Alignments for a candidate for pcaF in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for pcaF in Klebsiella michiganensis M5al

Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate BWI76_RS13135 BWI76_RS13135 3-oxoadipyl-CoA thiolase

Query= SwissProt::P0C7L2
         (401 letters)



>FitnessBrowser__Koxy:BWI76_RS13135
          Length = 401

 Score =  654 bits (1688), Expect = 0.0
 Identities = 333/401 (83%), Positives = 361/401 (90%)

Query: 1   MREAFICDGIRTPIGRYGGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQA 60
           MR+AFICDGIRTPIGRYGGAL+S+RADDLAAIPLRELL RNP+ D   IDDVILGCANQA
Sbjct: 1   MRDAFICDGIRTPIGRYGGALASMRADDLAAIPLRELLSRNPKFDPASIDDVILGCANQA 60

Query: 61  GEDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESM 120
           GEDNRNVA MATLLAG P +V GTT+NRLCGSGLDA+GFAARAIKAG+ DL+IAGGVESM
Sbjct: 61  GEDNRNVAHMATLLAGYPHTVPGTTVNRLCGSGLDAIGFAARAIKAGEADLMIAGGVESM 120

Query: 121 SRAPFVMGKAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTDSMPETAENVAELLKISRED 180
           SRAPFVMGKA++A+ RQAE+FDTTIGWRFVNPLM Q+FGTDSMPETAENVAELL ISR D
Sbjct: 121 SRAPFVMGKASAAYQRQAELFDTTIGWRFVNPLMQQRFGTDSMPETAENVAELLNISRAD 180

Query: 181 QDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLRGLKA 240
           QD+FA RSQQR+A+AQ  GILA+EIVPV +   KG V+ +  DEH R ETTLEQL  LK 
Sbjct: 181 QDAFAYRSQQRSARAQRDGILAQEIVPVPIIGGKGAVSTVYEDEHPRAETTLEQLSRLKT 240

Query: 241 PFRANGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVEPRLMGLGPV 300
           PFR  GV+TAGNASGVNDGAAALIIAS Q A AQGLTPRARIVAMATAGVEP+LMGLGPV
Sbjct: 241 PFRKGGVVTAGNASGVNDGAAALIIASSQQAIAQGLTPRARIVAMATAGVEPKLMGLGPV 300

Query: 301 PATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDAPHVNPNGGAIALGHPLG 360
           PA R+VLERAGLSI DMD+IELNEAFAAQALGVLR+LGL DDAPHVNPNGGAIALGHPLG
Sbjct: 301 PAVRKVLERAGLSIKDMDLIELNEAFAAQALGVLRQLGLADDAPHVNPNGGAIALGHPLG 360

Query: 361 MSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMILERV 401
           MSGARLAL+AS EL RR+GRYALCTMCIGVGQGIAMILERV
Sbjct: 361 MSGARLALSASLELQRRSGRYALCTMCIGVGQGIAMILERV 401


Lambda     K      H
   0.319    0.135    0.384 

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: 599
Number of extensions: 8
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: 401
Length of database: 401
Length adjustment: 31
Effective length of query: 370
Effective length of database: 370
Effective search space:   136900
Effective search space used:   136900
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_RS13135 BWI76_RS13135 (3-oxoadipyl-CoA thiolase)
to HMM TIGR02430 (pcaF: 3-oxoadipyl-CoA thiolase (EC 2.3.1.174))

# 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/TIGR02430.hmm
# target sequence database:        /tmp/gapView.5732.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02430  [M=400]
Accession:   TIGR02430
Description: pcaF: 3-oxoadipyl-CoA thiolase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   3.9e-219  713.5   7.5   4.3e-219  713.3   7.5    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS13135  BWI76_RS13135 3-oxoadipyl-CoA th


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS13135  BWI76_RS13135 3-oxoadipyl-CoA thiolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  713.3   7.5  4.3e-219  4.3e-219       1     400 []       2     401 .]       2     401 .] 1.00

  Alignments for each domain:
  == domain 1  score: 713.3 bits;  conditional E-value: 4.3e-219
                               TIGR02430   1 kevyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarmaa 71 
                                             ++++i+d+irtpiGrygG+l+s+raddlaa+pl++ll+rnp+ d a+iddvilGcanqaGednrnva ma+
  lcl|FitnessBrowser__Koxy:BWI76_RS13135   2 RDAFICDGIRTPIGRYGGALASMRADDLAAIPLRELLSRNPKFDPASIDDVILGCANQAGEDNRNVAHMAT 72 
                                             689******************************************************************** PP

                               TIGR02430  72 llaGlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakledt 142
                                             llaG+p++vpgttvnrlcgsglda+g+aaraikaGeadl+iaGGvesmsrapfv+Gka +a+ r+a+l+dt
  lcl|FitnessBrowser__Koxy:BWI76_RS13135  73 LLAGYPHTVPGTTVNRLCGSGLDAIGFAARAIKAGEADLMIAGGVESMSRAPFVMGKASAAYQRQAELFDT 143
                                             *********************************************************************** PP

                               TIGR02430 143 tiGwrfvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpveikqkk 213
                                             tiGwrfvnp +++ +G+dsmpetaenvae +++sr+dqdafa+rsqqr a+aq  G++a+eivpv i + k
  lcl|FitnessBrowser__Koxy:BWI76_RS13135 144 TIGWRFVNPLMQQRFGTDSMPETAENVAELLNISRADQDAFAYRSQQRSARAQRDGILAQEIVPVPIIGGK 214
                                             *********************************************************************** PP

                               TIGR02430 214 GeetvvdkdehlraettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrhgltprarilaa 284
                                             G  ++v +deh+raettle+l++lk+++r++g+vtaGnasGvndGaaal++as + + ++gltprari+a+
  lcl|FitnessBrowser__Koxy:BWI76_RS13135 215 GAVSTVYEDEHPRAETTLEQLSRLKTPFRKGGVVTAGNASGVNDGAAALIIASSQQAIAQGLTPRARIVAM 285
                                             *********************************************************************** PP

                               TIGR02430 285 asaGveprvmGlgpvpavkkllaraglsledldvielneafaaqalavlrelgladddarvnpnGGaialG 355
                                             a+aGvep++mGlgpvpav+k+l+ragls++d+d+ielneafaaqal+vlr+lgladd+ +vnpnGGaialG
  lcl|FitnessBrowser__Koxy:BWI76_RS13135 286 ATAGVEPKLMGLGPVPAVRKVLERAGLSIKDMDLIELNEAFAAQALGVLRQLGLADDAPHVNPNGGAIALG 356
                                             *********************************************************************** PP

                               TIGR02430 356 hplGasGarlvltalkqleksggryalatlciGvGqGialvierv 400
                                             hplG+sGarl+l+a+ +l++++gryal+t+ciGvGqGia+++erv
  lcl|FitnessBrowser__Koxy:BWI76_RS13135 357 HPLGMSGARLALSASLELQRRSGRYALCTMCIGVGQGIAMILERV 401
                                             ********************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (400 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.04
//
[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