Alignments for a candidate for astE in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for astE in Marinobacter adhaerens HP15

Align succinylglutamate desuccinylase (EC 3.5.1.96) (characterized)
to candidate GFF3091 HP15_3034 succinylglutamate desuccinylase

Query= BRENDA::O50177
         (332 letters)



>FitnessBrowser__Marino:GFF3091
          Length = 351

 Score =  227 bits (579), Expect = 3e-64
 Identities = 129/309 (41%), Positives = 178/309 (57%), Gaps = 6/309 (1%)

Query: 26  DGTRLHWLAEGALEVTPIGARDN--GVDLLLSAGIHGNETAPIELLERLIRKVAAGTLKP 83
           DGTR+   A G L++ P  AR N     +++SAG+HGNETAPIE+L RL+ ++  G  + 
Sbjct: 35  DGTRISRKAVGVLDIVPPAARSNPNAEAIIVSAGVHGNETAPIEVLNRLVSELIEGEWEL 94

Query: 84  AARVLFLFGNPEAIRRGERYVEQDMNRLFNGRHEEGSGN---EAFRAAELERLAQVFFSK 140
           A  VL + GNP A+  G+R++E ++NRLF+G H         EA RA ELE   + F   
Sbjct: 95  ACPVLLIMGNPPAMVAGKRFLEVNLNRLFDGAHSRNEYEGLAEAARAQELEEACRQFAMA 154

Query: 141 TERVHLHYDLHTAIRGSKIEQFALYPWAEGRQHSRSELARLRDAGIEAVLLQNKPGITFS 200
             +   HYDLHTAIR S  E+FALYP+ EGR     +   L +A +E +LLQ+K G TFS
Sbjct: 155 NPQALYHYDLHTAIRPSHRERFALYPFVEGRTVPVDQCDFLLEAEVETLLLQHKAGTTFS 214

Query: 201 AYTYGQLGAEAFTLELGKARPFGENQEVNLERLERSLELLIDGSEEQPDGSRLDGLKLFS 260
           +++   L AE+FT+ELGK RPFG+N       +  +L     G          D L +F 
Sbjct: 215 SFSSSLLKAESFTVELGKVRPFGQNDLGRFSGIRDALRRRFKGQPSPAPQPPFDHLTVFE 274

Query: 261 VSREVIKHSDHFRLHLDDDVANFTELSPGYLLAEDIGGTRWVVDEVGARIIFPNPRVKNG 320
           V  E++    +FR H+ DDVANFTE  PG ++ ED   T + V      I+FPNP V  G
Sbjct: 275 VVHEILNTGKNFRFHIPDDVANFTEYQPGTVIWED-DETSYRVGHSPEAIVFPNPEVPVG 333

Query: 321 LRAGILVVP 329
            R G+++ P
Sbjct: 334 HRVGLMIRP 342


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: 298
Number of extensions: 13
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: 332
Length of database: 351
Length adjustment: 29
Effective length of query: 303
Effective length of database: 322
Effective search space:    97566
Effective search space used:    97566
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 GFF3091 HP15_3034 (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.28566.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
      7e-98  313.8   0.0    7.7e-98  313.7   0.0    1.0  1  lcl|FitnessBrowser__Marino:GFF3091  HP15_3034 succinylglutamate desu


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF3091  HP15_3034 succinylglutamate desuccinylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  313.7   0.0   7.7e-98   7.7e-98      19     318 ..      34     340 ..      13     341 .. 0.92

  Alignments for each domain:
  == domain 1  score: 313.7 bits;  conditional E-value: 7.7e-98
                           TIGR03242  19 aknvklrwldeGvlelePe....aeaekslvisaGihGnetaPielleqllsdiaagklqlkvrlLlilGnpaal 89 
                                           + ++   + Gvl ++P     +   +++++saG+hGnetaPie+l++l+s++++g+ +l + +Lli+Gnp+a+
  lcl|FitnessBrowser__Marino:GFF3091  34 PDGTRISRKAVGVLDIVPPaarsNPNAEAIIVSAGVHGNETAPIEVLNRLVSELIEGEWELACPVLLIMGNPPAM 108
                                         66777888899******987776777899********************************************** PP

                           TIGR03242  90 rkgkRyleedlnRlfgGryq..eleeskeklRaeeLeqvveaffeagkasearyhyDlhtaiRasklekfallPy 162
                                          +gkR+le +lnRlf G +   e+e   e+ Ra+eLe++ ++f  a  ++   yhyDlhtaiR s+ e+fal+P 
  lcl|FitnessBrowser__Marino:GFF3091 109 VAGKRFLEVNLNRLFDGAHSrnEYEGLAEAARAQELEEACRQFAMANPQA--LYHYDLHTAIRPSHRERFALYPF 181
                                         ******************9633688899**************98887777..6*********************9 PP

                           TIGR03242 163 q.ekpfdkellewlaaadldavllhkekggtfshfssekleaeactlelGkarPfGendlsqfqaitealralis 236
                                           ++     + ++l +a+++++ll++++g+tfs fss  l+ae++t+elGk+rPfG+ndl +f+ i +alr+   
  lcl|FitnessBrowser__Marino:GFF3091 182 VeGRTVPVDQCDFLLEAEVETLLLQHKAGTTFSSFSSSLLKAESFTVELGKVRPFGQNDLGRFSGIRDALRRRFK 256
                                         8899999*******************************************************************9 PP

                           TIGR03242 237 deaiparkke..elklfevvesilkksdsfelhvaedasnftefakGtllaedkderyrveeeeerilfPnakva 309
                                         ++  pa +    +l  fevv++il +  +f++h+++d+ nfte++ Gt++ ed ++ yrv ++ e i+fPn++v 
  lcl|FitnessBrowser__Marino:GFF3091 257 GQPSPAPQPPfdHLTVFEVVHEILNTGKNFRFHIPDDVANFTEYQPGTVIWEDDETSYRVGHSPEAIVFPNPEVP 331
                                         988877664444*************************************************************** PP

                           TIGR03242 310 nGlRaglll 318
                                          G R gl++
  lcl|FitnessBrowser__Marino:GFF3091 332 VGHRVGLMI 340
                                         ********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (319 nodes)
Target sequences:                          1  (351 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: 12.29
//
[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