Alignments for a candidate for fadA in Sinorhizobium fredii NGR234

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Sinorhizobium fredii NGR234

Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate WP_015888208.1 NGR_RS10290 3-oxoadipyl-CoA thiolase

Query= metacyc::MONOMER-3207
         (400 letters)



>NCBI__GCF_000018545.1:WP_015888208.1
          Length = 400

 Score =  545 bits (1405), Expect = e-160
 Identities = 278/401 (69%), Positives = 330/401 (82%), Gaps = 2/401 (0%)

Query: 1   MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60
           MRD +ICD IRTPIGRFGG+L+ VRADDL A+PL+AL+E N +V W+ VD++ FGCANQA
Sbjct: 1   MRDAYICDYIRTPIGRFGGSLSAVRADDLGAIPLRALMERNASVDWEAVDDLIFGCANQA 60

Query: 61  GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120
           GEDNRNVARM+LLLAGLP ++PG T+NRLC SGMDA+  A RAI +GE EL IAGGVESM
Sbjct: 61  GEDNRNVARMSLLLAGLPVAVPGTTINRLCGSGMDAVIAAARAIKAGEAELMIAGGVESM 120

Query: 121 SRAPFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRAD 180
           SRAPFV+ KA+S +SR+ ++ DTTIGWRF+NPLMK+QYGVDSMPET +NVA+D++VSR  
Sbjct: 121 SRAPFVLPKADSAFSRHAEIHDTTIGWRFVNPLMKAQYGVDSMPETGENVAEDFKVSREA 180

Query: 181 QDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGE-TIVERDEHLRPETTLEALTKLKP 239
           QDAFA+RSQ KAAAAQA G  A EIV V I  KKGE  +V+RDEH R  TT+EAL KLK 
Sbjct: 181 QDAFAVRSQAKAAAAQANGRLAREIVAVTIPQKKGEAVVVDRDEHPR-ATTIEALAKLKA 239

Query: 240 VNGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPV 299
                 +VTAGNASGVNDGAAALI+AS EA +KHGL P AR+LG A+ GV PR+MGIGP+
Sbjct: 240 PFRAGGSVTAGNASGVNDGAAALIIASEEAARKHGLRPIARILGGATAGVPPRIMGIGPL 299

Query: 300 PAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLG 359
           PA +KL  RLG+    FDVIELNEAFASQGLAVLRELG+ADD P+VN NGGAIALGHPL 
Sbjct: 300 PASQKLMARLGITQDQFDVIELNEAFASQGLAVLRELGIADDDPRVNRNGGAIALGHPLA 359

Query: 360 MSGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400
           MSGAR+  TA  +L ++GGR  L+TMC+GVGQG+A+A+ERV
Sbjct: 360 MSGARITGTAALELAETGGRYSLSTMCIGVGQGIAVALERV 400


Lambda     K      H
   0.318    0.134    0.383 

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: 513
Number of extensions: 17
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: 400
Length of database: 400
Length adjustment: 31
Effective length of query: 369
Effective length of database: 369
Effective search space:   136161
Effective search space used:   136161
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_015888208.1 NGR_RS10290 (3-oxoadipyl-CoA thiolase)
to HMM TIGR01930 (acetyl-CoA C-acyltransferase (EC 2.3.1.16))

# 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/TIGR01930.hmm
# target sequence database:        /tmp/gapView.286844.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01930  [M=385]
Accession:   TIGR01930
Description: AcCoA-C-Actrans: acetyl-CoA C-acyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.4e-136  439.2   5.1   7.2e-136  439.0   5.1    1.0  1  NCBI__GCF_000018545.1:WP_015888208.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000018545.1:WP_015888208.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  439.0   5.1  7.2e-136  7.2e-136       1     385 []       6     398 ..       6     398 .. 0.95

  Alignments for each domain:
  == domain 1  score: 439.0 bits;  conditional E-value: 7.2e-136
                             TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikellera.gldpekidevilGnvlqageq.aniaReaalaaglp 71 
                                           i d++Rtpig++ggsl+ ++a+dL+a  +++l+er+  +d e++d++i+G++ qage+  n+aR+ +l aglp
  NCBI__GCF_000018545.1:WP_015888208.1   6 ICDYIRTPIGRFGGSLSAVRADDLGAIPLRALMERNaSVDWEAVDDLIFGCANQAGEDnRNVARMSLLLAGLP 78 
                                           7899******************************************************9************** PP

                             TIGR01930  72 esvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl 144
                                             vp++t+nr+C+Sg++Av+ aa++ikaGea++++aGGvEsmSr+p++l+++   +s+  ++a+ +d+++   
  NCBI__GCF_000018545.1:WP_015888208.1  79 VAVPGTTINRLCGSGMDAVIAAARAIKAGEAELMIAGGVESMSRAPFVLPKA---DSAFSRHAEIHDTTIGWR 148
                                           **************************************************97...555556667777444333 PP

                             TIGR01930 145 ........vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk...kkvvs 206
                                                   ++   sm et en+a+++++sRe qD++a+rS+ kaa+A+++g++++eiv v++++k   ++vv+
  NCBI__GCF_000018545.1:WP_015888208.1 149 fvnplmkaQYGVDSMPETGENVAEDFKVSREAQDAFAVRSQAKAAAAQANGRLAREIVAVTIPQKkgeAVVVD 221
                                           77888998778889*************************************************999*9999** PP

                             TIGR01930 207 kDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdp 279
                                           +De++r  tt+e+LakLk+ f+   gs vtAgN+s++nDGAaal+++see+a+++gl+p+ari + a+agv+p
  NCBI__GCF_000018545.1:WP_015888208.1 222 RDEHPR-ATTIEALAKLKAPFRA-GGS-VTAGNASGVNDGAAALIIASEEAARKHGLRPIARILGGATAGVPP 291
                                           ******.899***********96.796.********************************************* PP

                             TIGR01930 280 eemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsld.lekvNvnGGAiAlGHPlGasGar 351
                                           ++mg+gp pA++k++++ g++ +++d++E+nEAFA+q lav +elg  d + +vN nGGAiAlGHPl++sGar
  NCBI__GCF_000018545.1:WP_015888208.1 292 RIMGIGPLPASQKLMARLGITQDQFDVIELNEAFASQGLAVLRELGIADdDPRVNRNGGAIALGHPLAMSGAR 364
                                           **********************************************866799********************* PP

                             TIGR01930 352 ivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                           i+ t + eL+e g++y l t+C+g GqG+Av le
  NCBI__GCF_000018545.1:WP_015888208.1 365 ITGTAALELAETGGRYSLSTMCIGVGQGIAVALE 398
                                           *******************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 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: 15.02
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 2024 update 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