Alignments for a candidate for astE in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Alignments for a candidate for astE in Shewanella amazonensis SB2B

Align Succinylglutamate desuccinylase; EC 3.5.1.96 (uncharacterized)
to candidate 6937552 Sama_1708 succinylglutamate desuccinylase (RefSeq)

Query= curated2:A4Y6M4
         (344 letters)



>FitnessBrowser__SB2B:6937552
          Length = 348

 Score =  502 bits (1293), Expect = e-147
 Identities = 254/347 (73%), Positives = 283/347 (81%), Gaps = 4/347 (1%)

Query: 1   MLQALLDSKDFLALTLAHPEQFDGEFSFNLGDHTQVEVWDTGVIVFEPIQ-NEGKDIVLS 59
           ML  L   KDFL LTL++PE  D      L  HT V +WDTGV+VFEP+  N  KDIVLS
Sbjct: 1   MLNLLQGCKDFLHLTLSNPEHLDPIAPQPLYGHTLVSLWDTGVLVFEPVDGNSHKDIVLS 60

Query: 60  CGVHGNETAPIELCNSLIKQLLQQKIIAKQRTLFLIGNPLAINNGTRIIDENMNRLFSGE 119
            GVHGNETAPIELCN LI+ +L+ ++  K+R LFLIGNP AINNGTRI+DENMNRLFSGE
Sbjct: 61  SGVHGNETAPIELCNGLIQDVLEGRLQVKERVLFLIGNPAAINNGTRIVDENMNRLFSGE 120

Query: 120 HSNPPGLVNPERVRAKKLEAYVDRFFTAAAD---GRQRIHYDLHTAMRASKHEKFAIYPY 176
           HS  PGL NPERVRAKKLE YV RFF   A+   GRQRIHYDLHTA+R SKHEKFAIYPY
Sbjct: 121 HSRGPGLSNPERVRAKKLETYVTRFFEKGAEKGEGRQRIHYDLHTAIRGSKHEKFAIYPY 180

Query: 177 RPGRAFSGEQIMFLAASGVDTVLFHHEPTTTFSYFSSERYGADAFTIELGKVYPMGQNDM 236
           RPGRAFSGEQIMFLAASGVDTVLFHHEPTTTFSYFSSE + ADAFTIELGKVYPMGQNDM
Sbjct: 181 RPGRAFSGEQIMFLAASGVDTVLFHHEPTTTFSYFSSELFRADAFTIELGKVYPMGQNDM 240

Query: 237 TRFIATHEMFMRLITAKPLELDAFDADKVNLYQVCRVINKHFDDFEFTFATDVENFRSFP 296
           ++F  T EMF RLI A+PLEL  FD  +VNLYQVCRVINK  DDFEFTF+TDVENF +FP
Sbjct: 241 SKFANTREMFKRLICAEPLELAPFDETQVNLYQVCRVINKEVDDFEFTFSTDVENFSAFP 300

Query: 297 KGFVLAREGGQEIKVEHEFESVVFPNAKVPIGNRTVICLIPAVNADV 343
           +G V+AR+GG++I VE E E+VVFPNAKVP+G RTVI L+PAVN  V
Sbjct: 301 RGHVIARQGGKDILVEQEAEAVVFPNAKVPVGQRTVIMLVPAVNPHV 347


Lambda     K      H
   0.323    0.139    0.412 

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: 464
Number of extensions: 10
Number of successful extensions: 3
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: 344
Length of database: 348
Length adjustment: 29
Effective length of query: 315
Effective length of database: 319
Effective search space:   100485
Effective search space used:   100485
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 49 (23.5 bits)

Align candidate 6937552 Sama_1708 (succinylglutamate desuccinylase (RefSeq))
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.20741.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.6e-107  345.5   0.0   1.8e-107  345.3   0.0    1.0  1  lcl|FitnessBrowser__SB2B:6937552  Sama_1708 succinylglutamate desu


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6937552  Sama_1708 succinylglutamate desuccinylase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  345.3   0.0  1.8e-107  1.8e-107       1     319 []      10     340 ..      10     340 .. 0.91

  Alignments for each domain:
  == domain 1  score: 345.3 bits;  conditional E-value: 1.8e-107
                         TIGR03242   1 dflaltlekkep...evtqgeaknvklrwldeGvlelePe.aeaekslvisaGihGnetaPielleqllsdiaagkl 73 
                                       dfl+ltl++ e     + q       + + d+Gvl  eP   + +k++v+s+G+hGnetaPiel + l++d+++g+l
  lcl|FitnessBrowser__SB2B:6937552  10 DFLHLTLSNPEHldpIAPQPLYGHTLVSLWDTGVLVFEPVdGNSHKDIVLSSGVHGNETAPIELCNGLIQDVLEGRL 86 
                                       677888776543311333333455556799*********9456789******************************* PP

                         TIGR03242  74 qlkvrlLlilGnpaalrkgkRyleedlnRlfgGryqele..eskeklRaeeLeqvveaffeagkasea...ryhyDl 145
                                       q+k r+L+++Gnpaa+++g R ++e++nRlf+G++ +    +  e+ Ra++Le +v++ffe+g +  +   r hyDl
  lcl|FitnessBrowser__SB2B:6937552  87 QVKERVLFLIGNPAAINNGTRIVDENMNRLFSGEHSRGPglSNPERVRAKKLETYVTRFFEKGAEKGEgrqRIHYDL 163
                                       ***********************************8865225579*****************998765677****** PP

                         TIGR03242 146 htaiRasklekfallPyq.ekpfdkellewlaaadldavllhkekggtfshfssekleaeactlelGkarPfGendl 221
                                       htaiR+sk+ekfa++Py+ ++ f+ e++ +laa+++d+vl+h+e+++tfs+fsse + a+a+t+elGk+ P G+nd+
  lcl|FitnessBrowser__SB2B:6937552 164 HTAIRGSKHEKFAIYPYRpGRAFSGEQIMFLAASGVDTVLFHHEPTTTFSYFSSELFRADAFTIELGKVYPMGQNDM 240
                                       ***************************************************************************** PP

                         TIGR03242 222 sqfqaitealralisdeaiparkke..elklfevvesilkksdsfelhvaedasnftefakGtllaedkderyrvee 296
                                       s+f+++ e  ++li  e +    ++  +++l++v + i k+ d+fe+  + d++nf+ f++G+++a++  ++  ve+
  lcl|FitnessBrowser__SB2B:6937552 241 SKFANTREMFKRLICAEPLELAPFDetQVNLYQVCRVINKEVDDFEFTFSTDVENFSAFPRGHVIARQGGKDILVEQ 317
                                       ***************99887776665599************************************************ PP

                         TIGR03242 297 eeerilfPnakvanGlRaglllv 319
                                       e+e ++fPnakv  G+R +++lv
  lcl|FitnessBrowser__SB2B:6937552 318 EAEAVVFPNAKVPVGQRTVIMLV 340
                                       *********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (319 nodes)
Target sequences:                          1  (348 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: 8.26
//
[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