Alignments for a candidate for kbl in Sphingomonas koreensis DSMZ 15582

GapMind for catabolism of small carbon sources

Alignments for a candidate for kbl in Sphingomonas koreensis DSMZ 15582

Align 2-amino-3-ketobutyrate coenzyme A ligase (EC 2.3.1.29) (characterized)
to candidate Ga0059261_2606 Ga0059261_2606 2-amino-3-ketobutyrate coenzyme A ligase (EC 2.3.1.29)

Query= reanno::Phaeo:GFF3380
         (395 letters)



>FitnessBrowser__Korea:Ga0059261_2606
          Length = 401

 Score =  449 bits (1155), Expect = e-131
 Identities = 238/400 (59%), Positives = 293/400 (73%), Gaps = 6/400 (1%)

Query: 1   MSTDFLTDISKTLEEIKADGLYKRERMITSPQGGEIRV--GDAAVINLCANNYLGLADHP 58
           M+  F   I   L  I+ADGL K ER++T+PQG  +R+  G  +++NLCANNYLGLA  P
Sbjct: 1   MAGGFYDRIEAELSAIRADGLMKPERVLTTPQGAAVRIEGGPPSMLNLCANNYLGLAADP 60

Query: 59  DLIAAARGVMDDKGFGMASVRFICGTQDIHRELEQRLAKFLGKDDAILFAACFDANGGLF 118
            ++ AA     + G G+ASVRFICGTQ +H++LE   A +LG DDAILFAA FDANGG+F
Sbjct: 61  RVVEAAIAATRNWGAGLASVRFICGTQTLHKQLEAETAAYLGYDDAILFAAAFDANGGVF 120

Query: 119 EPLLGPEDAIISDSLNHASIIDGIRLCKAKRYRYLNSDMNDLEAWLKQAREDGARHIMIA 178
           EPLL  EDAI+SD+LNHASIIDG+RL KAKRYRY  SD+ DLE  L  AR DGAR I+IA
Sbjct: 121 EPLLSAEDAIVSDTLNHASIIDGVRLSKAKRYRYATSDIADLERVLTTARADGARTILIA 180

Query: 179 TDGVFSMDGYLAKLPEIRALADKYDAIVMVDDCHATGFMGATGAGTPEHFGV--DVDIVT 236
           TDGVFSMDG +A L EI ALA ++DA+++VDDCHATG +G  G G+    GV   VDI+T
Sbjct: 181 TDGVFSMDGAIAPLDEIAALAQRFDALLLVDDCHATGIIGEGGRGSGAFRGVADKVDILT 240

Query: 237 GTLGKALGGAIGGYIAGPQPVIDLLRQRARPYLFSNSLPPSIVAAGLEAIRLV--EEGNG 294
           GT GKALGGA+GG++A  QPVIDLLRQRARPYLFSN+L P+I  A L AI +   +EG+ 
Sbjct: 241 GTYGKALGGAMGGFVAARQPVIDLLRQRARPYLFSNALAPAICGASLAAIGIAASDEGDA 300

Query: 295 LRAQLFENAKYWRAGLEKLGFDLLPGEHPIIPVMLGEAQLAQDMASRLFDEGVYVSGFFF 354
           LR  L  NA  +R  L   GFDLLPGEHPIIPVML +A  AQ  A+ L D GV V+GF F
Sbjct: 301 LRRHLAANAALFRDRLTHAGFDLLPGEHPIIPVMLHDAAKAQRAAAELIDAGVLVAGFSF 360

Query: 355 PVVPRGQARIRTQMNAALTRDELDRALAAFGKVGKELGIL 394
           PVVP G+ARIRTQM+A LT D++++A   F  VG++L ++
Sbjct: 361 PVVPHGKARIRTQMSAGLTADQVEQAADIFVSVGRKLDLI 400


Lambda     K      H
   0.322    0.141    0.415 

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: 497
Number of extensions: 19
Number of successful extensions: 4
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: 395
Length of database: 401
Length adjustment: 31
Effective length of query: 364
Effective length of database: 370
Effective search space:   134680
Effective search space used:   134680
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 (21.9 bits)
S2: 50 (23.9 bits)

Align candidate Ga0059261_2606 Ga0059261_2606 (2-amino-3-ketobutyrate coenzyme A ligase (EC 2.3.1.29))
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.11197.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   9.6e-177  573.7   1.3   1.1e-176  573.5   1.3    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_2606  Ga0059261_2606 2-amino-3-ketobut


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_2606  Ga0059261_2606 2-amino-3-ketobutyrate coenzyme A ligase (EC 2.3.1.29)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  573.5   1.3  1.1e-176  1.1e-176       1     393 []       5     400 ..       5     400 .. 0.98

  Alignments for each domain:
  == domain 1  score: 573.5 bits;  conditional E-value: 1.1e-176
                                 TIGR01822   1 lkailaaelesireaGlfkkeriitspqkadirvadG.revlnfcannylGlsdhpeviqaakdaldeh 68 
                                               +++ ++ael +ir++Gl k er++t+pq+a +r+  G  ++ln+cannylGl+  p+v++aa +a ++ 
  lcl|FitnessBrowser__Korea:Ga0059261_2606   5 FYDRIEAELSAIRADGLMKPERVLTTPQGAAVRIEGGpPSMLNLCANNYLGLAADPRVVEAAIAATRNW 73 
                                               67899*****************************888889***************************** PP

                                 TIGR01822  69 GfGlssvrficGtqdlhkelekklaeflgtedailyascfdangGlfeallgeedaiisdalnhasiid 137
                                               G+Gl+svrficGtq lhk+le++ a++lg +dail+a++fdangG+fe+ll++edai+sd+lnhasiid
  lcl|FitnessBrowser__Korea:Ga0059261_2606  74 GAGLASVRFICGTQTLHKQLEAETAAYLGYDDAILFAAAFDANGGVFEPLLSAEDAIVSDTLNHASIID 142
                                               ********************************************************************* PP

                                 TIGR01822 138 GvrlckakryryenadledleaklkearaagarlrliatdGvfsmdGtiapldeicalaekydalvlvd 206
                                               Gvrl kakryry+ +d++dle+ l+ ara+gar+ liatdGvfsmdG iapldei+ala+++dal+lvd
  lcl|FitnessBrowser__Korea:Ga0059261_2606 143 GVRLSKAKRYRYATSDIADLERVLTTARADGARTILIATDGVFSMDGAIAPLDEIAALAQRFDALLLVD 211
                                               ********************************************************************* PP

                                 TIGR01822 207 echatGflGatGrGsaelldvldkvdiitgtlGkalGGasGGfttakkevvellrqrsrpylfsnslap 275
                                               +chatG++G+ GrGs  +++v dkvdi+tgt GkalGGa+GGf +a+++v++llrqr+rpylfsn+lap
  lcl|FitnessBrowser__Korea:Ga0059261_2606 212 DCHATGIIGEGGRGSGAFRGVADKVDILTGTYGKALGGAMGGFVAARQPVIDLLRQRARPYLFSNALAP 280
                                               ********************************************************************* PP

                                 TIGR01822 276 avvgasikvlell..easnelrdklventryfrekleaaGfdvkpaehaiipvmlydaklaqklaerll 342
                                               a+ gas++++ +   ++++ lr +l++n+  fr++l+ aGfd+ p+eh+iipvml+da +aq+ a++l+
  lcl|FitnessBrowser__Korea:Ga0059261_2606 281 AICGASLAAIGIAasDEGDALRRHLAANAALFRDRLTHAGFDLLPGEHPIIPVMLHDAAKAQRAAAELI 349
                                               *********99862267889************************************************* PP

                                 TIGR01822 343 eeGiyviGffypvvpkGqarirvqlsaaheeeqldkaveafvkvGrelgvi 393
                                               + G+ v Gf++pvvp G+arir+q+sa+ + +q+++a + fv vGr+l++i
  lcl|FitnessBrowser__Korea:Ga0059261_2606 350 DAGVLVAGFSFPVVPHGKARIRTQMSAGLTADQVEQAADIFVSVGRKLDLI 400
                                               ***********************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (401 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: 6.92
//
[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