GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aspA in Dietzia timorensis ID05-A0528

Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate WP_067478856.1 BJL86_RS15630 aspartate ammonia-lyase

Query= BRENDA::P0AC38
         (478 letters)



>NCBI__GCF_001659785.1:WP_067478856.1
          Length = 499

 Score =  640 bits (1650), Expect = 0.0
 Identities = 315/473 (66%), Positives = 379/473 (80%)

Query: 6   RIEEDLLGTREVPADAYYGVHTLRAIENFYISNNKISDIPEFVRGMVMVKKAAAMANKEL 65
           R+EEDLLG + VPA+AYYGVHT RAIENF IS   I+DIP+F+RGMV VKKA A+AN+++
Sbjct: 20  RVEEDLLGEKAVPAEAYYGVHTARAIENFPISKLTINDIPDFIRGMVQVKKATALANRDM 79

Query: 66  QTIPKSVANAIIAACDEVLNNGKCMDQFPVDVYQGGAGTSVNMNTNEVLANIGLELMGHQ 125
             + +    AI+ ACD+VL+ G+CMDQFP   +QGGAGTS+NMNTNEV+AN+ LE MG +
Sbjct: 80  GVLTEEKCEAIVWACDQVLDEGRCMDQFPSCQFQGGAGTSINMNTNEVIANLALEHMGVE 139

Query: 126 KGEYQYLNPNDHVNKCQSTNDAYPTGFRIAVYSSLIKLVDAINQLREGFERKAVEFQDIL 185
           KG Y  ++PND VN+ QSTNDAYP+GFR+A++++L +   A+  LRE F  KA  F+D+L
Sbjct: 140 KGRYDVISPNDDVNRSQSTNDAYPSGFRLALWAALERYEKALIALREAFYDKAEAFRDVL 199

Query: 186 KMGRTQLQDAVPMTLGQEFRAFSILLKEEVKNIQRTAELLLEVNLGATAIGTGLNTPKEY 245
           KMGRTQLQDAVPM+LGQE  A+++ L EE+  +  +A+ LL +NLGATAIGTG+NTP  Y
Sbjct: 200 KMGRTQLQDAVPMSLGQELGAYAVNLDEEMSVLASSAKTLLALNLGATAIGTGVNTPPHY 259

Query: 246 SPLAVKKLAEVTGFPCVPAEDLIEATSDCGAYVMVHGALKRLAVKMSKICNDLRLLSSGP 305
               ++ L EVTG P   AEDLIEAT D G YV+VH ALKR AVK+SKICNDLRLLSSGP
Sbjct: 260 QESVIEHLKEVTGLPVSGAEDLIEATQDTGDYVLVHAALKRTAVKISKICNDLRLLSSGP 319

Query: 306 RAGLNEINLPELQAGSSIMPAKVNPVVPEVVNQVCFKVIGNDTTVTMAAEAGQLQLNVME 365
           RAGLNEINLPE+QAGSSIMPAKVNPV+PEVVNQVCFKVIGND TV+ AAEAGQLQLNVME
Sbjct: 320 RAGLNEINLPEMQAGSSIMPAKVNPVIPEVVNQVCFKVIGNDVTVSAAAEAGQLQLNVME 379

Query: 366 PVIGQAMFESVHILTNACYNLLEKCINGITANKEVCEGYVYNSIGIVTYLNPFIGHHNGD 425
           P I Q+MFES+ +LTNACY L EKC+ GITAN+E+   +V NSIGIVTYLNP IGHHNGD
Sbjct: 380 PAIAQSMFESIDLLTNACYTLAEKCVAGITANEEIARNFVMNSIGIVTYLNPIIGHHNGD 439

Query: 426 IVGKICAETGKSVREVVLERGLLTEAELDDIFSVQNLMHPAYKAKRYTDESEQ 478
           +VGK CA +G+ VREVVLE GLL E ELDDI S QNL+HP +K  RY D+  Q
Sbjct: 440 LVGKECARSGRGVREVVLEMGLLDEEELDDILSPQNLLHPEFKGTRYLDKMRQ 492


Lambda     K      H
   0.317    0.134    0.381 

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: 654
Number of extensions: 13
Number of successful extensions: 1
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: 478
Length of database: 499
Length adjustment: 34
Effective length of query: 444
Effective length of database: 465
Effective search space:   206460
Effective search space used:   206460
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate WP_067478856.1 BJL86_RS15630 (aspartate ammonia-lyase)
to HMM TIGR00839 (aspA: aspartate ammonia-lyase (EC 4.3.1.1))

# 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/TIGR00839.hmm
# target sequence database:        /tmp/gapView.1860874.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00839  [M=468]
Accession:   TIGR00839
Description: aspA: aspartate ammonia-lyase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.6e-231  753.6   0.2   5.3e-231  753.4   0.2    1.0  1  NCBI__GCF_001659785.1:WP_067478856.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001659785.1:WP_067478856.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  753.4   0.2  5.3e-231  5.3e-231       1     467 [.      20     487 ..      20     488 .. 1.00

  Alignments for each domain:
  == domain 1  score: 753.4 bits;  conditional E-value: 5.3e-231
                             TIGR00839   1 riekdllGekeveaevyyGiqtlrasenfaisnekisdvpefvkalvlvkkaaalanvelkaidekiakaiva 73 
                                           r+e+dllGek v+ae+yyG++t ra+enf+is+ +i+d+p+f++++v+vkka+alan +++ ++e+  +aiv 
  NCBI__GCF_001659785.1:WP_067478856.1  20 RVEEDLLGEKAVPAEAYYGVHTARAIENFPISKLTINDIPDFIRGMVQVKKATALANRDMGVLTEEKCEAIVW 92 
                                           89*********************************************************************** PP

                             TIGR00839  74 acdeile.GkyldqfivdviqGGaGtsvnmntnevianlalellGhkkGeyqflnpndhvnksqstndaypta 145
                                           acd++l+ G+++dqf++  +qGGaGts+nmntnevianlale +G +kG y +++pnd vn+sqstndayp++
  NCBI__GCF_001659785.1:WP_067478856.1  93 ACDQVLDeGRCMDQFPSCQFQGGAGTSINMNTNEVIANLALEHMGVEKGRYDVISPNDDVNRSQSTNDAYPSG 165
                                           ******99***************************************************************** PP

                             TIGR00839 146 lkiavyesleklvdkiealrdafeqkakefadvlkmGrtqlqdavpltlGqefeayalllerdvkrikrtrel 218
                                           +++a++  le+  +++ alr+af +ka+ f+dvlkmGrtqlqdavp+ lGqe+ aya+ l++++  + ++++ 
  NCBI__GCF_001659785.1:WP_067478856.1 166 FRLALWAALERYEKALIALREAFYDKAEAFRDVLKMGRTQLQDAVPMSLGQELGAYAVNLDEEMSVLASSAKT 238
                                           ************************************************************************* PP

                             TIGR00839 219 llevnlGataiGtGlnadkeysklvvkklaevtGlplvpaenlieatsdtgayvevsgalkriavklskvcnd 291
                                           ll +nlGataiGtG+n++++y++ v+ +l+evtGlp+ +ae+lieat+dtg yv v++alkr+avk+sk+cnd
  NCBI__GCF_001659785.1:WP_067478856.1 239 LLALNLGATAIGTGVNTPPHYQESVIEHLKEVTGLPVSGAEDLIEATQDTGDYVLVHAALKRTAVKISKICND 311
                                           ************************************************************************* PP

                             TIGR00839 292 lrllssGpraGlneinlpelqaGssimpakvnpvvpevvnqvcfkviGndttvtlaaeaGqlqlnvlepviaf 364
                                           lrllssGpraGlneinlpe+qaGssimpakvnpv+pevvnqvcfkviGnd tv+ aaeaGqlqlnv+ep ia+
  NCBI__GCF_001659785.1:WP_067478856.1 312 LRLLSSGPRAGLNEINLPEMQAGSSIMPAKVNPVIPEVVNQVCFKVIGNDVTVSAAAEAGQLQLNVMEPAIAQ 384
                                           ************************************************************************* PP

                             TIGR00839 365 allesisiltnaiesltdkcveGitanekicedyvfnsiGivtalnpfiGyekaalvakeaiktgksvrdvvl 437
                                           +++esi++ltna+++l +kcv Gitane+i +++v+nsiGivt+lnp iG+++++lv+ke++++g++vr+vvl
  NCBI__GCF_001659785.1:WP_067478856.1 385 SMFESIDLLTNACYTLAEKCVAGITANEEIARNFVMNSIGIVTYLNPIIGHHNGDLVGKECARSGRGVREVVL 457
                                           ************************************************************************* PP

                             TIGR00839 438 ekdllteeelddilsvenllkpaykakklk 467
                                           e +ll eeelddils++nll+p +k+ ++ 
  NCBI__GCF_001659785.1:WP_067478856.1 458 EMGLLDEEELDDILSPQNLLHPEFKGTRYL 487
                                           ************************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (468 nodes)
Target sequences:                          1  (499 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 20.63
//
[ok]

This GapMind analysis is from Sep 24 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