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_4132 Ga0059261_4132 succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71)

Query= SwissProt::Q8ZPV0
         (492 letters)



>FitnessBrowser__Korea:Ga0059261_4132
          Length = 471

 Score =  472 bits (1214), Expect = e-137
 Identities = 247/457 (54%), Positives = 314/457 (68%), Gaps = 6/457 (1%)

Query: 20  TNPVSAEILWQGNDANAAQVAEACQAARAAFPRWARQPFAARQAIVEKFAALLEAHKAEL 79
           TNP + E LW+G  A+A   A A + AR AFP WA Q   AR AI+ ++AA+L   K  L
Sbjct: 8   TNPATGETLWEGPVASAEDCARAVERARTAFPAWAAQSPDARAAILTRYAAVLGERKDAL 67

Query: 80  TEVIARETGKPRWEAATEVTAMINKIAISIKAYHARTGAQKSELVDGAATLRHRPHGVLA 139
            E IARETGKP WE ATEV +MI K+AISI+A  AR G ++S +  G A L HRPHGV+A
Sbjct: 68  AEAIARETGKPLWETATEVASMIGKVAISIEAMAARAGTRESAMPFGRAVLAHRPHGVMA 127

Query: 140 VFGPYNFPGHLPNGHIVPALLAGNTLIFKPSELTPWTGETVIKLWERAGLPAGVLNLVQG 199
           V GPYNFPGHLPNGHIVPALLAGNTL+FKPSE TP  G+ +++    AG+P  V  L+QG
Sbjct: 128 VLGPYNFPGHLPNGHIVPALLAGNTLVFKPSEETPLVGQLMVEALHAAGIPEDVAILLQG 187

Query: 200 GRETGQALSSLDDLDGLLFTGSASTGYQLHRQLSGQPEKILALEMGGNNPLIIEDAANID 259
           GRETG AL S  D+DGLLFTGSA  G    R  + +P  ILALE+GGNNPL+  D    +
Sbjct: 188 GRETGAALVS-QDIDGLLFTGSAGAGMHFRRSFAERPAVILALELGGNNPLVAWD-GEPE 245

Query: 260 AAVHLTLQSAFITAGQRCTCARRLLVKQGAQGDAFLARLVDVAGRLQPGRWDDDPQPFIG 319
           A   + + S FIT GQRC+CARRL+V +GA GDA +  +  ++ RL+ GRWD+ P+PF+G
Sbjct: 246 AVASIVVASTFITTGQRCSCARRLIVPEGAAGDAIVDAVAALSDRLRIGRWDETPEPFMG 305

Query: 320 GLISAQAAQHVMEAWRQREALGGRTLLAPRKVKEGTS--LLTPGIIELTGVADVPDEEVF 377
            L+S  AA+           LG R  + P    EG S   + P I+++TG+ +VPDEE+F
Sbjct: 306 PLVSTGAAERAAAQVAALVGLGARE-IRPFGGVEGRSGAFVRPAILDVTGL-EVPDEEIF 363

Query: 378 GPLLNVWRYAHFDEAIRLANNTRFGLSCGLVSTDRAQFEQLLLEARAGIVNWNKPLTGAA 437
            P+L V R A FD A+  AN TRFGL+ GL+S D A + +   +ARAG+VN N+P TGAA
Sbjct: 364 APVLQVRRVADFDAALAAANQTRFGLAAGLISDDDALWARFQAQARAGVVNRNRPTTGAA 423

Query: 438 STAPFGGVGASGNHRPSAWYAADYCAWPMASLESPEL 474
           S+ PFGG+G SGNHRPSA+YAADYCA+P+ASLE+  +
Sbjct: 424 SSMPFGGLGDSGNHRPSAYYAADYCAYPVASLEAERI 460


Lambda     K      H
   0.319    0.134    0.411 

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: 711
Number of extensions: 32
Number of successful extensions: 4
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: 492
Length of database: 471
Length adjustment: 34
Effective length of query: 458
Effective length of database: 437
Effective search space:   200146
Effective search space used:   200146
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate Ga0059261_4132 Ga0059261_4132 (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.15515.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.1e-203  663.2   3.3   1.5e-203  662.8   3.3    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_4132  Ga0059261_4132 succinylglutamic 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_4132  Ga0059261_4132 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 !  662.8   3.3  1.5e-203  1.5e-203      15     475 ..       5     463 ..       2     470 .. 0.98

  Alignments for each domain:
  == domain 1  score: 662.8 bits;  conditional E-value: 1.5e-203
                                 TIGR03240  15 lesldpvtqevlwqgkaasaaqvekavkaarkafpawarlsleeriavvkrfaelleeekeelaeviak 83 
                                               ++s++p+t+e+lw+g  asa++ ++av+ ar+afpawa+ s ++r+a+++r+a++l e+k++lae+ia+
  lcl|FitnessBrowser__Korea:Ga0059261_4132   5 FASTNPATGETLWEGPVASAEDCARAVERARTAFPAWAAQSPDARAAILTRYAAVLGERKDALAEAIAR 73 
                                               789****************************************************************** PP

                                 TIGR03240  84 etgkplweartevasmvakvaisikayeertGekeseladakavlrhrphGvlavfGpynfpGhlpnGh 152
                                               etgkplwe++tevasm++kvaisi+a + r+G++es+++ ++avl hrphGv+av+GpynfpGhlpnGh
  lcl|FitnessBrowser__Korea:Ga0059261_4132  74 ETGKPLWETATEVASMIGKVAISIEAMAARAGTRESAMPFGRAVLAHRPHGVMAVLGPYNFPGHLPNGH 142
                                               ********************************************************************* PP

                                 TIGR03240 153 ivpallaGntvvfkpseltplvaeetvklwekaGlpaGvlnlvqGaretGkalaaeedidGllftGssn 221
                                               ivpallaGnt+vfkpse+tplv++ +v+++++aG+p+ v  l+qG+retG al+++ didGllftGs+ 
  lcl|FitnessBrowser__Korea:Ga0059261_4132 143 IVPALLAGNTLVFKPSEETPLVGQLMVEALHAAGIPEDVAILLQGGRETGAALVSQ-DIDGLLFTGSAG 210
                                               ******************************************************98.9*********** PP

                                 TIGR03240 222 tGallhrqlagrpekilalelGGnnplvveevkdidaavhlivqsafisaGqrctcarrllvkdgaeGd 290
                                               +G++++r +a+rp +ilalelGGnnplv ++  + +a++  +v s+fi++Gqrc+carrl+v++ga Gd
  lcl|FitnessBrowser__Korea:Ga0059261_4132 211 AGMHFRRSFAERPAVILALELGGNNPLVAWDG-EPEAVASIVVASTFITTGQRCSCARRLIVPEGAAGD 278
                                               ****************************9996.589********************************* PP

                                 TIGR03240 291 allerlvevaerltvgkydaepqpflGavisekaakellaaqekllalggksllelkqlee.eaalltp 358
                                               a+++++ ++++rl++g++d+ p+pf+G+++s+ aa++  a  + l+ lg++++  +  +e  + a+++p
  lcl|FitnessBrowser__Korea:Ga0059261_4132 279 AIVDAVAALSDRLRIGRWDETPEPFMGPLVSTGAAERAAAQVAALVGLGAREIRPFGGVEGrSGAFVRP 347
                                               *************************************999999***************9984568**** PP

                                 TIGR03240 359 giidvtevaevpdeeyfgpllkvlrykdfdealaeanntrfGlaaGllsddrelydkflleiraGivnw 427
                                               +i+dvt++ evpdee f+p+l+v r++dfd+ala+an+trfGlaaGl+sdd++l+ +f  ++raG+vn 
  lcl|FitnessBrowser__Korea:Ga0059261_4132 348 AILDVTGL-EVPDEEIFAPVLQVRRVADFDAALAAANQTRFGLAAGLISDDDALWARFQAQARAGVVNR 415
                                               *******8.9*********************************************************** PP

                                 TIGR03240 428 nkpltGassaapfGGiGasGnhrpsayyaadycaypvasleadslalp 475
                                               n+p+tGa+s++pfGG+G sGnhrpsayyaadycaypvaslea+++a  
  lcl|FitnessBrowser__Korea:Ga0059261_4132 416 NRPTTGAASSMPFGGLGDSGNHRPSAYYAADYCAYPVASLEAERIADQ 463
                                               *******************************************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (484 nodes)
Target sequences:                          1  (471 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 7.26
//
[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