Alignments for a candidate for astD in Amantichitinum ursilacus IGB-41

GapMind for catabolism of small carbon sources

Alignments for a candidate for astD in Amantichitinum ursilacus IGB-41

Align Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized)
to candidate WP_053935844.1 WG78_RS00590 succinylglutamate-semialdehyde dehydrogenase

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1974
         (488 letters)



>NCBI__GCF_001294205.1:WP_053935844.1
          Length = 485

 Score =  644 bits (1660), Expect = 0.0
 Identities = 318/484 (65%), Positives = 385/484 (79%)

Query: 4   LYIAGEWLAGGGEAFESLNPVTQQVLWSGVGATAGQVESAVQAARQAFPDWARRTLEERI 63
           L I GEW AG GE ++S NPVTQ ++W G  A A +V++AV  AR AF  WAR+  E R+
Sbjct: 2   LMINGEWRAGSGERWQSRNPVTQHIVWDGQAANAAEVDAAVANARAAFKSWARQEPEARL 61

Query: 64  SVLEAFAAALKNHADELAHTIGEETGKPLWEAATEVTSMVNKIAISVQSYRERTGEKSGP 123
           +V   FA  LK +   LA TIG ETGKP WEA TEVTSM+NK+ IS+++  ERTG K   
Sbjct: 62  AVARNFAELLKTNQAMLADTIGLETGKPRWEALTEVTSMINKVDISIRALDERTGSKEAT 121

Query: 124 LGDATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVLFKPSELTPKVAELTVK 183
            GDA AVLRH+PHGV+AVFGPYNFPGHLPNGHIVPAL+AGN V+FKPSEL P VA+ T +
Sbjct: 122 QGDALAVLRHRPHGVLAVFGPYNFPGHLPNGHIVPALIAGNCVVFKPSELAPLVAQKTAE 181

Query: 184 CWIEAGLPAGVLNLLQGARETGIALAANPGIDGLFFTGSSRTGNHLHQQFAGRPDKILAL 243
            W+ AGLPAGVLNLLQG R+TGIAL+ + GIDGL FTGS+ TG HLH+QFAG+PDK+LAL
Sbjct: 182 LWLAAGLPAGVLNLLQGGRDTGIALSKHAGIDGLLFTGSATTGYHLHRQFAGQPDKMLAL 241

Query: 244 EMGGNNPLVVDQVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDSLLARLVAVS 303
           EMGGNNPL+V+QVAD++AA++ ++QSAF+SAGQRCTCARRLLVPQG+WGD+ + RL  V+
Sbjct: 242 EMGGNNPLIVEQVADVNAALHHVVQSAFVSAGQRCTCARRLLVPQGSWGDAFIDRLSEVT 301

Query: 304 STLSVGAFDQQPAPFMGSVVSLGAAKALMDAQEHLLANGAVALLEMTQPQAQSALLTPGI 363
             L+VGA+D +P PFMG+V+SL AA+ L+ AQ  L A GA ++L M +    +ALL+PGI
Sbjct: 302 RNLTVGAWDAEPQPFMGAVISLHAAEQLLKAQTELHAMGAASILTMRRLVEGTALLSPGI 361

Query: 364 LDVSAVADRPDEELFGPLLQVIRYADFEAAIAEANDTAYGLAAGLLSDSEARYQQFWLES 423
           LDV+ VA  PD+E FGPLLQV RYADF  AI  AN T YGLAAGLLSD EA+Y+ FWLES
Sbjct: 362 LDVTHVAHLPDDEYFGPLLQVQRYADFNEAITLANRTRYGLAAGLLSDDEAQYRTFWLES 421

Query: 424 RAGIVNWNKQLTGAASSAPFGGVGASGNHRASAYYAADYCAYPVASLETPSLVLPSALTP 483
           RAGIVNWNK LTGA+S+APFGGVGASGNHR SA+YAADYCA+PVASLE+ +L LP  L P
Sbjct: 422 RAGIVNWNKPLTGASSAAPFGGVGASGNHRPSAWYAADYCAWPVASLESNALTLPGQLPP 481

Query: 484 GVKM 487
           G+ +
Sbjct: 482 GLTL 485


Lambda     K      H
   0.316    0.132    0.388 

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: 750
Number of extensions: 28
Number of successful extensions: 1
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: 488
Length of database: 485
Length adjustment: 34
Effective length of query: 454
Effective length of database: 451
Effective search space:   204754
Effective search space used:   204754
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 WP_053935844.1 WG78_RS00590 (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.2952462.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.3e-252  822.4   1.0   7.1e-252  822.2   1.0    1.0  1  NCBI__GCF_001294205.1:WP_053935844.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001294205.1:WP_053935844.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  822.2   1.0  7.1e-252  7.1e-252       2     483 ..       3     484 ..       2     485 .] 1.00

  Alignments for each domain:
  == domain 1  score: 822.2 bits;  conditional E-value: 7.1e-252
                             TIGR03240   2 fidGkwraGqGeslesldpvtqevlwqgkaasaaqvekavkaarkafpawarlsleeriavvkrfaelleeek 74 
                                            i+G+wraG+Ge  +s++pvtq+ +w+g+aa+aa+v++av+ ar+af++war + e+r+av ++faell+ ++
  NCBI__GCF_001294205.1:WP_053935844.1   3 MINGEWRAGSGERWQSRNPVTQHIVWDGQAANAAEVDAAVANARAAFKSWARQEPEARLAVARNFAELLKTNQ 75 
                                           69*********************************************************************** PP

                             TIGR03240  75 eelaeviaketgkplweartevasmvakvaisikayeertGekeseladakavlrhrphGvlavfGpynfpGh 147
                                           + la++i+ etgkp+wea tev+sm++kv+isi+a++ertG+ke++ +da avlrhrphGvlavfGpynfpGh
  NCBI__GCF_001294205.1:WP_053935844.1  76 AMLADTIGLETGKPRWEALTEVTSMINKVDISIRALDERTGSKEATQGDALAVLRHRPHGVLAVFGPYNFPGH 148
                                           ************************************************************************* PP

                             TIGR03240 148 lpnGhivpallaGntvvfkpseltplvaeetvklwekaGlpaGvlnlvqGaretGkalaaeedidGllftGss 220
                                           lpnGhivpal+aGn+vvfkpsel+plva++t +lw +aGlpaGvlnl+qG+r+tG al+++ +idGllftGs+
  NCBI__GCF_001294205.1:WP_053935844.1 149 LPNGHIVPALIAGNCVVFKPSELAPLVAQKTAELWLAAGLPAGVLNLLQGGRDTGIALSKHAGIDGLLFTGSA 221
                                           ************************************************************************* PP

                             TIGR03240 221 ntGallhrqlagrpekilalelGGnnplvveevkdidaavhlivqsafisaGqrctcarrllvkdgaeGdall 293
                                           +tG++lhrq+ag+p+k+lale+GGnnpl+ve+v+d++aa h++vqsaf+saGqrctcarrllv++g++Gda++
  NCBI__GCF_001294205.1:WP_053935844.1 222 TTGYHLHRQFAGQPDKMLALEMGGNNPLIVEQVADVNAALHHVVQSAFVSAGQRCTCARRLLVPQGSWGDAFI 294
                                           ************************************************************************* PP

                             TIGR03240 294 erlvevaerltvgkydaepqpflGavisekaakellaaqekllalggksllelkqleeeaalltpgiidvtev 366
                                           +rl ev+++ltvg++daepqpf+Gavis +aa++ll+aq++l+a+g++s+l++++l e++all+pgi+dvt+v
  NCBI__GCF_001294205.1:WP_053935844.1 295 DRLSEVTRNLTVGAWDAEPQPFMGAVISLHAAEQLLKAQTELHAMGAASILTMRRLVEGTALLSPGILDVTHV 367
                                           ************************************************************************* PP

                             TIGR03240 367 aevpdeeyfgpllkvlrykdfdealaeanntrfGlaaGllsddrelydkflleiraGivnwnkpltGassaap 439
                                           a++pd+eyfgpll+v ry+df+ea++ an tr+GlaaGllsdd+++y++f+le+raGivnwnkpltGassaap
  NCBI__GCF_001294205.1:WP_053935844.1 368 AHLPDDEYFGPLLQVQRYADFNEAITLANRTRYGLAAGLLSDDEAQYRTFWLESRAGIVNWNKPLTGASSAAP 440
                                           ************************************************************************* PP

                             TIGR03240 440 fGGiGasGnhrpsayyaadycaypvasleadslalpatlspGlk 483
                                           fGG+GasGnhrpsa+yaadyca+pvasle++ l+lp +l pGl+
  NCBI__GCF_001294205.1:WP_053935844.1 441 FGGVGASGNHRPSAWYAADYCAWPVASLESNALTLPGQLPPGLT 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 28.75
//
[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 2024 update 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