GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kbl in Echinicola vietnamensis KMM 6221, DSM 17526

Align 2-amino-3-ketobutyrate coenzyme A ligase (EC 2.3.1.29) (characterized)
to candidate Echvi_0145 Echvi_0145 2-amino-3-ketobutyrate coenzyme A ligase

Query= reanno::Cup4G11:RR42_RS28295
         (400 letters)



>FitnessBrowser__Cola:Echvi_0145
          Length = 397

 Score =  542 bits (1397), Expect = e-159
 Identities = 256/389 (65%), Positives = 322/389 (82%)

Query: 11  IRQELESIEQAGLFKTERVIASPQGSLIRTTDGKEVINLCANNYLGLSSHPEVVEAAHRA 70
           + +EL+ I  AGL+K+ER+I SPQG+ I T++GK+V+N CANNYLGLSSHP+V+EAA  A
Sbjct: 9   LEKELKEISDAGLYKSERIITSPQGAEISTSEGKQVLNFCANNYLGLSSHPKVIEAAKNA 68

Query: 71  LGERGFGLSSVRFICGTQDLHKSLEARLASFLGTEDTILYGSAFDANGGLFETLLGSDDA 130
           +   G+G+SSVRFICGTQD+HK LE +++ FLGTEDTILY +AFDANGG+FE +LG +DA
Sbjct: 69  IDTHGYGMSSVRFICGTQDIHKELERKISEFLGTEDTILYAAAFDANGGVFEPILGPEDA 128

Query: 131 VISDELNHASIIDGIRLCKAKRFRYKNNDLEDLREQLKAADAAGARFKLVFTDGVFSMDG 190
           +ISD LNHASIIDG+RLCKA RFRYK+ND+EDL  QLK A+A GA+ K++ TDG FSMDG
Sbjct: 129 IISDALNHASIIDGVRLCKAMRFRYKHNDMEDLETQLKEANAKGAKQKIIVTDGAFSMDG 188

Query: 191 TIARLDEIREICDEFGALLGIDECHATGFLGQRGRGSHEHRGIFGKVDIITGTLGKALGG 250
           TIA++D+I  + +++ AL+  DECH+TGF+G+ GRG HE +G+ GK+DIITGTLGKALGG
Sbjct: 189 TIAQMDKIVALAEQYDALVMSDECHSTGFIGKTGRGVHELKGVMGKMDIITGTLGKALGG 248

Query: 251 ASGGFTSGRKEVVALLRQRSRPYLFSNTVAPCIVGATLKVLDLLEADTTLRDKLERNARY 310
           ASGGFTSGRKE++ +LRQRSRPYLFSNT+AP I GA++ V DLL   T LRDKLE N  Y
Sbjct: 249 ASGGFTSGRKEIIDILRQRSRPYLFSNTLAPAITGASIAVFDLLSETTELRDKLEDNTTY 308

Query: 311 FRGKLGTLGFDVKPGDHPIIPVMVYDAEKAQRLSRRLLELGVYVIGFFYPVVPRGQARIR 370
           FR K+   GFD+KPG HPI+P+M+YDA  +Q+++ +LLE GVYVIGF+YPVVP+GQARIR
Sbjct: 309 FREKMTAAGFDIKPGVHPIVPIMLYDAVLSQQMAEKLLERGVYVIGFYYPVVPKGQARIR 368

Query: 371 VQISALHDSAELDQALEAFEIAGKELGII 399
           VQISA HD   LD A+EAF   GKELG+I
Sbjct: 369 VQISAAHDRKHLDAAIEAFTEVGKELGVI 397


Lambda     K      H
   0.321    0.140    0.402 

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: 546
Number of extensions: 10
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: 400
Length of database: 397
Length adjustment: 31
Effective length of query: 369
Effective length of database: 366
Effective search space:   135054
Effective search space used:   135054
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 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate Echvi_0145 Echvi_0145 (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.3930585.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   5.3e-220  716.1   0.5   6.1e-220  715.9   0.5    1.0  1  lcl|FitnessBrowser__Cola:Echvi_0145  Echvi_0145 2-amino-3-ketobutyrat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_0145  Echvi_0145 2-amino-3-ketobutyrate coenzyme A ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  715.9   0.5  6.1e-220  6.1e-220       2     393 .]       6     397 .]       5     397 .] 0.99

  Alignments for each domain:
  == domain 1  score: 715.9 bits;  conditional E-value: 6.1e-220
                            TIGR01822   2 kailaaelesireaGlfkkeriitspqkadirvadGrevlnfcannylGlsdhpeviqaakdaldehGfGlssv 75 
                                          k  l++el+ i +aGl+k+eriitspq+a+i +++G++vlnfcannylGls+hp+vi+aak+a+d+hG+G+ssv
  lcl|FitnessBrowser__Cola:Echvi_0145   6 KPKLEKELKEISDAGLYKSERIITSPQGAEISTSEGKQVLNFCANNYLGLSSHPKVIEAAKNAIDTHGYGMSSV 79 
                                          567999******************************************************************** PP

                            TIGR01822  76 rficGtqdlhkelekklaeflgtedailyascfdangGlfeallgeedaiisdalnhasiidGvrlckakryry 149
                                          rficGtqd+hkele+k++eflgted+ilya++fdangG+fe++lg+edaiisdalnhasiidGvrlcka r+ry
  lcl|FitnessBrowser__Cola:Echvi_0145  80 RFICGTQDIHKELERKISEFLGTEDTILYAAAFDANGGVFEPILGPEDAIISDALNHASIIDGVRLCKAMRFRY 153
                                          ************************************************************************** PP

                            TIGR01822 150 enadledleaklkearaagarlrliatdGvfsmdGtiapldeicalaekydalvlvdechatGflGatGrGsae 223
                                          +++d+edle++lkea+a+ga++++i+tdG+fsmdGtia++d+i+alae+ydalv+ dech+tGf+G+tGrG++e
  lcl|FitnessBrowser__Cola:Echvi_0145 154 KHNDMEDLETQLKEANAKGAKQKIIVTDGAFSMDGTIAQMDKIVALAEQYDALVMSDECHSTGFIGKTGRGVHE 227
                                          ************************************************************************** PP

                            TIGR01822 224 lldvldkvdiitgtlGkalGGasGGfttakkevvellrqrsrpylfsnslapavvgasikvlelleasnelrdk 297
                                          l++v++k+diitgtlGkalGGasGGft+++ke++++lrqrsrpylfsn+lapa+ gasi+v++ll++++elrdk
  lcl|FitnessBrowser__Cola:Echvi_0145 228 LKGVMGKMDIITGTLGKALGGASGGFTSGRKEIIDILRQRSRPYLFSNTLAPAITGASIAVFDLLSETTELRDK 301
                                          ************************************************************************** PP

                            TIGR01822 298 lventryfrekleaaGfdvkpaehaiipvmlydaklaqklaerlleeGiyviGffypvvpkGqarirvqlsaah 371
                                          l++nt yfrek++aaGfd+kp+ h+i+p+mlyda l+q++ae+lle+G+yviGf+ypvvpkGqarirvq+saah
  lcl|FitnessBrowser__Cola:Echvi_0145 302 LEDNTTYFREKMTAAGFDIKPGVHPIVPIMLYDAVLSQQMAEKLLERGVYVIGFYYPVVPKGQARIRVQISAAH 375
                                          ************************************************************************** PP

                            TIGR01822 372 eeeqldkaveafvkvGrelgvi 393
                                          ++++ld+a+eaf++vG+elgvi
  lcl|FitnessBrowser__Cola:Echvi_0145 376 DRKHLDAAIEAFTEVGKELGVI 397
                                          ********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (397 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 23.03
//
[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