Aligments for a candidate for kbl in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Aligments for a candidate for kbl in Phaeobacter inhibens BS107

Align 2-amino-3-ketobutyrate coenzyme A ligase (EC 2.3.1.29) (characterized)
to candidate GFF3380 PGA1_c34330 2-amino-3-ketobutyrate coenzyme A ligase Kbl

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



>FitnessBrowser__Phaeo:GFF3380
          Length = 395

 Score =  786 bits (2030), Expect = 0.0
 Identities = 395/395 (100%), Positives = 395/395 (100%)

Query: 1   MSTDFLTDISKTLEEIKADGLYKRERMITSPQGGEIRVGDAAVINLCANNYLGLADHPDL 60
           MSTDFLTDISKTLEEIKADGLYKRERMITSPQGGEIRVGDAAVINLCANNYLGLADHPDL
Sbjct: 1   MSTDFLTDISKTLEEIKADGLYKRERMITSPQGGEIRVGDAAVINLCANNYLGLADHPDL 60

Query: 61  IAAARGVMDDKGFGMASVRFICGTQDIHRELEQRLAKFLGKDDAILFAACFDANGGLFEP 120
           IAAARGVMDDKGFGMASVRFICGTQDIHRELEQRLAKFLGKDDAILFAACFDANGGLFEP
Sbjct: 61  IAAARGVMDDKGFGMASVRFICGTQDIHRELEQRLAKFLGKDDAILFAACFDANGGLFEP 120

Query: 121 LLGPEDAIISDSLNHASIIDGIRLCKAKRYRYLNSDMNDLEAWLKQAREDGARHIMIATD 180
           LLGPEDAIISDSLNHASIIDGIRLCKAKRYRYLNSDMNDLEAWLKQAREDGARHIMIATD
Sbjct: 121 LLGPEDAIISDSLNHASIIDGIRLCKAKRYRYLNSDMNDLEAWLKQAREDGARHIMIATD 180

Query: 181 GVFSMDGYLAKLPEIRALADKYDAIVMVDDCHATGFMGATGAGTPEHFGVDVDIVTGTLG 240
           GVFSMDGYLAKLPEIRALADKYDAIVMVDDCHATGFMGATGAGTPEHFGVDVDIVTGTLG
Sbjct: 181 GVFSMDGYLAKLPEIRALADKYDAIVMVDDCHATGFMGATGAGTPEHFGVDVDIVTGTLG 240

Query: 241 KALGGAIGGYIAGPQPVIDLLRQRARPYLFSNSLPPSIVAAGLEAIRLVEEGNGLRAQLF 300
           KALGGAIGGYIAGPQPVIDLLRQRARPYLFSNSLPPSIVAAGLEAIRLVEEGNGLRAQLF
Sbjct: 241 KALGGAIGGYIAGPQPVIDLLRQRARPYLFSNSLPPSIVAAGLEAIRLVEEGNGLRAQLF 300

Query: 301 ENAKYWRAGLEKLGFDLLPGEHPIIPVMLGEAQLAQDMASRLFDEGVYVSGFFFPVVPRG 360
           ENAKYWRAGLEKLGFDLLPGEHPIIPVMLGEAQLAQDMASRLFDEGVYVSGFFFPVVPRG
Sbjct: 301 ENAKYWRAGLEKLGFDLLPGEHPIIPVMLGEAQLAQDMASRLFDEGVYVSGFFFPVVPRG 360

Query: 361 QARIRTQMNAALTRDELDRALAAFGKVGKELGILS 395
           QARIRTQMNAALTRDELDRALAAFGKVGKELGILS
Sbjct: 361 QARIRTQMNAALTRDELDRALAAFGKVGKELGILS 395


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: 684
Number of extensions: 9
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: 395
Length of database: 395
Length adjustment: 31
Effective length of query: 364
Effective length of database: 364
Effective search space:   132496
Effective search space used:   132496
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 GFF3380 PGA1_c34330 (2-amino-3-ketobutyrate coenzyme A ligase Kbl)
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.4605.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
     2e-193  628.6   0.0   2.3e-193  628.4   0.0    1.0  1  lcl|FitnessBrowser__Phaeo:GFF3380  PGA1_c34330 2-amino-3-ketobutyra


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF3380  PGA1_c34330 2-amino-3-ketobutyrate coenzyme A ligase Kbl
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  628.4   0.0  2.3e-193  2.3e-193       5     393 .]       9     394 ..       5     394 .. 0.99

  Alignments for each domain:
  == domain 1  score: 628.4 bits;  conditional E-value: 2.3e-193
                          TIGR01822   5 laaelesireaGlfkkeriitspqkadirvadGrevlnfcannylGlsdhpeviqaakdaldehGfGlssvrficG 80 
                                        +++ le i+++Gl+k+er+itspq+ +irv d   v+n+cannylGl+dhp++i+aa+  +d++GfG++svrficG
  lcl|FitnessBrowser__Phaeo:GFF3380   9 ISKTLEEIKADGLYKRERMITSPQGGEIRVGD-AAVINLCANNYLGLADHPDLIAAARGVMDDKGFGMASVRFICG 83 
                                        67789*************************65.68***************************************** PP

                          TIGR01822  81 tqdlhkelekklaeflgtedailyascfdangGlfeallgeedaiisdalnhasiidGvrlckakryryenadled 156
                                        tqd+h+ele++la+flg++dail+a+cfdangGlfe+llg+edaiisd+lnhasiidG+rlckakryry n+d++d
  lcl|FitnessBrowser__Phaeo:GFF3380  84 TQDIHRELEQRLAKFLGKDDAILFAACFDANGGLFEPLLGPEDAIISDSLNHASIIDGIRLCKAKRYRYLNSDMND 159
                                        **************************************************************************** PP

                          TIGR01822 157 leaklkearaagarlrliatdGvfsmdGtiapldeicalaekydalvlvdechatGflGatGrGsaelldvldkvd 232
                                        lea lk+ar++gar+ +iatdGvfsmdG +a+l ei+ala+kyda+v+vd+chatGf+GatG G+ e ++v   vd
  lcl|FitnessBrowser__Phaeo:GFF3380 160 LEAWLKQAREDGARHIMIATDGVFSMDGYLAKLPEIRALADKYDAIVMVDDCHATGFMGATGAGTPEHFGV--DVD 233
                                        **********************************************************************9..7** PP

                          TIGR01822 233 iitgtlGkalGGasGGfttakkevvellrqrsrpylfsnslapavvgasikvlelleasnelrdklventryfrek 308
                                        i+tgtlGkalGGa+GG+ +++++v++llrqr+rpylfsnsl+p++v+a+++++ l+e++n lr +l en++y+r+ 
  lcl|FitnessBrowser__Phaeo:GFF3380 234 IVTGTLGKALGGAIGGYIAGPQPVIDLLRQRARPYLFSNSLPPSIVAAGLEAIRLVEEGNGLRAQLFENAKYWRAG 309
                                        **************************************************************************** PP

                          TIGR01822 309 leaaGfdvkpaehaiipvmlydaklaqklaerlleeGiyviGffypvvpkGqarirvqlsaaheeeqldkaveafv 384
                                        le +Gfd+ p+eh+iipvml++a+laq++a+rl +eG+yv Gff+pvvp+Gqarir+q+ aa ++++ld+a+ af 
  lcl|FitnessBrowser__Phaeo:GFF3380 310 LEKLGFDLLPGEHPIIPVMLGEAQLAQDMASRLFDEGVYVSGFFFPVVPRGQARIRTQMNAALTRDELDRALAAFG 385
                                        **************************************************************************** PP

                          TIGR01822 385 kvGrelgvi 393
                                        kvG+elg++
  lcl|FitnessBrowser__Phaeo:GFF3380 386 KVGKELGIL 394
                                        ******985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (395 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: 7.01
//
[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, 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

GapMind for catabolism of small carbon sources