GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fadA in Azospirillum brasilense Sp245

Align Acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate AZOBR_RS20220 AZOBR_RS20220 acetyl-CoA acetyltransferase

Query= reanno::SB2B:6935813
         (387 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS20220 AZOBR_RS20220 acetyl-CoA
           acetyltransferase
          Length = 382

 Score =  342 bits (876), Expect = 1e-98
 Identities = 201/384 (52%), Positives = 254/384 (66%), Gaps = 11/384 (2%)

Query: 5   VIVDCIRTPMGRSKGGVFRNVRAETLSAELMKALLLRNPGVDPNTIEDVIWGCVQQTLEQ 64
           VI    R+P   +  G    VR + L A ++ AL+ R  GV+P  IEDV+ GC     EQ
Sbjct: 9   VIAGYARSPFAFANKGELAKVRPDDLLAHVVAALVERT-GVNPQDIEDVVVGCAFPEGEQ 67

Query: 65  GFNIARNASLLAGVPKTAGAVTVNRLCGSSMEALHQASRAIMTGMGDTFIIGGVEHMGHV 124
           G NIAR  S LA +P TAGA T+NR CGSSM+A+HQA+ AI  G G+ F+ GG+E M  V
Sbjct: 68  GMNIARTVSFLAKLPLTAGATTINRYCGSSMQAIHQAAGAIQMGAGEVFLCGGIESMSRV 127

Query: 125 PM-NHGVDFHPGLAANVAKASGMMGLTAEMLGKLHGISREMQDQFAVRSHQRAHAASIEG 183
           PM  +    HPGL  +  +A   MG+TAE + + + ISR  Q+  A  SH +A AA   G
Sbjct: 128 PMMGYNPLPHPGLKDHYPEAYCSMGVTAENVARRYEISRADQEAMAAESHAKAAAAQQAG 187

Query: 184 RFANEIYAIEGHDANGALIKVDYDEVIRPETTLESLAGLRPVFDPANGTVTAGTSSALSD 243
           R A EI AI+      A   V+ D  IRP T+ E+L+GL+P F  A+G+VTAGTSS L+D
Sbjct: 188 RLAEEIVAIQT-----AAGLVERDGCIRPGTSGETLSGLKPAF-LADGSVTAGTSSPLTD 241

Query: 244 GAAAMLVMEEEKARALGLTIRARVRSMAVAGCDAAIMGYGPVPATQKALARAGLSIQDMD 303
           GA+A+LV  E  A+A GL I AR+RS+AVAGC   +MG GPVPA QKALARAGLSI+D+D
Sbjct: 242 GASAVLVTTEAYAKANGLPILARIRSVAVAGCAPEVMGLGPVPAAQKALARAGLSIRDID 301

Query: 304 VIELNEAFAAQSLPCVKDLGLMDVVEDKVNLNGGAIALGHPLGCSGARISTTLINLMEHK 363
           VIELNEAFAAQ++ C++DL   D+   KVNL+GGAIALGHPLG +GARI+     L++ +
Sbjct: 302 VIELNEAFAAQAIACMRDL---DIDPAKVNLDGGAIALGHPLGATGARITGKAAALLKRE 358

Query: 364 DATLGLATMCIGLGQGIATVFERV 387
                LAT CIG GQGIATV E V
Sbjct: 359 GKQFALATQCIGGGQGIATVLEAV 382


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: 433
Number of extensions: 19
Number of successful extensions: 5
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: 387
Length of database: 382
Length adjustment: 30
Effective length of query: 357
Effective length of database: 352
Effective search space:   125664
Effective search space used:   125664
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 AZOBR_RS20220 AZOBR_RS20220 (acetyl-CoA acetyltransferase)
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.26935.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.2e-134  432.7   8.1   7.4e-134  432.4   8.1    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS20220  AZOBR_RS20220 acetyl-CoA acetylt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS20220  AZOBR_RS20220 acetyl-CoA acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  432.4   8.1  7.4e-134  7.4e-134       1     385 []      10     380 ..      10     380 .. 0.97

  Alignments for each domain:
  == domain 1  score: 432.4 bits;  conditional E-value: 7.4e-134
                                 TIGR01930   1 ivdavRtpig.klggslkelsaedLlaavikelleragldpekidevilGnvlqageq.aniaReaala 67 
                                               i +++R+p++ + +g l++++++dLla+v+ +l+er+g++p++i++v++G+++++geq +niaR++ + 
  lcl|FitnessBrowser__azobra:AZOBR_RS20220  10 IAGYARSPFAfANKGELAKVRPDDLLAHVVAALVERTGVNPQDIEDVVVGCAFPEGEQgMNIARTVSFL 78 
                                               67899*****977******************************************************** PP

                                 TIGR01930  68 aglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakl 136
                                               a+lp +  a+t+nr+C+S++qA+++aa +i++G+ +v++ GG+EsmSrvp++  +       ++g ++ 
  lcl|FitnessBrowser__azobra:AZOBR_RS20220  79 AKLPLTAGATTINRYCGSSMQAIHQAAGAIQMGAGEVFLCGGIESMSRVPMMGYNP----LPHPGLKDH 143
                                               ***************************************************98886....677766666 PP

                                 TIGR01930 137 edqllkdlvktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgkkkvv 205
                                               +        ++  smg+tAen+a++y+isR +q++ a++Sh kaa+A+++g++++eiv ++    +  v
  lcl|FitnessBrowser__azobra:AZOBR_RS20220 144 YP-------EAYCSMGVTAENVARRYEISRADQEAMAAESHAKAAAAQQAGRLAEEIVAIQTA--AGLV 203
                                               65.......8899*********************************************97776..5899 PP

                                 TIGR01930 206 skDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaav 274
                                               ++D +irp+t+ e+L++Lkpaf   +gs vtAg ss+l+DGA+a+l+++e+ ak+ gl +lari+s+av
  lcl|FitnessBrowser__azobra:AZOBR_RS20220 204 ERDGCIRPGTSGETLSGLKPAFLA-DGS-VTAGTSSPLTDGASAVLVTTEAYAKANGLPILARIRSVAV 270
                                               **********************95.9*7.**************************************** PP

                                 TIGR01930 275 agvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGH 343
                                               ag+ pe+mglgpvpA +kaL++aglsi+did++E+nEAFAaq++a++++l+ +d++kvN  GGAiAlGH
  lcl|FitnessBrowser__azobra:AZOBR_RS20220 271 AGCAPEVMGLGPVPAAQKALARAGLSIRDIDVIELNEAFAAQAIACMRDLD-IDPAKVNLDGGAIALGH 338
                                               ***************************************************.88*************** PP

                                 TIGR01930 344 PlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                               PlGa+Gari+ + +  Lk++gk+++lat C+ggGqG+A++le
  lcl|FitnessBrowser__azobra:AZOBR_RS20220 339 PLGATGARITGKAAALLKREGKQFALATQCIGGGQGIATVLE 380
                                               ****************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (382 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: 7.61
//
[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