvvfkpseltplvaeetvklwekaGlpaGvlnlvqGaretGkalaaeedidGllftGssntGallhrql 230
                                           laGn+vvfkpse tp v+e +v+ +++aG+p+Gv+  + G+ e Gk+la ++++dGllftGs+++G+ lhrq+
  NCBI__GCF_900177405.1:WP_085219240.1 146 LAGNAVVFKPSEKTPAVGERLVRYFHEAGVPEGVVRCLIGGPEQGKSLAGHPGLDGLLFTGSARAGMALHRQF 218
                                           ************************************************************************* PP

                             TIGR03240 231 agrpekilalelGGnnplvveevkdidaavhlivqsafisaGqrctcarrllvkdgaeGdallerlvevaerl 303
                                           a+ p+kilalelGGnnplvv+++ di+aa+  +vqsaf+saGqrct arrl+v+dg++ + l+e ++++++r+
  NCBI__GCF_900177405.1:WP_085219240.1 219 AETPHKILALELGGNNPLVVWQAPDIHAAAVIAVQSAFLSAGQRCTAARRLIVEDGKH-EQLVETILKLTDRI 290
                                           ******************************************************9987.6799********** PP

                             TIGR03240 304 tvgkydaepqpflGavisekaakellaaqekllalggksllelkqleeeaalltpgiidvtevaevpdeeyfg 376
                                            v++ +a+p+pf+G+v+ + aa++l aa  +l+ +ggk l +l++ + ++ +ltp+i+dvt+v+++pd e+fg
  NCBI__GCF_900177405.1:WP_085219240.1 291 IVDHPHANPAPFMGPVVDNGAADQLQAAYLDLVLKGGKPLKHLERPDDGKPFLTPSILDVTGVSDRPDAELFG 363
                                           ************************************************************************* PP

                             TIGR03240 377 pllkvlrykdfdealaeanntrfGlaaGllsddrelydkflleiraGivnwnkpltGassaapfGGiGasGnh 449
                                           p+l+++r++dfd+alaeanntrfGlaa l+  + +lyd+f+ ++raG+vnwnkp++Ga s+apfGG+G sGnh
  NCBI__GCF_900177405.1:WP_085219240.1 364 PVLQIVRVADFDAALAEANNTRFGLAASLIGGSPQLYDRFWANVRAGVVNWNKPTNGAPSSAPFGGVGISGNH 436
                                           ************************************************************************* PP

                             TIGR03240 450 rpsayyaadycaypvasleadsla 473
                                           rpsa+yaadycaypv+s ea++  
  NCBI__GCF_900177405.1:WP_085219240.1 437 RPSAFYAADYCAYPVTSSEAEQAR 460
                                           ********************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (484 nodes)
Target sequences:                          1  (477 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: 00:00:00.00
# Mc/sec: 26.45
//
[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