Alignments for a candidate for astD in Sphingomonas koreensis DSMZ 15582

GapMind for catabolism of small carbon sources

Alignments for a candidate for astD in Sphingomonas koreensis DSMZ 15582

Align N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized)
to candidate Ga0059261_1495 Ga0059261_1495 succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71)

Query= SwissProt::O50174
         (487 letters)



>FitnessBrowser__Korea:Ga0059261_1495
          Length = 480

 Score =  454 bits (1168), Expect = e-132
 Identities = 241/460 (52%), Positives = 305/460 (66%), Gaps = 7/460 (1%)

Query: 15  GETLESLDPVGQGVVWSGRGADATQVDAAVCAAREAFPAWARRPLEQRIELLERFAATLK 74
           G  + S +P    V+W     D   VDA V AAR ++  WA RPL  RIE L RFA  ++
Sbjct: 12  GSEIISTEPATGAVLWRRPIGD---VDAEVAAARASWADWAARPLTYRIEALRRFANVVR 68

Query: 75  SRADELARVIGEETGKPLWESATEVTSMVNKVAISVQAFRERTGEK--SGPLADATAVLR 132
            +++    +I  ETGKPLWE+ TEV +++ KV ISV AF ERTG++    P+    A LR
Sbjct: 69  QKSEAFTDLIARETGKPLWEARTEVETVIAKVDISVTAFSERTGQRRIEAPMNTRLA-LR 127

Query: 133 HKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNCVVFKPSELTPKVAELTLKAWIQAGLPA 192
           HKPHGV+AV GPYNFP HLPNGHIVPALLAGN VVFKPSE TP      ++ +  AG+P 
Sbjct: 128 HKPHGVLAVLGPYNFPAHLPNGHIVPALLAGNAVVFKPSEKTPATGAFLVECYHAAGIPE 187

Query: 193 GVLNLVQGGRETGVALAAHRGLDGLFFTGSSRTGNLLHSQFGGQPQKILALEMGGNNPLV 252
           G + L+ GG + G ALA H G+DGL FTGS+RTG  L+  F  +P+KILALEMGGNNP++
Sbjct: 188 GCIRLLIGGPDEGKALAGHDGIDGLLFTGSARTGIALNRAFAAKPEKILALEMGGNNPIL 247

Query: 253 VEEVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDALLARLVAVSATLRVGRFD 312
           V    D+ +A   +IQSAF SAGQRCT ARRL+V +  + D LL  +  +   L VG   
Sbjct: 248 VWSTPDIYSAAVLVIQSAFTSAGQRCTAARRLIVDEKLY-DPLLEEVNKLIGRLIVGEPH 306

Query: 313 EQPAPFMGAVISLSAAEHLLKAQEHLIGKGAQPLLAMTQPIDGAALLTPGILDVSAVAER 372
             PAPFMG VI    A+ L ++   L   G +PL  M +P+DG   LTP ++D++   E+
Sbjct: 307 ADPAPFMGPVIDNDTADLLTESFLELSFMGGRPLRHMERPVDGRPFLTPAMIDMTDAKEK 366

Query: 373 PDEEFFGPLLQVIRYSDFAAAIREANATQYGLAAGLLSDSRERFEQFLVESRAGIVNWNK 432
           PD E FGP+LQVIR   F  AI EAN T+YGL+A L+S   + ++QF    RAGIVNWN+
Sbjct: 367 PDVELFGPILQVIRARTFEEAIAEANNTRYGLSASLVSQDPKLYDQFWANIRAGIVNWNR 426

Query: 433 QLTGAASSAPFGGIGASGNHRPSAYYAADYCAYPVASLES 472
              GA+S+APFGGIG SGNHRPSA+YAADYCAYPV S E+
Sbjct: 427 PTNGASSAAPFGGIGWSGNHRPSAFYAADYCAYPVVSSEA 466


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: 695
Number of extensions: 32
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: 480
Length adjustment: 34
Effective length of query: 453
Effective length of database: 446
Effective search space:   202038
Effective search space used:   202038
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 Ga0059261_1495 Ga0059261_1495 (succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71))
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.27142.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.5e-187  610.1   0.0   1.9e-187  609.8   0.0    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_1495  Ga0059261_1495 succinylglutamic 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_1495  Ga0059261_1495 succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  609.8   0.0  1.9e-187  1.9e-187      10     474 ..      10     471 ..       4     476 .. 0.97

  Alignments for each domain:
  == domain 1  score: 609.8 bits;  conditional E-value: 1.9e-187
                                 TIGR03240  10 GqGeslesldpvtqevlwqgkaasaaqvekavkaarkafpawarlsleeriavvkrfaelleeekeela 78 
                                                +G+++ s++p+t++vlw+       +v++ v+aar+++++wa+++l  ri+ ++rfa++++++ e+++
  lcl|FitnessBrowser__Korea:Ga0059261_1495  10 MSGSEIISTEPATGAVLWRRPI---GDVDAEVAAARASWADWAARPLTYRIEALRRFANVVRQKSEAFT 75 
                                               57999*************9765...6799**************************************** PP

                                 TIGR03240  79 eviaketgkplweartevasmvakvaisikayeertGekeselad.akavlrhrphGvlavfGpynfpG 146
                                               ++ia+etgkplweartev++++akv+is+ a++ertG+++ e +  ++  lrh+phGvlav+Gpynfp 
  lcl|FitnessBrowser__Korea:Ga0059261_1495  76 DLIARETGKPLWEARTEVETVIAKVDISVTAFSERTGQRRIEAPMnTRLALRHKPHGVLAVLGPYNFPA 144
                                               ***************************************99888615678******************* PP

                                 TIGR03240 147 hlpnGhivpallaGntvvfkpseltplvaeetvklwekaGlpaGvlnlvqGaretGkalaaeedidGll 215
                                               hlpnGhivpallaGn+vvfkpse tp ++  +v+++++aG+p+G + l+ G+ + Gkala +++idGll
  lcl|FitnessBrowser__Korea:Ga0059261_1495 145 HLPNGHIVPALLAGNAVVFKPSEKTPATGAFLVECYHAAGIPEGCIRLLIGGPDEGKALAGHDGIDGLL 213
                                               ********************************************************************* PP

                                 TIGR03240 216 ftGssntGallhrqlagrpekilalelGGnnplvveevkdidaavhlivqsafisaGqrctcarrllvk 284
                                               ftGs++tG  l+r +a +pekilale+GGnnp++v+++ di +a+ l++qsaf saGqrct arrl+v+
  lcl|FitnessBrowser__Korea:Ga0059261_1495 214 FTGSARTGIALNRAFAAKPEKILALEMGGNNPILVWSTPDIYSAAVLVIQSAFTSAGQRCTAARRLIVD 282
                                               ******************************************************************997 PP

                                 TIGR03240 285 dgaeGdallerlvevaerltvgkydaepqpflGavisekaakellaaqekllalggksllelkqleeea 353
                                               ++   d lle++ ++  rl vg+ +a+p+pf+G+vi + +a+ l ++  +l+ +gg+ l ++++   + 
  lcl|FitnessBrowser__Korea:Ga0059261_1495 283 EK-LYDPLLEEVNKLIGRLIVGEPHADPAPFMGPVIDNDTADLLTESFLELSFMGGRPLRHMERPVDGR 350
                                               65.6799************************************************************** PP

                                 TIGR03240 354 alltpgiidvtevaevpdeeyfgpllkvlrykdfdealaeanntrfGlaaGllsddrelydkflleira 422
                                                +ltp++id+t+ +e pd e+fgp+l+v+r ++f+ea+aeanntr+Gl+a l+s+d +lyd+f+ +ira
  lcl|FitnessBrowser__Korea:Ga0059261_1495 351 PFLTPAMIDMTDAKEKPDVELFGPILQVIRARTFEEAIAEANNTRYGLSASLVSQDPKLYDQFWANIRA 419
                                               ********************************************************************* PP

                                 TIGR03240 423 GivnwnkpltGassaapfGGiGasGnhrpsayyaadycaypvasleadslal 474
                                               Givnwn+p++GassaapfGGiG sGnhrpsa+yaadycaypv s ea++  +
  lcl|FitnessBrowser__Korea:Ga0059261_1495 420 GIVNWNRPTNGASSAAPFGGIGWSGNHRPSAFYAADYCAYPVVSSEAEQARV 471
                                               ***********************************************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (484 nodes)
Target sequences:                          1  (480 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: 9.65
//
[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