Alignments for a candidate for kbl in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for kbl in Klebsiella michiganensis M5al

Align 2-amino-3-ketobutyrate coenzyme A ligase (EC 2.3.1.29) (characterized)
to candidate BWI76_RS27255 BWI76_RS27255 glycine C-acetyltransferase

Query= reanno::Koxy:BWI76_RS27255
         (397 letters)



>FitnessBrowser__Koxy:BWI76_RS27255
          Length = 397

 Score =  781 bits (2016), Expect = 0.0
 Identities = 397/397 (100%), Positives = 397/397 (100%)

Query: 1   MRGDFYKQLTNDLDTARAEGLFKEERIITSAQQADITVGGSQVINFCANNYLGLANHPEL 60
           MRGDFYKQLTNDLDTARAEGLFKEERIITSAQQADITVGGSQVINFCANNYLGLANHPEL
Sbjct: 1   MRGDFYKQLTNDLDTARAEGLFKEERIITSAQQADITVGGSQVINFCANNYLGLANHPEL 60

Query: 61  IAAAKSGMDSHGFGMASVRFICGTQDSHKALEKKLADFLGMEDAILYSSCFDANGGLFET 120
           IAAAKSGMDSHGFGMASVRFICGTQDSHKALEKKLADFLGMEDAILYSSCFDANGGLFET
Sbjct: 61  IAAAKSGMDSHGFGMASVRFICGTQDSHKALEKKLADFLGMEDAILYSSCFDANGGLFET 120

Query: 121 LLGAEDAIISDALNHASIIDGVRLCKAKRFRYANNDMVELEARLKEARDAGARHVLIATD 180
           LLGAEDAIISDALNHASIIDGVRLCKAKRFRYANNDMVELEARLKEARDAGARHVLIATD
Sbjct: 121 LLGAEDAIISDALNHASIIDGVRLCKAKRFRYANNDMVELEARLKEARDAGARHVLIATD 180

Query: 181 GVFSMDGVIANLKGVCDLADKYDALVMVDDSHAVGFVGENGRGSHEYCDVMGRVDIITGT 240
           GVFSMDGVIANLKGVCDLADKYDALVMVDDSHAVGFVGENGRGSHEYCDVMGRVDIITGT
Sbjct: 181 GVFSMDGVIANLKGVCDLADKYDALVMVDDSHAVGFVGENGRGSHEYCDVMGRVDIITGT 240

Query: 241 LGKALGGASGGYTAARKEVVEWLRQRSRPYLFSNSLAPAIVAASIKVLEMVEAGSELRDR 300
           LGKALGGASGGYTAARKEVVEWLRQRSRPYLFSNSLAPAIVAASIKVLEMVEAGSELRDR
Sbjct: 241 LGKALGGASGGYTAARKEVVEWLRQRSRPYLFSNSLAPAIVAASIKVLEMVEAGSELRDR 300

Query: 301 LWSNARLFREKMTAAGFILAGADHAIIPVMLGEATVAQEFARELQKEGIYVTGFFYPVVP 360
           LWSNARLFREKMTAAGFILAGADHAIIPVMLGEATVAQEFARELQKEGIYVTGFFYPVVP
Sbjct: 301 LWSNARLFREKMTAAGFILAGADHAIIPVMLGEATVAQEFARELQKEGIYVTGFFYPVVP 360

Query: 361 KGQARIRTQMSAAHTPEQIERAVEAFTRIGKQLGVIA 397
           KGQARIRTQMSAAHTPEQIERAVEAFTRIGKQLGVIA
Sbjct: 361 KGQARIRTQMSAAHTPEQIERAVEAFTRIGKQLGVIA 397


Lambda     K      H
   0.321    0.136    0.390 

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: 695
Number of extensions: 19
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: 397
Length of database: 397
Length adjustment: 31
Effective length of query: 366
Effective length of database: 366
Effective search space:   133956
Effective search space used:   133956
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 BWI76_RS27255 BWI76_RS27255 (glycine C-acetyltransferase)
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.11147.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   3.3e-223  726.6   3.1   3.8e-223  726.5   3.1    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS27255  BWI76_RS27255 glycine C-acetyltr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS27255  BWI76_RS27255 glycine C-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  726.5   3.1  3.8e-223  3.8e-223       1     393 []       5     396 ..       5     396 .. 1.00

  Alignments for each domain:
  == domain 1  score: 726.5 bits;  conditional E-value: 3.8e-223
                               TIGR01822   1 lkailaaelesireaGlfkkeriitspqkadirvadGrevlnfcannylGlsdhpeviqaakdaldehGfG 71 
                                             ++++l+++l+++r++Glfk+eriits+q+adi+v  G++v+nfcannylGl++hpe+i+aak+++d+hGfG
  lcl|FitnessBrowser__Koxy:BWI76_RS27255   5 FYKQLTNDLDTARAEGLFKEERIITSAQQADITV-GGSQVINFCANNYLGLANHPELIAAAKSGMDSHGFG 74 
                                             6789******************************.99********************************** PP

                               TIGR01822  72 lssvrficGtqdlhkelekklaeflgtedailyascfdangGlfeallgeedaiisdalnhasiidGvrlc 142
                                             ++svrficGtqd+hk lekkla+flg+edaily+scfdangGlfe+llg+edaiisdalnhasiidGvrlc
  lcl|FitnessBrowser__Koxy:BWI76_RS27255  75 MASVRFICGTQDSHKALEKKLADFLGMEDAILYSSCFDANGGLFETLLGAEDAIISDALNHASIIDGVRLC 145
                                             *********************************************************************** PP

                               TIGR01822 143 kakryryenadledleaklkearaagarlrliatdGvfsmdGtiapldeicalaekydalvlvdechatGf 213
                                             kakr+ry+n+d+ +lea+lkear+agar++liatdGvfsmdG+ia+l+ +c+la+kydalv+vd++ha+Gf
  lcl|FitnessBrowser__Koxy:BWI76_RS27255 146 KAKRFRYANNDMVELEARLKEARDAGARHVLIATDGVFSMDGVIANLKGVCDLADKYDALVMVDDSHAVGF 216
                                             *********************************************************************** PP

                               TIGR01822 214 lGatGrGsaelldvldkvdiitgtlGkalGGasGGfttakkevvellrqrsrpylfsnslapavvgasikv 284
                                             +G++GrGs+e++dv+++vdiitgtlGkalGGasGG+t+a+kevve+lrqrsrpylfsnslapa+v+asikv
  lcl|FitnessBrowser__Koxy:BWI76_RS27255 217 VGENGRGSHEYCDVMGRVDIITGTLGKALGGASGGYTAARKEVVEWLRQRSRPYLFSNSLAPAIVAASIKV 287
                                             *********************************************************************** PP

                               TIGR01822 285 lelleasnelrdklventryfrekleaaGfdvkpaehaiipvmlydaklaqklaerlleeGiyviGffypv 355
                                             le++ea++elrd+l++n+r frek++aaGf +++a+haiipvml++a++aq++a++l++eGiyv+Gffypv
  lcl|FitnessBrowser__Koxy:BWI76_RS27255 288 LEMVEAGSELRDRLWSNARLFREKMTAAGFILAGADHAIIPVMLGEATVAQEFARELQKEGIYVTGFFYPV 358
                                             *********************************************************************** PP

                               TIGR01822 356 vpkGqarirvqlsaaheeeqldkaveafvkvGrelgvi 393
                                             vpkGqarir+q+saah+ eq+++aveaf+++G++lgvi
  lcl|FitnessBrowser__Koxy:BWI76_RS27255 359 VPKGQARIRTQMSAAHTPEQIERAVEAFTRIGKQLGVI 396
                                             ************************************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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.47
//
[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