Alignments for a candidate for kbl in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for kbl in Cupriavidus basilensis 4G11

Align 2-amino-3-ketobutyrate coenzyme A ligase (EC 2.3.1.29) (characterized)
to candidate RR42_RS28295 RR42_RS28295 2-amino-3-ketobutyrate CoA ligase

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



>FitnessBrowser__Cup4G11:RR42_RS28295
          Length = 400

 Score =  786 bits (2030), Expect = 0.0
 Identities = 400/400 (100%), Positives = 400/400 (100%)

Query: 1   MPTTDAFYAAIRQELESIEQAGLFKTERVIASPQGSLIRTTDGKEVINLCANNYLGLSSH 60
           MPTTDAFYAAIRQELESIEQAGLFKTERVIASPQGSLIRTTDGKEVINLCANNYLGLSSH
Sbjct: 1   MPTTDAFYAAIRQELESIEQAGLFKTERVIASPQGSLIRTTDGKEVINLCANNYLGLSSH 60

Query: 61  PEVVEAAHRALGERGFGLSSVRFICGTQDLHKSLEARLASFLGTEDTILYGSAFDANGGL 120
           PEVVEAAHRALGERGFGLSSVRFICGTQDLHKSLEARLASFLGTEDTILYGSAFDANGGL
Sbjct: 61  PEVVEAAHRALGERGFGLSSVRFICGTQDLHKSLEARLASFLGTEDTILYGSAFDANGGL 120

Query: 121 FETLLGSDDAVISDELNHASIIDGIRLCKAKRFRYKNNDLEDLREQLKAADAAGARFKLV 180
           FETLLGSDDAVISDELNHASIIDGIRLCKAKRFRYKNNDLEDLREQLKAADAAGARFKLV
Sbjct: 121 FETLLGSDDAVISDELNHASIIDGIRLCKAKRFRYKNNDLEDLREQLKAADAAGARFKLV 180

Query: 181 FTDGVFSMDGTIARLDEIREICDEFGALLGIDECHATGFLGQRGRGSHEHRGIFGKVDII 240
           FTDGVFSMDGTIARLDEIREICDEFGALLGIDECHATGFLGQRGRGSHEHRGIFGKVDII
Sbjct: 181 FTDGVFSMDGTIARLDEIREICDEFGALLGIDECHATGFLGQRGRGSHEHRGIFGKVDII 240

Query: 241 TGTLGKALGGASGGFTSGRKEVVALLRQRSRPYLFSNTVAPCIVGATLKVLDLLEADTTL 300
           TGTLGKALGGASGGFTSGRKEVVALLRQRSRPYLFSNTVAPCIVGATLKVLDLLEADTTL
Sbjct: 241 TGTLGKALGGASGGFTSGRKEVVALLRQRSRPYLFSNTVAPCIVGATLKVLDLLEADTTL 300

Query: 301 RDKLERNARYFRGKLGTLGFDVKPGDHPIIPVMVYDAEKAQRLSRRLLELGVYVIGFFYP 360
           RDKLERNARYFRGKLGTLGFDVKPGDHPIIPVMVYDAEKAQRLSRRLLELGVYVIGFFYP
Sbjct: 301 RDKLERNARYFRGKLGTLGFDVKPGDHPIIPVMVYDAEKAQRLSRRLLELGVYVIGFFYP 360

Query: 361 VVPRGQARIRVQISALHDSAELDQALEAFEIAGKELGIIQ 400
           VVPRGQARIRVQISALHDSAELDQALEAFEIAGKELGIIQ
Sbjct: 361 VVPRGQARIRVQISALHDSAELDQALEAFEIAGKELGIIQ 400


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: 766
Number of extensions: 15
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 RR42_RS28295 RR42_RS28295 (2-amino-3-ketobutyrate CoA 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.32656.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.3e-211  688.4   0.1   1.5e-211  688.2   0.1    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS28295  RR42_RS28295 2-amino-3-ketobutyr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS28295  RR42_RS28295 2-amino-3-ketobutyrate CoA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  688.2   0.1  1.5e-211  1.5e-211       1     393 []       7     399 ..       7     399 .. 1.00

  Alignments for each domain:
  == domain 1  score: 688.2 bits;  conditional E-value: 1.5e-211
                                 TIGR01822   1 lkailaaelesireaGlfkkeriitspqkadirvadGrevlnfcannylGlsdhpeviqaakdaldehG 69 
                                               ++a +++elesi++aGlfk er+i+spq++ ir++dG+ev+n+cannylGls+hpev++aa+ al e+G
  lcl|FitnessBrowser__Cup4G11:RR42_RS28295   7 FYAAIRQELESIEQAGLFKTERVIASPQGSLIRTTDGKEVINLCANNYLGLSSHPEVVEAAHRALGERG 75 
                                               57899**************************************************************** PP

                                 TIGR01822  70 fGlssvrficGtqdlhkelekklaeflgtedailyascfdangGlfeallgeedaiisdalnhasiidG 138
                                               fGlssvrficGtqdlhk+le++la+flgted+ily+s+fdangGlfe+llg++da+isd+lnhasiidG
  lcl|FitnessBrowser__Cup4G11:RR42_RS28295  76 FGLSSVRFICGTQDLHKSLEARLASFLGTEDTILYGSAFDANGGLFETLLGSDDAVISDELNHASIIDG 144
                                               ********************************************************************* PP

                                 TIGR01822 139 vrlckakryryenadledleaklkearaagarlrliatdGvfsmdGtiapldeicalaekydalvlvde 207
                                               +rlckakr+ry+n+dledl+ +lk+a+aagar +l++tdGvfsmdGtia+ldei++++++++al+ +de
  lcl|FitnessBrowser__Cup4G11:RR42_RS28295 145 IRLCKAKRFRYKNNDLEDLREQLKAADAAGARFKLVFTDGVFSMDGTIARLDEIREICDEFGALLGIDE 213
                                               ********************************************************************* PP

                                 TIGR01822 208 chatGflGatGrGsaelldvldkvdiitgtlGkalGGasGGfttakkevvellrqrsrpylfsnslapa 276
                                               chatGflG++GrGs+e +++++kvdiitgtlGkalGGasGGft+++kevv+llrqrsrpylfsn++ap 
  lcl|FitnessBrowser__Cup4G11:RR42_RS28295 214 CHATGFLGQRGRGSHEHRGIFGKVDIITGTLGKALGGASGGFTSGRKEVVALLRQRSRPYLFSNTVAPC 282
                                               ********************************************************************* PP

                                 TIGR01822 277 vvgasikvlelleasnelrdklventryfrekleaaGfdvkpaehaiipvmlydaklaqklaerlleeG 345
                                               +vga++kvl+llea ++lrdkl++n+ryfr kl ++Gfdvkp++h+iipvm+yda++aq+l++rlle G
  lcl|FitnessBrowser__Cup4G11:RR42_RS28295 283 IVGATLKVLDLLEADTTLRDKLERNARYFRGKLGTLGFDVKPGDHPIIPVMVYDAEKAQRLSRRLLELG 351
                                               ********************************************************************* PP

                                 TIGR01822 346 iyviGffypvvpkGqarirvqlsaaheeeqldkaveafvkvGrelgvi 393
                                               +yviGffypvvp+Gqarirvq+sa h+ ++ld+a+eaf  +G+elg+i
  lcl|FitnessBrowser__Cup4G11:RR42_RS28295 352 VYVIGFFYPVVPRGQARIRVQISALHDSAELDQALEAFEIAGKELGII 399
                                               **********************************************97 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.17
//
[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