GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fadA in Echinicola vietnamensis KMM 6221, DSM 17526

Align 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 (characterized)
to candidate Echvi_1071 Echvi_1071 acetyl-CoA acetyltransferases

Query= SwissProt::O32177
         (391 letters)



>lcl|FitnessBrowser__Cola:Echvi_1071 Echvi_1071 acetyl-CoA
           acetyltransferases
          Length = 391

 Score =  411 bits (1057), Expect = e-119
 Identities = 210/389 (53%), Positives = 265/389 (68%), Gaps = 2/389 (0%)

Query: 3   EAVIVSGARTPVGKAKKGSLATVRPDDLGAICVKETLKRAGGYEGN-IDDLIIGCATPEA 61
           +A I+ G RT VGKAKKG     RPDDL    +K+ +    G E   +DDLI+G A PEA
Sbjct: 2   DAYIIKGYRTAVGKAKKGGFRFYRPDDLAVDVIKKLIADTPGLEAERVDDLIVGNAVPEA 61

Query: 62  EQGLNMARNIGALAGLPYTVPAITVNRYCSSGLQSIAYAAEKIMLGAYDTAIAGGAESMS 121
           EQG+ M R I  +A L   VP   +NRYC SGL++IA A  KI  G  D  IAGG ESMS
Sbjct: 62  EQGMQMGRMISLMA-LGKVVPGFIINRYCGSGLEAIALATAKIKSGMADCIIAGGTESMS 120

Query: 122 QVPMMGHVTRPNLALAEKAPEYYMSMGHTAEQVAKKYGVSREDQDAFAVRSHQNAAKALA 181
            VPMMG+ T  N  +A + P+YY+SMG TAE++AK Y +SRED D FAV SH+ A  A+ 
Sbjct: 121 MVPMMGYKTALNWKIASEHPDYYLSMGLTAEELAKDYDISREDSDQFAVTSHERAISAIK 180

Query: 182 EGKFKDEIVPVEVTVTEIGEDHKPMEKQFVFSQDEGVRPQTTADILSTLRPAFSVDGTVT 241
           EG+FK+EIVP+EV  T +    K   + F    DEG RP T  D+L  L+PAF   G VT
Sbjct: 181 EGRFKEEIVPIEVEETFVDASGKRQTRTFTVDTDEGPRPGTNMDVLGGLKPAFKQGGQVT 240

Query: 242 AGNSSQTSDGAAAVMLMDREKADALGLAPLVKFRSFAVGGVPPEVMGIGPVEAIPRALKL 301
           AGNSSQTSDGAA  ++M       L L P+ +  S++V GV P +MGIGP EA+P+ALK 
Sbjct: 241 AGNSSQTSDGAAFTVVMSERMVKELNLEPVARLVSYSVAGVDPRIMGIGPKEAVPKALKQ 300

Query: 302 AGLQLQDIGLFELNEAFASQAIQVIRELGIDEEKVNVNGGAIALGHPLGCTGTKLTLSLI 361
           AG+++ DI L ELNEAFA+QA+ VIR L +D   VNVNGGA+ALGHPLGCTG KLT+ +I
Sbjct: 301 AGMKMSDISLVELNEAFAAQALAVIRALDMDPNTVNVNGGAVALGHPLGCTGAKLTVQMI 360

Query: 362 HEMKRRNEQFGVVTMCIGGGMGAAGVFEL 390
           +E++RRN+++G+VT C+GGG G AGV EL
Sbjct: 361 NELRRRNQKYGMVTACVGGGQGVAGVVEL 389


Lambda     K      H
   0.316    0.133    0.377 

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: 426
Number of extensions: 17
Number of successful extensions: 3
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: 391
Length of database: 391
Length adjustment: 31
Effective length of query: 360
Effective length of database: 360
Effective search space:   129600
Effective search space used:   129600
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 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate Echvi_1071 Echvi_1071 (acetyl-CoA acetyltransferases)
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.6363.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   6.9e-140  452.2   1.4   7.9e-140  452.1   1.4    1.0  1  lcl|FitnessBrowser__Cola:Echvi_1071  Echvi_1071 acetyl-CoA acetyltran


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_1071  Echvi_1071 acetyl-CoA acetyltransferases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  452.1   1.4  7.9e-140  7.9e-140       1     385 []       5     388 ..       5     388 .. 0.96

  Alignments for each domain:
  == domain 1  score: 452.1 bits;  conditional E-value: 7.9e-140
                            TIGR01930   1 ivdavRtpig.klggslkelsaedLlaavikellera.gldpekidevilGnvlqageq.aniaReaalaaglp 71 
                                          i++++Rt++g + +g ++  +++dL++ vik+l++ + gl++e++d++i+Gn+++++eq ++++R++ l a l+
  lcl|FitnessBrowser__Cola:Echvi_1071   5 IIKGYRTAVGkAKKGGFRFYRPDDLAVDVIKKLIADTpGLEAERVDDLIVGNAVPEAEQgMQMGRMISLMA-LG 77 
                                          899*******9569*********************************************999***999976.99 PP

                            TIGR01930  72 esvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdlv 145
                                          + vp++ +nr+C+Sgl+A+ala +kik+G+ad+++aGG EsmS vp++  +      l+ + a+ +        
  lcl|FitnessBrowser__Cola:Echvi_1071  78 KVVPGFIINRYCGSGLEAIALATAKIKSGMADCIIAGGTESMSMVPMMGYKT----ALNWKIASEHP------- 140
                                          99*********************************************88886....44444445555....... PP

                            TIGR01930 146 ktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk...........kkvvskD 208
                                          +  lsmg tAe+lak+y+isRe+ D++a+ Sh++a +Ai+eg+fk+eivp+ev+++           + +v++D
  lcl|FitnessBrowser__Cola:Echvi_1071 141 DYYLSMGLTAEELAKDYDISREDSDQFAVTSHERAISAIKEGRFKEEIVPIEVEETfvdasgkrqtrTFTVDTD 214
                                          567***************************************************99*********99999**** PP

                            TIGR01930 209 egirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeem 282
                                          eg+rp+t+++ L++Lkpafk+  g+ vtAgNssq++DGAa++++mse+++kel+l+p+ar+vs++vagvdp++m
  lcl|FitnessBrowser__Cola:Echvi_1071 215 EGPRPGTNMDVLGGLKPAFKQ-GGQ-VTAGNSSQTSDGAAFTVVMSERMVKELNLEPVARLVSYSVAGVDPRIM 286
                                          *******************95.797.************************************************ PP

                            TIGR01930 283 glgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltl 356
                                          g+gp +A++kaLk+ag+++sdi lvE+nEAFAaq+lav+++l+ +d++ vNvnGGA+AlGHPlG++Ga +++++
  lcl|FitnessBrowser__Cola:Echvi_1071 287 GIGPKEAVPKALKQAGMKMSDISLVELNEAFAAQALAVIRALD-MDPNTVNVNGGAVALGHPLGCTGAKLTVQM 359
                                          *******************************************.88**************************** PP

                            TIGR01930 357 lkeLkergkkyGlatlCvggGqGaAvile 385
                                          ++eL++r++kyG++t+CvggGqG+A ++e
  lcl|FitnessBrowser__Cola:Echvi_1071 360 INELRRRNQKYGMVTACVGGGQGVAGVVE 388
                                          *************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (391 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: 7.36
//
[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 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