GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Magnetospirillum magneticum AMB-1

Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate WP_011385133.1 AMB_RS13850 3-oxoadipyl-CoA thiolase

Query= metacyc::MONOMER-15952
         (401 letters)



>NCBI__GCF_000009985.1:WP_011385133.1
          Length = 400

 Score =  567 bits (1460), Expect = e-166
 Identities = 291/401 (72%), Positives = 329/401 (82%), Gaps = 1/401 (0%)

Query: 1   MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60
           M EALI D  RTPIGRYAG+LA VR DDL A P+KAL+ARH  LDWS VD+V YGCANQA
Sbjct: 1   MTEALICDYTRTPIGRYAGSLAGVRTDDLAAHPIKALMARHAGLDWSRVDEVAYGCANQA 60

Query: 61  GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120
           GEDNRNVARMA LLAGLP S+ GTTLNRLCGSG+DAVG AARA+  GEA LM+AGGVESM
Sbjct: 61  GEDNRNVARMALLLAGLPHSIGGTTLNRLCGSGMDAVGYAARAVMTGEAELMIAGGVESM 120

Query: 121 SRAPFVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISRAD 180
           SRAPFVM K++ AF R A ++DTTIGWRFVN LM++ +G DSMPETAENVA QFNISR D
Sbjct: 121 SRAPFVMNKADSAFSRDARLYDTTIGWRFVNALMEKAYGTDSMPETAENVAEQFNISRED 180

Query: 181 QDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKLGT 240
           QDAFA RSQ KA+AA  NGR A+EI  V +  RKG   +V HDEHPR +TT+E LAKL  
Sbjct: 181 QDAFAARSQAKASAAQKNGRFAQEISPVTLPARKGDPVVVSHDEHPR-ETTVEALAKLKA 239

Query: 241 PFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIGPV 300
           PFR GGS+TAGNASGVNDGA ALL+AS  AA+ HGL   AR++GMATAGVEPRIMGIGPV
Sbjct: 240 PFRAGGSITAGNASGVNDGAAALLIASPAAAKAHGLTPIARILGMATAGVEPRIMGIGPV 299

Query: 301 PATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGHPLG 360
           PAT+K+L   GL +AD+DV+E NEAFAAQ LA  R+LGLADDD+RVNPNGGAIALGHPLG
Sbjct: 300 PATQKLLARLGLTMADLDVMEFNEAFAAQALACTRQLGLADDDQRVNPNGGAIALGHPLG 359

Query: 361 MSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIERI 401
           MSGAR+V TA  +L +  GR AL TMCIGVGQGIA+ IER+
Sbjct: 360 MSGARIVGTAALQLAQTGGRRALSTMCIGVGQGIAMAIERV 400


Lambda     K      H
   0.319    0.134    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: 552
Number of extensions: 18
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: 401
Length of database: 400
Length adjustment: 31
Effective length of query: 370
Effective length of database: 369
Effective search space:   136530
Effective search space used:   136530
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 WP_011385133.1 AMB_RS13850 (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.12175.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     8e-212  689.4  12.7     9e-212  689.2  12.7    1.0  1  lcl|NCBI__GCF_000009985.1:WP_011385133.1  AMB_RS13850 3-oxoadipyl-CoA thio


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_011385133.1  AMB_RS13850 3-oxoadipyl-CoA thiolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  689.2  12.7    9e-212    9e-212       2     400 .]       3     400 .]       2     400 .] 1.00

  Alignments for each domain:
  == domain 1  score: 689.2 bits;  conditional E-value: 9e-212
                                 TIGR02430   2 evyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarma 70 
                                               e+ i+d  rtpiGry+Gsl+ vr+ddlaa p+kal+ar++ ld++ +d+v +GcanqaGednrnvarma
  lcl|NCBI__GCF_000009985.1:WP_011385133.1   3 EALICDYTRTPIGRYAGSLAGVRTDDLAAHPIKALMARHAGLDWSRVDEVAYGCANQAGEDNRNVARMA 71 
                                               789****************************************************************** PP

                                 TIGR02430  71 allaGlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakl 139
                                               +llaGlp+s+ gtt+nrlcgsg+da+g+aara+ +Gea+l+iaGGvesmsrapfv+ kadsafsr+a+l
  lcl|NCBI__GCF_000009985.1:WP_011385133.1  72 LLLAGLPHSIGGTTLNRLCGSGMDAVGYAARAVMTGEAELMIAGGVESMSRAPFVMNKADSAFSRDARL 140
                                               ********************************************************************* PP

                                 TIGR02430 140 edttiGwrfvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpve 208
                                                dttiGwrfvn  +++ yG+dsmpetaenvae+f++sredqdafa rsq++++aaq++G fa+ei pv+
  lcl|NCBI__GCF_000009985.1:WP_011385133.1 141 YDTTIGWRFVNALMEKAYGTDSMPETAENVAEQFNISREDQDAFAARSQAKASAAQKNGRFAQEISPVT 209
                                               ********************************************************************* PP

                                 TIGR02430 209 ikqkkGeetvvdkdehlraettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrhgltp 277
                                               ++ +kG+++vv++deh+r ett+ealaklka++r++g++taGnasGvndGaaall+as  a+k+hgltp
  lcl|NCBI__GCF_000009985.1:WP_011385133.1 210 LPARKGDPVVVSHDEHPR-ETTVEALAKLKAPFRAGGSITAGNASGVNDGAAALLIASPAAAKAHGLTP 277
                                               ******************.************************************************** PP

                                 TIGR02430 278 rarilaaasaGveprvmGlgpvpavkkllaraglsledldvielneafaaqalavlrelgladddarvn 346
                                                aril++a+aGvepr+mG+gpvpa++kllar+gl+++dldv+e+neafaaqala++r+lgladdd+rvn
  lcl|NCBI__GCF_000009985.1:WP_011385133.1 278 IARILGMATAGVEPRIMGIGPVPATQKLLARLGLTMADLDVMEFNEAFAAQALACTRQLGLADDDQRVN 346
                                               ********************************************************************* PP

                                 TIGR02430 347 pnGGaialGhplGasGarlvltalkqleksggryalatlciGvGqGialvierv 400
                                               pnGGaialGhplG+sGar+v ta  ql+++ggr+al+t+ciGvGqGia++ierv
  lcl|NCBI__GCF_000009985.1:WP_011385133.1 347 PNGGAIALGHPLGMSGARIVGTAALQLAQTGGRRALSTMCIGVGQGIAMAIERV 400
                                               *****************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (400 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 9.51
//
[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:

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:

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:

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:

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