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

GapMind for catabolism of small carbon sources

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

Align succinylglutamate desuccinylase (EC 3.5.1.96) (characterized)
to candidate WP_053935846.1 WG78_RS00600 succinylglutamate desuccinylase

Query= BRENDA::O50177
         (332 letters)



>NCBI__GCF_001294205.1:WP_053935846.1
          Length = 336

 Score =  261 bits (667), Expect = 2e-74
 Identities = 151/331 (45%), Positives = 201/331 (60%), Gaps = 6/331 (1%)

Query: 5   GKLLDLTLAGREPTEKIQLTADGTRLHWLAEGALEVTPIGARDNGVDLLLSAGIHGNETA 64
           G  L  TLAG+           G  +  + EG +   P   + + + L++S G+HGNETA
Sbjct: 4   GSFLAQTLAGKTTLGLPFYLPHGANVQIMDEGVIRFGPRDPQSSPLHLVISCGVHGNETA 63

Query: 65  PIELLERLIRKVAAGTLKPAARVLFLFGNPEAIRRGERYVEQDMNRLFNGRHEEGSGNEA 124
           P+EL+ERLI  + +G LKP ARV+F+ GN  A+R G R+V+QDMNRLF    E    +E+
Sbjct: 64  PVELVERLIAALLSGELKPRARVMFVLGNVAALRAGTRFVQQDMNRLFCRIPEASDDDES 123

Query: 125 FRAAELERLAQVFFSKT---ERVHLHYDLHTAIRGSKIEQFALYPWA-EGRQHSRSELAR 180
            RA  LE     FFS+    ++  LHYDLHTAI GS+IE+FA+YP   EG+    + +AR
Sbjct: 124 RRATMLEMHLMRFFSRAIQDDKPRLHYDLHTAIHGSQIEKFAIYPRPNEGQNFQPAAVAR 183

Query: 181 LRDAGIEAVLLQNKPGITFSAYTYGQLGAEAFTLELGKARPFGENQEVNLERLERSLELL 240
           L   G+ AVLLQ     TFS ++    GA AFT+ELG+A PFG+N  ++L ++E  L  L
Sbjct: 184 LARGGVSAVLLQTSTAPTFSYFSSRHCGATAFTVELGRAAPFGQNAALDLSQMEAHLRAL 243

Query: 241 IDGSEEQPDGSRLDGLKLFSVSREVIKHSDHFRLHLDDDVANFTELSPGYLLAEDIGGTR 300
           I G E   D S    +++F VSRE+IK S+ F L +D    NFT L  G  LA D G   
Sbjct: 244 I-GGEVPMDDSAPASMQVFRVSREIIKRSEAFELFIDAKTDNFTPLIQGQPLARD-GDQT 301

Query: 301 WVVDEVGARIIFPNPRVKNGLRAGILVVPAK 331
           W VDEVGARIIFPNP V  G RAG+++VP +
Sbjct: 302 WTVDEVGARIIFPNPDVAVGQRAGLVIVPTE 332


Lambda     K      H
   0.319    0.138    0.399 

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: 275
Number of extensions: 11
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: 332
Length of database: 336
Length adjustment: 28
Effective length of query: 304
Effective length of database: 308
Effective search space:    93632
Effective search space used:    93632
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: 49 (23.5 bits)

Align candidate WP_053935846.1 WG78_RS00600 (succinylglutamate desuccinylase)
to HMM TIGR03242 (astE: succinylglutamate desuccinylase (EC 3.5.1.96))

# 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/TIGR03242.hmm
# target sequence database:        /tmp/gapView.3095537.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03242  [M=319]
Accession:   TIGR03242
Description: arg_catab_astE: succinylglutamate desuccinylase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.4e-103  331.2   0.0   3.9e-103  331.1   0.0    1.0  1  NCBI__GCF_001294205.1:WP_053935846.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001294205.1:WP_053935846.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  331.1   0.0  3.9e-103  3.9e-103       2     319 .]       6     329 ..       5     329 .. 0.93

  Alignments for each domain:
  == domain 1  score: 331.1 bits;  conditional E-value: 3.9e-103
                             TIGR03242   2 flaltlekkep.evtqgeaknvklrwldeGvlelePe..aeaekslvisaGihGnetaPielleqllsdiaag 71 
                                           fla tl+ k++  +     ++++++ +deGv++  P+  ++    lvis G+hGnetaP+el+e+l++++++g
  NCBI__GCF_001294205.1:WP_053935846.1   6 FLAQTLAGKTTlGLPFYLPHGANVQIMDEGVIRFGPRdpQSSPLHLVISCGVHGNETAPVELVERLIAALLSG 78 
                                           7777777777745556668999***************555566789*************************** PP

                             TIGR03242  72 klqlkvrlLlilGnpaalrkgkRyleedlnRlfgGryqeleeskeklRaeeLeqvveaffeagkasea.ryhy 143
                                           +l+ ++r++++lGn aalr+g R++++d+nRlf+ r  e +  +e +Ra+ Le ++++ff+++ + ++ r+hy
  NCBI__GCF_001294205.1:WP_053935846.1  79 ELKPRARVMFVLGNVAALRAGTRFVQQDMNRLFC-RIPEASDDDESRRATMLEMHLMRFFSRAIQDDKpRLHY 150
                                           *********************************9.7779999*********************998777**** PP

                             TIGR03242 144 DlhtaiRasklekfallPyq..ekpfdkellewlaaadldavllhkekggtfshfssekleaeactlelGkar 214
                                           Dlhtai +s++ekfa++P    +++f+ + +++la  ++ avll+++++ tfs+fss++++a+a+t+elG+a 
  NCBI__GCF_001294205.1:WP_053935846.1 151 DLHTAIHGSQIEKFAIYPRPneGQNFQPAAVARLARGGVSAVLLQTSTAPTFSYFSSRHCGATAFTVELGRAA 223
                                           *****************97645899************************************************ PP

                             TIGR03242 215 PfGendlsqfqaitealralisdeaiparkke.elklfevvesilkksdsfelhvaedasnftefakGtllae 286
                                           PfG+n    +++++++lrali +e    +++   ++ f+v ++i+k+s++fel++ +++ nft++ +G+ la+
  NCBI__GCF_001294205.1:WP_053935846.1 224 PFGQNAALDLSQMEAHLRALIGGEVPMDDSAPaSMQVFRVSREIIKRSEAFELFIDAKTDNFTPLIQGQPLAR 296
                                           *********************7776555555579*************************************** PP

                             TIGR03242 287 dkderyrveeeeerilfPnakvanGlRaglllv 319
                                           d d+ ++v e ++ri+fPn++va G+Ragl++v
  NCBI__GCF_001294205.1:WP_053935846.1 297 DGDQTWTVDEVGARIIFPNPDVAVGQRAGLVIV 329
                                           ******************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (319 nodes)
Target sequences:                          1  (336 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: 19.13
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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