Alignments for a candidate for astE in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for astE in Klebsiella michiganensis M5al

Align Succinylglutamate desuccinylase; EC 3.5.1.96 (characterized)
to candidate BWI76_RS11690 BWI76_RS11690 succinylglutamate desuccinylase

Query= SwissProt::Q8ZPU8
         (322 letters)



>FitnessBrowser__Koxy:BWI76_RS11690
          Length = 321

 Score =  415 bits (1066), Expect = e-121
 Identities = 209/320 (65%), Positives = 243/320 (75%), Gaps = 1/320 (0%)

Query: 1   MDNFLALTLSGTTPRVTQGKGAGFRWRWLGHGLLELTPDAPVDRALILSAGIHGNETAPV 60
           MD+FLALTL+G  P    G+ A FRW W+  G+L+L P  P DR+L+LS+G+HGNETAPV
Sbjct: 1   MDDFLALTLAGRLPHHFHGQTAQFRWHWIDCGILQLVPHEPCDRSLVLSSGLHGNETAPV 60

Query: 61  EMLDKLLSALYSGSLTLTWRVLVVLGNPQALAAGIRYCHSDMNRMFGGRWQSFAESDETR 120
           E+ D LL  L+ G   L WR+LV+ GNPQAL A  RY HSD+NRMFG RW++F+ SDET 
Sbjct: 61  EITDLLLRQLFRGETPLRWRLLVIFGNPQALRANKRYLHSDINRMFGERWRAFSASDETV 120

Query: 121 RARELELSLETFFSSGQARVRWHLDLHTAIRGSHHLRFGVLPQRDRPWETDFLAWLGAAG 180
           RAR+LE +L  F+++  A  RWHLDLHTAIRGS H RFGVLP R++PW+  FL WLGAAG
Sbjct: 121 RARQLEHALARFYAA-TAGERWHLDLHTAIRGSLHTRFGVLPAREKPWDEGFLRWLGAAG 179

Query: 181 LEALVFHQAPGGTFTHFSSEHFGALSCTLELGKALPFRQNDLTQFNVTSQALSALLSGVE 240
           LEALVFHQ PGGTFTHFSSE FGALSCTLELGKALPF  NDL  F  T +ALS LL+G  
Sbjct: 180 LEALVFHQQPGGTFTHFSSERFGALSCTLELGKALPFGDNDLRLFAATQRALSLLLAGEL 239

Query: 241 TSTSFSPPLRYRVVSQITRHSDKFALYMDAQTLNFTAFAKGTLLAEEGDKRVTVTHDVEY 300
           T      PLRYRVV QITR SD+F L+M AQTLNFT F+ GTLLAE+GD R  V  + EY
Sbjct: 240 TLEDEHTPLRYRVVQQITRSSDRFQLHMSAQTLNFTLFSFGTLLAEDGDTRYVVEGEQEY 299

Query: 301 VLFPNPSVACGLRAGLMLER 320
           VLFPNPSVA G RAGLML+R
Sbjct: 300 VLFPNPSVAFGQRAGLMLQR 319


Lambda     K      H
   0.322    0.136    0.418 

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: 391
Number of extensions: 12
Number of successful extensions: 2
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: 322
Length of database: 321
Length adjustment: 28
Effective length of query: 294
Effective length of database: 293
Effective search space:    86142
Effective search space used:    86142
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 (21.9 bits)
S2: 48 (23.1 bits)

Align candidate BWI76_RS11690 BWI76_RS11690 (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.14499.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   1.4e-131  424.5   0.0   1.6e-131  424.3   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS11690  BWI76_RS11690 succinylglutamate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS11690  BWI76_RS11690 succinylglutamate desuccinylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  424.3   0.0  1.6e-131  1.6e-131       1     319 []       3     318 ..       3     318 .. 0.99

  Alignments for each domain:
  == domain 1  score: 424.3 bits;  conditional E-value: 1.6e-131
                               TIGR03242   1 dflaltlekkepevtqgeaknvklrwldeGvlelePeaeaekslvisaGihGnetaPielleqllsdiaag 71 
                                             dflaltl+ + p+  +g++ +++++w+d G+l+l+P++ +++slv+s+G+hGnetaP+e+ + ll+++++g
  lcl|FitnessBrowser__Koxy:BWI76_RS11690   3 DFLALTLAGRLPHHFHGQTAQFRWHWIDCGILQLVPHEPCDRSLVLSSGLHGNETAPVEITDLLLRQLFRG 73 
                                             8********************************************************************** PP

                               TIGR03242  72 klqlkvrlLlilGnpaalrkgkRyleedlnRlfgGryqeleeskeklRaeeLeqvveaffeagkasearyh 142
                                             + +l++rlL+i+Gnp+alr++kRyl++d+nR+fg r++ +++s+e+ Ra++Le+++++f++a+     r+h
  lcl|FitnessBrowser__Koxy:BWI76_RS11690  74 ETPLRWRLLVIFGNPQALRANKRYLHSDINRMFGERWRAFSASDETVRARQLEHALARFYAATAGE--RWH 142
                                             ************************************************************987665..9** PP

                               TIGR03242 143 yDlhtaiRasklekfallPyqekpfdkellewlaaadldavllhkekggtfshfssekleaeactlelGka 213
                                             +DlhtaiR+s++ +f++lP++ekp+d+ +l+wl+aa+l+a+++h+++ggtf+hfsse+++a +ctlelGka
  lcl|FitnessBrowser__Koxy:BWI76_RS11690 143 LDLHTAIRGSLHTRFGVLPAREKPWDEGFLRWLGAAGLEALVFHQQPGGTFTHFSSERFGALSCTLELGKA 213
                                             *********************************************************************** PP

                               TIGR03242 214 rPfGendlsqfqaitealralisdeaiparkkeelklfevvesilkksdsfelhvaedasnftefakGtll 284
                                             +PfG+ndl+ f+a+++al+ l+++e + ++++++l+ ++vv++i+++sd f+lh+++++ nft f+ Gtll
  lcl|FitnessBrowser__Koxy:BWI76_RS11690 214 LPFGDNDLRLFAATQRALSLLLAGELTLEDEHTPLR-YRVVQQITRSSDRFQLHMSAQTLNFTLFSFGTLL 283
                                             ***********************************9.********************************** PP

                               TIGR03242 285 aedkderyrveeeeerilfPnakvanGlRaglllv 319
                                             aed d+ry+ve e+e++lfPn++va G+Ragl+l+
  lcl|FitnessBrowser__Koxy:BWI76_RS11690 284 AEDGDTRYVVEGEQEYVLFPNPSVAFGQRAGLMLQ 318
                                             *********************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (319 nodes)
Target sequences:                          1  (321 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 8.19
//
[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