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

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.16388.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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.02
# Mc/sec: 7.64
//
[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