Alignments for a candidate for astD in Sphingopyxis indica DS15

GapMind for catabolism of small carbon sources

Alignments for a candidate for astD in Sphingopyxis indica DS15

Align N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized)
to candidate WP_089214372.1 CHB69_RS02540 succinylglutamate-semialdehyde dehydrogenase

Query= SwissProt::O50174
         (487 letters)



>NCBI__GCF_900188185.1:WP_089214372.1
          Length = 483

 Score =  459 bits (1182), Expect = e-134
 Identities = 247/462 (53%), Positives = 313/462 (67%), Gaps = 7/462 (1%)

Query: 16  ETLESLDPVGQGVVWSGRGADATQVDAAVCAAREAFPAWARRPLEQRIELLERFAATLKS 75
           E L S +P     +W G  +D   VDA V AAR+A+P WA +PL  R E L RFA  +K+
Sbjct: 3   EELISHEPATGAELWRGGISD---VDAEVAAARQAWPGWAAKPLAYRAETLRRFADRVKA 59

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

Query: 134 KPHGVVAVFGPYNFPGHLPNGHIVPALLAGNCVVFKPSELTPKVAELTLKAWIQAGLPAG 193
           KPHG +AV GPYNFP HLPNGHIVPALLAGN V+FKPSE TP V     + +  AG+P  
Sbjct: 119 KPHGALAVLGPYNFPAHLPNGHIVPALLAGNSVIFKPSEKTPAVGAKLAQLFHSAGVPEE 178

Query: 194 VLNLVQGGRETGVALAAHRGLDGLFFTGSSRTGNLLHSQFGGQPQKILALEMGGNNPLVV 253
           VL LV GG + G ALA H G+DGL FTGS+RTG  L+ QF  +P KILALEMGGNNP+VV
Sbjct: 179 VLRLVIGGPDQGKALAGHDGIDGLLFTGSARTGVALNRQFADRPGKILALEMGGNNPIVV 238

Query: 254 EEVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDALLARLVAVSATLRVGRFDE 313
            +  D+  A   ++QSAF+SAGQRCT ARRL+V Q    +AL+  +  ++  L V     
Sbjct: 239 WDTPDIRTAAMLVVQSAFLSAGQRCTNARRLIVRQTV-AEALIDEVRNLTNRLIVDHPHA 297

Query: 314 QPAPFMGAVISLSAAEHLLKAQEHLIGKGAQPLLAMTQPIDGAALLTPGILDVSAVAERP 373
            PAP+MG VI   AA+ L ++   L+  G Q +  MT+PI     LTPGI+DV+A+ ERP
Sbjct: 298 DPAPYMGPVIDNEAADGLTESFLILMSNGGQVIRHMTRPIADRPFLTPGIIDVTAMPERP 357

Query: 374 DEEFFGPLLQVIRYSDFAAAIREANATQYGLAAGLLSDSRERFEQFLVESRAGIVNWNKQ 433
           D E FGPLLQ++R   F AAI EAN T +GL+A L+  + + ++QF   +RAG++NWN+ 
Sbjct: 358 DIELFGPLLQLVRVDSFEAAIAEANNTAFGLSAALIGGTPQLYDQFWANARAGVINWNRP 417

Query: 434 LTGAASSAPFGGIGASGNHRPSAYYAADYCAYPVASLESPSV 475
             GA+S+APFGGIG SGNHRPSA+YAADYCAYPVAS ES ++
Sbjct: 418 TNGASSAAPFGGIGLSGNHRPSAFYAADYCAYPVASSESDAL 459


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: 666
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: 483
Length adjustment: 34
Effective length of query: 453
Effective length of database: 449
Effective search space:   203397
Effective search space used:   203397
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_089214372.1 CHB69_RS02540 (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.724454.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     1e-188  613.9   0.1   1.2e-188  613.7   0.1    1.0  1  NCBI__GCF_900188185.1:WP_089214372.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900188185.1:WP_089214372.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  613.7   0.1  1.2e-188  1.2e-188      13     474 ..       3     461 ..       1     467 [. 0.97

  Alignments for each domain:
  == domain 1  score: 613.7 bits;  conditional E-value: 1.2e-188
                             TIGR03240  13 eslesldpvtqevlwqgkaasaaqvekavkaarkafpawarlsleeriavvkrfaelleeekeelaeviaket 85 
                                           e+l s++p+t+++lw+g     ++v++ v+aar+a+p wa+ +l+ r++ ++rfa++++ ++e++a++ia+et
  NCBI__GCF_900188185.1:WP_089214372.1   3 EELISHEPATGAELWRGGI---SDVDAEVAAARQAWPGWAAKPLAYRAETLRRFADRVKADAESFADLIARET 72 
                                           567899**********975...6899*********************************************** PP

                             TIGR03240  86 gkplweartevasmvakvaisikayeertGekeselada.kavlrhrphGvlavfGpynfpGhlpnGhivpal 157
                                           gkplweartev+s++akv+is+kay+ert +++ e a + +  +rh+phG lav+Gpynfp hlpnGhivpal
  NCBI__GCF_900188185.1:WP_089214372.1  73 GKPLWEARTEVESVAAKVDISVKAYAERTPNRRIEGAMGlRHAVRHKPHGALAVLGPYNFPAHLPNGHIVPAL 145
                                           ******************************99877666535678***************************** PP

                             TIGR03240 158 laGntvvfkpseltplvaeetvklwekaGlpaGvlnlvqGaretGkalaaeedidGllftGssntGallhrql 230
                                           laGn+v+fkpse tp v+ ++ +l+++aG+p+ vl lv G+ + Gkala +++idGllftGs++tG  l+rq+
  NCBI__GCF_900188185.1:WP_089214372.1 146 LAGNSVIFKPSEKTPAVGAKLAQLFHSAGVPEEVLRLVIGGPDQGKALAGHDGIDGLLFTGSARTGVALNRQF 218
                                           ************************************************************************* PP

                             TIGR03240 231 agrpekilalelGGnnplvveevkdidaavhlivqsafisaGqrctcarrllvkdgaeGdallerlvevaerl 303
                                           a+rp kilale+GGnnp+vv+++ di +a+ l+vqsaf+saGqrct arrl+v+++   +al++++ ++++rl
  NCBI__GCF_900188185.1:WP_089214372.1 219 ADRPGKILALEMGGNNPIVVWDTPDIRTAAMLVVQSAFLSAGQRCTNARRLIVRQT-VAEALIDEVRNLTNRL 290
                                           *****************************************************986.679************* PP

                             TIGR03240 304 tvgkydaepqpflGavisekaakellaaqekllalggksllelkqleeeaalltpgiidvtevaevpdeeyfg 376
                                            v++ +a+p+p++G+vi ++aa+ l ++   l+ +gg+ + ++++  ++  +ltpgiidvt++ e+pd e+fg
  NCBI__GCF_900188185.1:WP_089214372.1 291 IVDHPHADPAPYMGPVIDNEAADGLTESFLILMSNGGQVIRHMTRPIADRPFLTPGIIDVTAMPERPDIELFG 363
                                           ************************************************************************* PP

                             TIGR03240 377 pllkvlrykdfdealaeanntrfGlaaGllsddrelydkflleiraGivnwnkpltGassaapfGGiGasGnh 449
                                           pll+++r+++f++a+aeannt+fGl+a l+    +lyd+f+ ++raG++nwn+p++GassaapfGGiG sGnh
  NCBI__GCF_900188185.1:WP_089214372.1 364 PLLQLVRVDSFEAAIAEANNTAFGLSAALIGGTPQLYDQFWANARAGVINWNRPTNGASSAAPFGGIGLSGNH 436
                                           ************************************************************************* PP

                             TIGR03240 450 rpsayyaadycaypvasleadslal 474
                                           rpsa+yaadycaypvas e+d l +
  NCBI__GCF_900188185.1:WP_089214372.1 437 RPSAFYAADYCAYPVASSESDALRA 461
                                           *********************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (484 nodes)
Target sequences:                          1  (483 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: 00:00:00.01
# Mc/sec: 16.80
//
[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