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 glycine C-acetyltransferase (EC 2.3.1.29) (characterized)
to candidate RR42_RS22865 RR42_RS22865 2-amino-3-ketobutyrate CoA ligase

Query= BRENDA::P0AB77
         (398 letters)



>FitnessBrowser__Cup4G11:RR42_RS22865
          Length = 400

 Score =  528 bits (1359), Expect = e-154
 Identities = 271/400 (67%), Positives = 313/400 (78%), Gaps = 2/400 (0%)

Query: 1   MRGEFYQQLTNDLETARAEGLFKEERIITSAQQADITVADGSHVINFCANNYLGLANHPD 60
           MR  +   L + L+T RA+G  K ER+I S Q ADI +A G HV+NFCANNYLGLA+   
Sbjct: 1   MRDRYLSHLRDTLDTIRADGFHKSERVIASPQAADIRLAGGEHVLNFCANNYLGLADDHR 60

Query: 61  LIAAAKAGMDSHGFGMASVRFICGTQDSHKELEQKLAAFLGMEDAILYSSCFDANGGLFE 120
           LI AA+ G++  GFGMASVRFICGTQ  HK LE  LA FL   D+ILYSSCFDANGGLFE
Sbjct: 61  LIEAARRGLEQDGFGMASVRFICGTQSVHKTLEAVLAKFLHTGDSILYSSCFDANGGLFE 120

Query: 121 TLLGAEDAIISDALNHASIIDGVRLCKAKRYRYANNDMQELEARLKEAREAGARHVLIAT 180
           TLL  +DA+ISD LNHASIIDGVRLCKA+RYRY NNDM +LE RL+EA  AGAR  LIAT
Sbjct: 121 TLLDDQDAVISDELNHASIIDGVRLCKARRYRYRNNDMADLETRLQEADAAGARFKLIAT 180

Query: 181 DGVFSMDGVIANLKGVCDLADKYDALVMVDDSHAVGFVGENGRGSHEYCDVMGRVDIITG 240
           DGVFSMDG+IA+LK +CDLAD+Y ALVMVDDSHAVGFVGE+GRG+ E C V GRVDIITG
Sbjct: 181 DGVFSMDGIIADLKSICDLADRYGALVMVDDSHAVGFVGEHGRGTPELCGVEGRVDIITG 240

Query: 241 TLGKALGGASGGYTAARKEVVEWLRQRSRPYLFSNSLAPAIVAASIKVLEMV--EAGSEL 298
           TLGKALGGASGGY AA +E+VE LRQRSRPYLFSNSLAP+I AA++KVLE++  E G+ L
Sbjct: 241 TLGKALGGASGGYVAAHREIVELLRQRSRPYLFSNSLAPSICAATLKVLELLASEEGAAL 300

Query: 299 RDRLWANARQFREQMSAAGFTLAGADHAIIPVMLGDAVVAQKFARELQKEGIYVTGFFYP 358
           R R+  N   FR +M+A GFTL    H IIPVMLGDA +A   A  L  E +YV GF +P
Sbjct: 301 RARVRENGEHFRREMTALGFTLVPGQHPIIPVMLGDAALASGMADALLAEHVYVVGFSFP 360

Query: 359 VVPKGQARIRTQMSAAHTPEQITRAVEAFTRIGKQLGVIA 398
           VVPKG+ARIRTQMSAAHT EQI RAV AF ++G++ G IA
Sbjct: 361 VVPKGRARIRTQMSAAHTAEQIERAVAAFAKVGRKFGAIA 400


Lambda     K      H
   0.320    0.135    0.388 

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: 537
Number of extensions: 14
Number of successful extensions: 2
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: 398
Length of database: 400
Length adjustment: 31
Effective length of query: 367
Effective length of database: 369
Effective search space:   135423
Effective search space used:   135423
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_RS22865 RR42_RS22865 (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.17986.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.1e-199  647.3   2.2   4.7e-199  647.1   2.2    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS22865  RR42_RS22865 2-amino-3-ketobutyr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS22865  RR42_RS22865 2-amino-3-ketobutyrate CoA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  647.1   2.2  4.7e-199  4.7e-199       4     393 .]       8     399 ..       5     399 .. 0.99

  Alignments for each domain:
  == domain 1  score: 647.1 bits;  conditional E-value: 4.7e-199
                                 TIGR01822   4 ilaaelesireaGlfkkeriitspqkadirvadGrevlnfcannylGlsdhpeviqaakdaldehGfGl 72 
                                               +l+  l++ir++G +k+er+i+spq adir+a G++vlnfcannylGl+d  ++i+aa+ +l++ GfG+
  lcl|FitnessBrowser__Cup4G11:RR42_RS22865   8 HLRDTLDTIRADGFHKSERVIASPQAADIRLAGGEHVLNFCANNYLGLADDHRLIEAARRGLEQDGFGM 76 
                                               78999**************************************************************** PP

                                 TIGR01822  73 ssvrficGtqdlhkelekklaeflgtedailyascfdangGlfeallgeedaiisdalnhasiidGvrl 141
                                               +svrficGtq++hk+le+ la+fl+t d+ily+scfdangGlfe+ll ++da+isd+lnhasiidGvrl
  lcl|FitnessBrowser__Cup4G11:RR42_RS22865  77 ASVRFICGTQSVHKTLEAVLAKFLHTGDSILYSSCFDANGGLFETLLDDQDAVISDELNHASIIDGVRL 145
                                               ********************************************************************* PP

                                 TIGR01822 142 ckakryryenadledleaklkearaagarlrliatdGvfsmdGtiapldeicalaekydalvlvdecha 210
                                               cka+ryry+n+d++dle++l+ea+aagar +liatdGvfsmdG ia+l+ ic+la++y+alv+vd++ha
  lcl|FitnessBrowser__Cup4G11:RR42_RS22865 146 CKARRYRYRNNDMADLETRLQEADAAGARFKLIATDGVFSMDGIIADLKSICDLADRYGALVMVDDSHA 214
                                               ********************************************************************* PP

                                 TIGR01822 211 tGflGatGrGsaelldvldkvdiitgtlGkalGGasGGfttakkevvellrqrsrpylfsnslapavvg 279
                                               +Gf+G++GrG+ el++v ++vdiitgtlGkalGGasGG+ +a++e+vellrqrsrpylfsnslap++ +
  lcl|FitnessBrowser__Cup4G11:RR42_RS22865 215 VGFVGEHGRGTPELCGVEGRVDIITGTLGKALGGASGGYVAAHREIVELLRQRSRPYLFSNSLAPSICA 283
                                               ********************************************************************* PP

                                 TIGR01822 280 asikvlell..easnelrdklventryfrekleaaGfdvkpaehaiipvmlydaklaqklaerlleeGi 346
                                               a++kvlell  e+++ lr ++ en ++fr +++a+Gf++ p++h+iipvml+da la+ +a+ ll e +
  lcl|FitnessBrowser__Cup4G11:RR42_RS22865 284 ATLKVLELLasEEGAALRARVRENGEHFRREMTALGFTLVPGQHPIIPVMLGDAALASGMADALLAEHV 352
                                               ********94457889***************************************************** PP

                                 TIGR01822 347 yviGffypvvpkGqarirvqlsaaheeeqldkaveafvkvGrelgvi 393
                                               yv+Gf++pvvpkG+arir+q+saah+ eq+++av af+kvGr++g+i
  lcl|FitnessBrowser__Cup4G11:RR42_RS22865 353 YVVGFSFPVVPKGRARIRTQMSAAHTAEQIERAVAAFAKVGRKFGAI 399
                                               *******************************************9986 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: 6.89
//
[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