Alignments for a candidate for astD in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for astD in Marinobacter adhaerens HP15

Align Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized)
to candidate GFF3096 HP15_3039 N-succinylglutamate 5-semialdehyde dehydrogenase

Query= reanno::SB2B:6938906
         (486 letters)



>FitnessBrowser__Marino:GFF3096
          Length = 491

 Score =  622 bits (1605), Expect = 0.0
 Identities = 310/481 (64%), Positives = 371/481 (77%), Gaps = 1/481 (0%)

Query: 4   FINGQWLAGEGKEMQSKNPANGEVIWQGKAAVPAQVQAAVMAARDAQFEWFMLGFEGRQA 63
           FI+G WL G G   +S  P  GE +W G++A    V AAV  AR+A  +W    F  RQA
Sbjct: 9   FIDGLWLPGHGPVFESVQPVTGETLWDGESANLEDVDAAVREARNAFVKWQRKSFAERQA 68

Query: 64  IVEAYRNELEANKAELAEVIAQETGKPRWETATEAAAMIGKIGLSVSAYHKRTGTEVNEG 123
           +VEA+   LEA+K ELA  I  ETGKP WE+ TE AAMIGKIG+SV AY+ RTGT  ++ 
Sbjct: 69  VVEAFGELLEAHKEELAHQIGLETGKPLWESRTEVAAMIGKIGISVKAYNDRTGTSESDV 128

Query: 124 AAGRAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNTVVFKPSELTPKVAELMLKL 183
           A G AVLRH+PHGVVAVFGPYNFPGHLPNGHIVPALLAGNTVVFKPSELTP VAEL +KL
Sbjct: 129 AGGHAVLRHRPHGVVAVFGPYNFPGHLPNGHIVPALLAGNTVVFKPSELTPGVAELTVKL 188

Query: 184 WEKAGLPAGVINLVQGEVETGKALASHPQLDGLFFTGSSRTGHLLHQQYAGHPGKILALE 243
           W KAG+P GVINLVQG   TGK+LA HP +DGLFFTGSS  GHLLH+Q+ G P KI+ALE
Sbjct: 189 WGKAGIPDGVINLVQGASATGKSLAGHPLIDGLFFTGSSTVGHLLHKQFGGQPEKIVALE 248

Query: 244 MGGNNPLIVKGVSDTRAAIHDIIQSAFISSGQRCTCARRLYVEKGAEGDKLLAGLVEAVK 303
           MGGNNPLIV+ V+D   A+H  +QSAF+S+GQRCTCARRL V KG +GD  +  LVE   
Sbjct: 249 MGGNNPLIVQDVADVDGAVHHALQSAFLSAGQRCTCARRLLVPKGKKGDAFIDRLVEVSA 308

Query: 304 AIKVGPWNADPQPFMGSMISETAAKGMLDAQRNLLNLGAKSLVEMTHLQAGTGLVSPGLI 363
            IKVG ++ADPQPFMGS+IS  AA+ +L AQ +LL  G KSL+EM  L++GTGL+SPG++
Sbjct: 309 RIKVGEFDADPQPFMGSVISSEAAEKLLAAQASLLEKGGKSLLEMKSLKSGTGLLSPGIV 368

Query: 364 DVTEVIELPDEEYFGPLLQVVRYTSFDEAIRLANDTRYGLSAGILADDKADYEYFLARIR 423
           D T  +++ DEE+FGPLL+V RY SFD+A+ LANDT YGLSAGIL DD+  YE  +  +R
Sbjct: 369 DATG-LDVTDEEFFGPLLKVYRYKSFDDALALANDTHYGLSAGILTDDRKLYERLVEEVR 427

Query: 424 AGIVNWNKQITGASGAAPFGGVGASGNHRASAFYAADYCAYPVASMEADSVTLPASLSPG 483
           AGIVNWN+ +TGAS AAPFGGVGASGNHR SA+YAADYCA+P+AS+EA    +P SL+PG
Sbjct: 428 AGIVNWNRPLTGASSAAPFGGVGASGNHRPSAYYAADYCAWPMASLEAGKSEMPESLAPG 487

Query: 484 L 484
           L
Sbjct: 488 L 488


Lambda     K      H
   0.317    0.133    0.393 

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: 805
Number of extensions: 23
Number of successful extensions: 2
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: 486
Length of database: 491
Length adjustment: 34
Effective length of query: 452
Effective length of database: 457
Effective search space:   206564
Effective search space used:   206564
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 (21.6 bits)
S2: 52 (24.6 bits)

Align candidate GFF3096 HP15_3039 (N-succinylglutamate 5-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.24992.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.8e-249  814.3   0.0     2e-249  814.1   0.0    1.0  1  lcl|FitnessBrowser__Marino:GFF3096  HP15_3039 N-succinylglutamate 5-


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF3096  HP15_3039 N-succinylglutamate 5-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  814.1   0.0    2e-249    2e-249       1     484 []       8     490 ..       8     490 .. 1.00

  Alignments for each domain:
  == domain 1  score: 814.1 bits;  conditional E-value: 2e-249
                           TIGR03240   1 lfidGkwraGqGeslesldpvtqevlwqgkaasaaqvekavkaarkafpawarlsleeriavvkrfaelleeeke 75 
                                         lfidG w  G+G  +es++pvt+e+lw+g++a+ ++v++av+ ar+af +w r s++er+avv+ f elle +ke
  lcl|FitnessBrowser__Marino:GFF3096   8 LFIDGLWLPGHGPVFESVQPVTGETLWDGESANLEDVDAAVREARNAFVKWQRKSFAERQAVVEAFGELLEAHKE 82 
                                         59************************************************************************* PP

                           TIGR03240  76 elaeviaketgkplweartevasmvakvaisikayeertGekeseladakavlrhrphGvlavfGpynfpGhlpn 150
                                         ela+ i+ etgkplwe+rteva+m++k+ is+kay++rtG++es++a ++avlrhrphGv+avfGpynfpGhlpn
  lcl|FitnessBrowser__Marino:GFF3096  83 ELAHQIGLETGKPLWESRTEVAAMIGKIGISVKAYNDRTGTSESDVAGGHAVLRHRPHGVVAVFGPYNFPGHLPN 157
                                         *************************************************************************** PP

                           TIGR03240 151 GhivpallaGntvvfkpseltplvaeetvklwekaGlpaGvlnlvqGaretGkalaaeedidGllftGssntGal 225
                                         GhivpallaGntvvfkpseltp vae tvklw kaG+p+Gv+nlvqGa  tGk+la ++ idGl+ftGss+ G+l
  lcl|FitnessBrowser__Marino:GFF3096 158 GHIVPALLAGNTVVFKPSELTPGVAELTVKLWGKAGIPDGVINLVQGASATGKSLAGHPLIDGLFFTGSSTVGHL 232
                                         *************************************************************************** PP

                           TIGR03240 226 lhrqlagrpekilalelGGnnplvveevkdidaavhlivqsafisaGqrctcarrllvkdgaeGdallerlveva 300
                                         lh+q++g+peki+ale+GGnnpl+v++v+d+d+avh+++qsaf+saGqrctcarrllv++g++Gda+++rlvev+
  lcl|FitnessBrowser__Marino:GFF3096 233 LHKQFGGQPEKIVALEMGGNNPLIVQDVADVDGAVHHALQSAFLSAGQRCTCARRLLVPKGKKGDAFIDRLVEVS 307
                                         *************************************************************************** PP

                           TIGR03240 301 erltvgkydaepqpflGavisekaakellaaqekllalggksllelkqleeeaalltpgiidvtevaevpdeeyf 375
                                         +r++vg++da+pqpf+G+vis++aa++llaaq++ll++ggkslle+k+l+++++ll+pgi+d t++ +v dee+f
  lcl|FitnessBrowser__Marino:GFF3096 308 ARIKVGEFDADPQPFMGSVISSEAAEKLLAAQASLLEKGGKSLLEMKSLKSGTGLLSPGIVDATGL-DVTDEEFF 381
                                         *****************************************************************8.9******* PP

                           TIGR03240 376 gpllkvlrykdfdealaeanntrfGlaaGllsddrelydkflleiraGivnwnkpltGassaapfGGiGasGnhr 450
                                         gpllkv+ryk+fd+ala an+t++Gl+aG+l+ddr+ly+++++e+raGivnwn+pltGassaapfGG+GasGnhr
  lcl|FitnessBrowser__Marino:GFF3096 382 GPLLKVYRYKSFDDALALANDTHYGLSAGILTDDRKLYERLVEEVRAGIVNWNRPLTGASSAAPFGGVGASGNHR 456
                                         *************************************************************************** PP

                           TIGR03240 451 psayyaadycaypvasleadslalpatlspGlkl 484
                                         psayyaadyca+p+aslea + ++p++l+pGl++
  lcl|FitnessBrowser__Marino:GFF3096 457 PSAYYAADYCAWPMASLEAGKSEMPESLAPGLNF 490
                                         *******************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (484 nodes)
Target sequences:                          1  (491 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 11.60
//
[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