GapMind for catabolism of small carbon sources

 

Aligments for a candidate for kbl in Dyella japonica UNC79MFTsu3.2

Align 2-amino-3-ketobutyrate coenzyme A ligase (EC 2.3.1.29) (characterized)
to candidate N515DRAFT_0037 N515DRAFT_0037 2-amino-3-ketobutyrate coenzyme A ligase

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



>lcl|FitnessBrowser__Dyella79:N515DRAFT_0037 N515DRAFT_0037
           2-amino-3-ketobutyrate coenzyme A ligase
          Length = 400

 Score =  512 bits (1319), Expect = e-150
 Identities = 251/397 (63%), Positives = 307/397 (77%), Gaps = 3/397 (0%)

Query: 3   TTDAFYAAIRQELESIEQAGLFKTERVIASPQGSLIRTTDGKEVINLCANNYLGLSSHPE 62
           TT A YAA   EL+SI + GLFK ERVI SPQ + I    G+ V+N CANNYLGL+ HP+
Sbjct: 6   TTQARYAA---ELDSIREQGLFKAERVIVSPQSAQIELEGGRRVLNFCANNYLGLADHPQ 62

Query: 63  VVEAAHRALGERGFGLSSVRFICGTQDLHKSLEARLASFLGTEDTILYGSAFDANGGLFE 122
           V++AA  AL   GFG++SVRFICGTQDLHK LE ++A F GTEDTILY + FDANGGL+E
Sbjct: 63  VIQAAKEALDSHGFGMASVRFICGTQDLHKQLEKKIAEFFGTEDTILYAACFDANGGLYE 122

Query: 123 TLLGSDDAVISDELNHASIIDGIRLCKAKRFRYKNNDLEDLREQLKAADAAGARFKLVFT 182
            LLG +DA+ISD LNHASIIDGIRLCKA+RFRY N D+ DL +QL+AADAAGAR KL+ T
Sbjct: 123 PLLGEEDAIISDALNHASIIDGIRLCKARRFRYANCDMADLEQQLQAADAAGARTKLITT 182

Query: 183 DGVFSMDGTIARLDEIREICDEFGALLGIDECHATGFLGQRGRGSHEHRGIFGKVDIITG 242
           DG FSMDG IA LD+I  +  ++ A++ IDECH TGFLG  GRGS E  G+  K+DI TG
Sbjct: 183 DGAFSMDGFIAPLDKIAALAAKYNAMVHIDECHCTGFLGASGRGSAEVNGVMDKIDIFTG 242

Query: 243 TLGKALGGASGGFTSGRKEVVALLRQRSRPYLFSNTVAPCIVGATLKVLDLLEADTTLRD 302
           TLGKALGGA GGFT+GR EV+ LLRQRSRPYLFSN++ P +V A LKV D+L +   LR 
Sbjct: 243 TLGKALGGALGGFTTGRAEVIELLRQRSRPYLFSNSLPPHVVAAALKVFDMLSSAGELRQ 302

Query: 303 KLERNARYFRGKLGTLGFDVKPGDHPIIPVMVYDAEKAQRLSRRLLELGVYVIGFFYPVV 362
           +++ N RYFR ++   GFD+KPG HPI+PVM+YDA+KAQ ++ RLL+ G+YV GFFYPVV
Sbjct: 303 RVQENTRYFREQMTQAGFDIKPGVHPIVPVMIYDAKKAQAMATRLLDEGIYVTGFFYPVV 362

Query: 363 PRGQARIRVQISALHDSAELDQALEAFEIAGKELGII 399
           P+GQARIR Q+SA H    LD+A+ AF   G+ELG+I
Sbjct: 363 PQGQARIRTQMSAAHTREHLDRAIAAFTKVGRELGVI 399


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: 527
Number of extensions: 7
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: 400
Length adjustment: 31
Effective length of query: 369
Effective length of database: 369
Effective search space:   136161
Effective search space used:   136161
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 N515DRAFT_0037 N515DRAFT_0037 (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.27267.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   8.3e-224  728.6   1.7   9.4e-224  728.4   1.7    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_0037  N515DRAFT_0037 2-amino-3-ketobut


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_0037  N515DRAFT_0037 2-amino-3-ketobutyrate coenzyme A ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  728.4   1.7  9.4e-224  9.4e-224       3     393 .]       9     399 ..       7     399 .. 0.99

  Alignments for each domain:
  == domain 1  score: 728.4 bits;  conditional E-value: 9.4e-224
                                    TIGR01822   3 ailaaelesireaGlfkkeriitspqkadirvadGrevlnfcannylGlsdhpeviqaakdaldeh 68 
                                                  a +aael+sire+Glfk er+i+spq+a+i +  Gr vlnfcannylGl+dhp+viqaak+ald+h
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0037   9 ARYAAELDSIREQGLFKAERVIVSPQSAQIELEGGRRVLNFCANNYLGLADHPQVIQAAKEALDSH 74 
                                                  6789************************************************************** PP

                                    TIGR01822  69 GfGlssvrficGtqdlhkelekklaeflgtedailyascfdangGlfeallgeedaiisdalnhas 134
                                                  GfG++svrficGtqdlhk+lekk+aef+gted+ilya+cfdangGl+e+llgeedaiisdalnhas
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0037  75 GFGMASVRFICGTQDLHKQLEKKIAEFFGTEDTILYAACFDANGGLYEPLLGEEDAIISDALNHAS 140
                                                  ****************************************************************** PP

                                    TIGR01822 135 iidGvrlckakryryenadledleaklkearaagarlrliatdGvfsmdGtiapldeicalaekyd 200
                                                  iidG+rlcka+r+ry+n+d++dle++l++a+aagar++li+tdG+fsmdG+iapld+i+ala ky+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0037 141 IIDGIRLCKARRFRYANCDMADLEQQLQAADAAGARTKLITTDGAFSMDGFIAPLDKIAALAAKYN 206
                                                  ****************************************************************** PP

                                    TIGR01822 201 alvlvdechatGflGatGrGsaelldvldkvdiitgtlGkalGGasGGfttakkevvellrqrsrp 266
                                                  a+v++dech+tGflGa+GrGsae+ +v+dk+di+tgtlGkalGGa+GGftt++ ev+ellrqrsrp
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0037 207 AMVHIDECHCTGFLGASGRGSAEVNGVMDKIDIFTGTLGKALGGALGGFTTGRAEVIELLRQRSRP 272
                                                  ****************************************************************** PP

                                    TIGR01822 267 ylfsnslapavvgasikvlelleasnelrdklventryfrekleaaGfdvkpaehaiipvmlydak 332
                                                  ylfsnsl+p+vv+a++kv+++l++++elr++++entryfre+++ aGfd+kp+ h+i+pvm+ydak
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0037 273 YLFSNSLPPHVVAAALKVFDMLSSAGELRQRVQENTRYFREQMTQAGFDIKPGVHPIVPVMIYDAK 338
                                                  ****************************************************************** PP

                                    TIGR01822 333 laqklaerlleeGiyviGffypvvpkGqarirvqlsaaheeeqldkaveafvkvGrelgvi 393
                                                  +aq +a+rll+eGiyv+Gffypvvp+Gqarir+q+saah++e+ld+a+ af+kvGrelgvi
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0037 339 KAQAMATRLLDEGIYVTGFFYPVVPQGQARIRTQMSAAHTREHLDRAIAAFTKVGRELGVI 399
                                                  ***********************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (400 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: 7.27
//
[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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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