Alignments for a candidate for astD in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for astD in Caulobacter crescentus NA1000

Align N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized)
to candidate CCNA_01679 CCNA_01679 succinylglutamic semialdehyde dehydrogenase

Query= SwissProt::Q8ZPV0
         (492 letters)



>FitnessBrowser__Caulo:CCNA_01679
          Length = 485

 Score =  472 bits (1214), Expect = e-137
 Identities = 244/471 (51%), Positives = 323/471 (68%), Gaps = 7/471 (1%)

Query: 3   LWINGDWITGQGERRRKTNPVSAEILWQGNDANAAQVAEACQAARAAFPRWARQPFAARQ 62
           L+I+G W  GQG     T+P + E +W    A  A VA+A  AAR AFP WA +P   R 
Sbjct: 5   LFIDGKWRAGQGAGLSSTDPATGEDVWSAATATPADVADAVAAARKAFPAWADRPREERI 64

Query: 63  AIVEKFAALLEAHKAELTEVIARETGKPRWEAATEVTAMINKIAISIKAYHARTGAQKSE 122
           AI+ ++  +L    A   E ++RETGK  WE   E+ +M  K+ +SI+AY  RTG  ++ 
Sbjct: 65  AILRRYKDILVERAAPYAEALSRETGKALWETRAELASMAGKVDLSIRAYDERTGVTENA 124

Query: 123 LVDGAATLRHRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNTLIFKPSELTPWTGETVIK 182
           +  G A LRHR HGV+AV GP+NFPGHLPNGHIVPALLAG+T++FKPSE TP  G+ +++
Sbjct: 125 MPFGRAVLRHRAHGVMAVLGPFNFPGHLPNGHIVPALLAGDTVVFKPSEETPLAGQLMVE 184

Query: 183 LWERAGLPAGVLNLVQGGRETGQALSSLDDLDGLLFTGSASTGYQLHRQLSGQPEKILAL 242
             E AG PAGV+NLVQGGRETGQAL +  D+DGLLFTGSA+ G    R  + +P+ ILAL
Sbjct: 185 ALEAAGAPAGVVNLVQGGRETGQALIA-QDIDGLLFTGSAAAGTYFRRYFADRPDVILAL 243

Query: 243 EMGGNNPLIIEDAANI-DAAVHLTLQSAFITAGQRCTCARRLLVKQGAQGDAFLARLVDV 301
           E+GGNNPL++ +A +  +A   L +QSAFIT GQRC+CARRL+V   A G A +   V +
Sbjct: 244 ELGGNNPLVVWNADDAPEAVAALIVQSAFITTGQRCSCARRLIVPDDASGAAIIEATVAL 303

Query: 302 AGRLQPGRWDDDPQPFIGGLISAQAAQHVMEAWRQREALGGRTLLAPRKVKE-GTSLLTP 360
           A RL  G W+ + +PF+G LIS +AA+   E      A  G+T+LA   V   G + L P
Sbjct: 304 AERLVIGAWNAENEPFMGPLISGRAAKAAREV---ASATPGKTILALDGVAGLGDAFLKP 360

Query: 361 GIIELTGVADVPDEEVFGPLLNVWRYAHFDEAIRLANNTRFGLSCGLVSTDRAQFEQLLL 420
           GI+++TG+ + PDEE+F PLL V R + FDEA+  AN TR+GLS GL+S +   +++ L 
Sbjct: 361 GIVDVTGL-ETPDEELFAPLLQVRRVSSFDEALAAANATRYGLSAGLISNESELWDKFLS 419

Query: 421 EARAGIVNWNKPLTGAASTAPFGGVGASGNHRPSAWYAADYCAWPMASLES 471
             RAG+VNWN+P TGAA + PFGG+GASGNHRPSA+YAADYCA+P+AS E+
Sbjct: 420 RIRAGVVNWNRPTTGAAGSMPFGGLGASGNHRPSAYYAADYCAYPVASFEA 470


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: 739
Number of extensions: 30
Number of successful extensions: 5
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: 485
Length adjustment: 34
Effective length of query: 458
Effective length of database: 451
Effective search space:   206558
Effective search space used:   206558
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 CCNA_01679 CCNA_01679 (succinylglutamic 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.15568.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.4e-235  766.1   2.0   8.3e-235  765.9   2.0    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_01679  CCNA_01679 succinylglutamic semi


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_01679  CCNA_01679 succinylglutamic semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  765.9   2.0  8.3e-235  8.3e-235       1     483 [.       5     484 ..       5     485 .] 0.99

  Alignments for each domain:
  == domain 1  score: 765.9 bits;  conditional E-value: 8.3e-235
                             TIGR03240   1 lfidGkwraGqGeslesldpvtqevlwqgkaasaaqvekavkaarkafpawarlsleeriavvkrfaelleee 73 
                                           lfidGkwraGqG+ l+s+dp+t+e++w++++a+ a+v++av+aarkafpawa+++ eeria+++r++++l+e+
  lcl|FitnessBrowser__Caulo:CCNA_01679   5 LFIDGKWRAGQGAGLSSTDPATGEDVWSAATATPADVADAVAAARKAFPAWADRPREERIAILRRYKDILVER 77 
                                           59*********************************************************************** PP

                             TIGR03240  74 keelaeviaketgkplweartevasmvakvaisikayeertGekeseladakavlrhrphGvlavfGpynfpG 146
                                           ++ +ae++++etgk+lwe+r+e+asm++kv++si+ay+ertG++e++++ ++avlrhr+hGv+av+Gp+nfpG
  lcl|FitnessBrowser__Caulo:CCNA_01679  78 AAPYAEALSRETGKALWETRAELASMAGKVDLSIRAYDERTGVTENAMPFGRAVLRHRAHGVMAVLGPFNFPG 150
                                           ************************************************************************* PP

                             TIGR03240 147 hlpnGhivpallaGntvvfkpseltplvaeetvklwekaGlpaGvlnlvqGaretGkalaaeedidGllftGs 219
                                           hlpnGhivpallaG+tvvfkpse+tpl+++ +v+++e+aG paGv+nlvqG+retG+al+a+ didGllftGs
  lcl|FitnessBrowser__Caulo:CCNA_01679 151 HLPNGHIVPALLAGDTVVFKPSEETPLAGQLMVEALEAAGAPAGVVNLVQGGRETGQALIAQ-DIDGLLFTGS 222
                                           *************************************************************9.9********* PP

                             TIGR03240 220 sntGallhrqlagrpekilalelGGnnplvveevkd.idaavhlivqsafisaGqrctcarrllvkdgaeGda 291
                                           +++G++++r++a+rp++ilalelGGnnplvv++++d  +a+++livqsafi++Gqrc+carrl+v+d+a+G+a
  lcl|FitnessBrowser__Caulo:CCNA_01679 223 AAAGTYFRRYFADRPDVILALELGGNNPLVVWNADDaPEAVAALIVQSAFITTGQRCSCARRLIVPDDASGAA 295
                                           ************************************7799999****************************** PP

                             TIGR03240 292 llerlvevaerltvgkydaepqpflGavisekaakellaaqekllalggksllelkqlee.eaalltpgiidv 363
                                           ++e++v++aerl++g+++ae++pf+G++is +aak   aa+e ++a++gk++l+l+ ++  ++a+l+pgi+dv
  lcl|FitnessBrowser__Caulo:CCNA_01679 296 IIEATVALAERLVIGAWNAENEPFMGPLISGRAAK---AAREVASATPGKTILALDGVAGlGDAFLKPGIVDV 365
                                           ***********************************...9******************99879*********** PP

                             TIGR03240 364 tevaevpdeeyfgpllkvlrykdfdealaeanntrfGlaaGllsddrelydkflleiraGivnwnkpltGass 436
                                           t++ e+pdee+f+pll+v r+++fdeala+an+tr+Gl+aGl+s+++el+dkfl++iraG+vnwn+p+tGa++
  lcl|FitnessBrowser__Caulo:CCNA_01679 366 TGL-ETPDEELFAPLLQVRRVSSFDEALAAANATRYGLSAGLISNESELWDKFLSRIRAGVVNWNRPTTGAAG 437
                                           **8.9******************************************************************** PP

                             TIGR03240 437 aapfGGiGasGnhrpsayyaadycaypvasleadslalpatlspGlk 483
                                           ++pfGG+GasGnhrpsayyaadycaypvas+ea++++ + ++++Glk
  lcl|FitnessBrowser__Caulo:CCNA_01679 438 SMPFGGLGASGNHRPSAYYAADYCAYPVASFEASMVVDTLKDIKGLK 484
                                           *********************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (484 nodes)
Target sequences:                          1  (485 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: 12.36
//
[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