GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kbl in Paraburkholderia bryophila 376MFSha3.1

Align 2-amino-3-ketobutyrate coenzyme A ligase (EC 2.3.1.29) (characterized)
to candidate H281DRAFT_03587 H281DRAFT_03587 2-amino-3-ketobutyrate coenzyme A ligase

Query= reanno::ANA3:7026975
         (397 letters)



>FitnessBrowser__Burk376:H281DRAFT_03587
          Length = 399

 Score =  541 bits (1395), Expect = e-158
 Identities = 275/395 (69%), Positives = 326/395 (82%), Gaps = 3/395 (0%)

Query: 6   FYAQINQQLADVKAEGLYKSERVIASPQQTAIQV-NHQEVVNFCANNYLGLANHPELIKA 64
           + A +   L  ++A+G YKSERVIASPQ   I++ N   V+NFCANNYLGLA+   LI+A
Sbjct: 5   YLAHLRGTLEQIRADGFYKSERVIASPQSADIRLANGTGVLNFCANNYLGLADDARLIEA 64

Query: 65  AQQGLDSHGFGMASVRFICGTQDIHKQLEASLSEFLGMEDTILYSSCFDANAGLFETLLD 124
           A+QGLD+ GFGMASVRFICGTQ +HKQLE++L+EFL  +D ILYSSCFDAN GLFETLLD
Sbjct: 65  AKQGLDNDGFGMASVRFICGTQTVHKQLESALAEFLQTDDCILYSSCFDANGGLFETLLD 124

Query: 125 AEDAIISDALNHASIIDGVRLCKAKRFRYANNDMADLETQLIAAKAAGARNILIATDGVF 184
             DAIISD LNHASIIDGVRL KAKRFRY NND+ADLE +L  A AAGAR  LIATDGVF
Sbjct: 125 ENDAIISDELNHASIIDGVRLSKAKRFRYKNNDLADLEAKLQEADAAGARYKLIATDGVF 184

Query: 185 SMDGVIANLQGVCDLADKYGALVMVDDSHAVGFVGLNGRGSHEHCGVMGRVDIITGTLGK 244
           SMDG+IA+L G+CDLAD+YGALVMVDDSHAVGFVG +GRG+ EHCGV+ RVDIITGTLGK
Sbjct: 185 SMDGIIADLAGICDLADRYGALVMVDDSHAVGFVGEHGRGTPEHCGVLSRVDIITGTLGK 244

Query: 245 ALGGASGGFTSGKKEVIDWLRQRSRPYLFSNSLAPSIVTASIHVLEMLKS--GQALREAV 302
           ALGGASGG+ + +KE++D LRQRSRPYLFSN+L PSI  AS+ VLE+L S  G  LRE V
Sbjct: 245 ALGGASGGYVAARKEIVDLLRQRSRPYLFSNTLTPSIAAASLKVLELLASDEGAQLRERV 304

Query: 303 WENSRYFREKMSAAGFTLGGADHAIIPVMIGDAKLASDFANRLLAEHIYVIGFSFPVVPK 362
            +N  +FR+KMSA GFTL   +H IIPVM+GDA+LAS  A+ LL E +YVIGFSFPVVPK
Sbjct: 305 RKNGAHFRDKMSALGFTLVPGEHPIIPVMLGDAQLASKMADALLNEGVYVIGFSFPVVPK 364

Query: 363 GQARIRTQMSAAHTREQLDKAIEAFTRIAKEMAII 397
           G+ARIRTQMSAAHT EQ+D+A++AF R+ +E+ +I
Sbjct: 365 GRARIRTQMSAAHTTEQIDRAVDAFARVGRELGVI 399


Lambda     K      H
   0.321    0.134    0.385 

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: 540
Number of extensions: 11
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: 397
Length of database: 399
Length adjustment: 31
Effective length of query: 366
Effective length of database: 368
Effective search space:   134688
Effective search space used:   134688
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: 50 (23.9 bits)

Align candidate H281DRAFT_03587 H281DRAFT_03587 (2-amino-3-ketobutyrate coenzyme A ligase)
to HMM TIGR01822 (kbl: glycine C-acetyltransferase (EC 2.3.1.29))

# 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/TIGR01822.hmm
# target sequence database:        /tmp/gapView.1978.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01822  [M=393]
Accession:   TIGR01822
Description: 2am3keto_CoA: glycine C-acetyltransferase
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-204  665.3   1.6   1.7e-204  665.1   1.6    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_03587  H281DRAFT_03587 2-amino-3-ketobu


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_03587  H281DRAFT_03587 2-amino-3-ketobutyrate coenzyme A ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  665.1   1.6  1.7e-204  1.7e-204       3     393 .]       7     399 .]       5     399 .] 0.99

  Alignments for each domain:
  == domain 1  score: 665.1 bits;  conditional E-value: 1.7e-204
                                    TIGR01822   3 ailaaelesireaGlfkkeriitspqkadirvadGrevlnfcannylGlsdhpeviqaakdaldeh 68 
                                                  a+l++ le ir++G +k+er+i+spq+adir+a+G+ vlnfcannylGl+d  ++i+aak++ld+ 
  lcl|FitnessBrowser__Burk376:H281DRAFT_03587   7 AHLRGTLEQIRADGFYKSERVIASPQSADIRLANGTGVLNFCANNYLGLADDARLIEAAKQGLDND 72 
                                                  68999************************************************************* PP

                                    TIGR01822  69 GfGlssvrficGtqdlhkelekklaeflgtedailyascfdangGlfeallgeedaiisdalnhas 134
                                                  GfG++svrficGtq +hk+le +laefl+t+d+ily+scfdangGlfe+ll e+daiisd+lnhas
  lcl|FitnessBrowser__Burk376:H281DRAFT_03587  73 GFGMASVRFICGTQTVHKQLESALAEFLQTDDCILYSSCFDANGGLFETLLDENDAIISDELNHAS 138
                                                  ****************************************************************** PP

                                    TIGR01822 135 iidGvrlckakryryenadledleaklkearaagarlrliatdGvfsmdGtiapldeicalaekyd 200
                                                  iidGvrl kakr+ry+n+dl+dleakl+ea+aagar++liatdGvfsmdG ia+l  ic+la++y+
  lcl|FitnessBrowser__Burk376:H281DRAFT_03587 139 IIDGVRLSKAKRFRYKNNDLADLEAKLQEADAAGARYKLIATDGVFSMDGIIADLAGICDLADRYG 204
                                                  ****************************************************************** PP

                                    TIGR01822 201 alvlvdechatGflGatGrGsaelldvldkvdiitgtlGkalGGasGGfttakkevvellrqrsrp 266
                                                  alv+vd++ha+Gf+G++GrG+ e ++vl +vdiitgtlGkalGGasGG+ +a+ke+v+llrqrsrp
  lcl|FitnessBrowser__Burk376:H281DRAFT_03587 205 ALVMVDDSHAVGFVGEHGRGTPEHCGVLSRVDIITGTLGKALGGASGGYVAARKEIVDLLRQRSRP 270
                                                  ****************************************************************** PP

                                    TIGR01822 267 ylfsnslapavvgasikvlell..easnelrdklventryfrekleaaGfdvkpaehaiipvmlyd 330
                                                  ylfsn+l+p++ +as+kvlell  +++++lr+++ +n  +fr+k++a+Gf++ p+eh+iipvml+d
  lcl|FitnessBrowser__Burk376:H281DRAFT_03587 271 YLFSNTLTPSIAAASLKVLELLasDEGAQLRERVRKNGAHFRDKMSALGFTLVPGEHPIIPVMLGD 336
                                                  *********************9444689************************************** PP

                                    TIGR01822 331 aklaqklaerlleeGiyviGffypvvpkGqarirvqlsaaheeeqldkaveafvkvGrelgvi 393
                                                  a+la+k+a+ ll+eG+yviGf++pvvpkG+arir+q+saah+ eq+d+av+af++vGrelgvi
  lcl|FitnessBrowser__Burk376:H281DRAFT_03587 337 AQLASKMADALLNEGVYVIGFSFPVVPKGRARIRTQMSAAHTTEQIDRAVDAFARVGRELGVI 399
                                                  *************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (399 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.70
//
[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