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.31664.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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.45
//
[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:

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:

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:

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:

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