GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fadA in Pedobacter sp. GW460-11-11-14-LB5

Align 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 (characterized)
to candidate CA265_RS17585 CA265_RS17585 acetyl-CoA acetyltransferase

Query= SwissProt::O32177
         (391 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS17585 CA265_RS17585 acetyl-CoA
           acetyltransferase
          Length = 391

 Score =  388 bits (996), Expect = e-112
 Identities = 199/389 (51%), Positives = 264/389 (67%), Gaps = 1/389 (0%)

Query: 3   EAVIVSGARTPVGKAKKGSLATVRPDDLGAICVKETLKRAGGYEGN-IDDLIIGCATPEA 61
           EA I++G RT VGKA +G     R DDL A  ++  +      +   IDD+I+G ATPEA
Sbjct: 2   EAYIIAGYRTAVGKAPRGVFRFTRADDLAAEVIRALVASVPNLDNEQIDDVIVGNATPEA 61

Query: 62  EQGLNMARNIGALAGLPYTVPAITVNRYCSSGLQSIAYAAEKIMLGAYDTAIAGGAESMS 121
           EQGLN+ R I  +      VP +TVNRYC+SGL +IA A  KI  G  D  IAGG E MS
Sbjct: 62  EQGLNIGRMISLMGLDTDKVPGVTVNRYCASGLDTIATAVAKIKAGMADCIIAGGVEVMS 121

Query: 122 QVPMMGHVTRPNLALAEKAPEYYMSMGHTAEQVAKKYGVSREDQDAFAVRSHQNAAKALA 181
            +P  G    PN  +A+  P++Y  MG TAE VAK+Y VSREDQDAF+++SH+ A  A+ 
Sbjct: 122 GMPFGGWKLVPNAEVAKNNPDWYWGMGLTAEAVAKEYNVSREDQDAFSLKSHEKAIHAIK 181

Query: 182 EGKFKDEIVPVEVTVTEIGEDHKPMEKQFVFSQDEGVRPQTTADILSTLRPAFSVDGTVT 241
            G  KD I+P+ V    +  + K   + +V   DEG R  TT D L+ L+P F   G+VT
Sbjct: 182 NGHLKDGILPITVNENYLDANLKKKTRSYVVDTDEGPRADTTLDKLAKLKPVFDAVGSVT 241

Query: 242 AGNSSQTSDGAAAVMLMDREKADALGLAPLVKFRSFAVGGVPPEVMGIGPVEAIPRALKL 301
           AGNSSQTSDGAA V+++  +K   L   P+ +  S+ + GVPP +MGIGP+EAIP+ALK 
Sbjct: 242 AGNSSQTSDGAAFVLVVSEKKMKELNAEPIARLVSYGIAGVPPRIMGIGPIEAIPKALKQ 301

Query: 302 AGLQLQDIGLFELNEAFASQAIQVIRELGIDEEKVNVNGGAIALGHPLGCTGTKLTLSLI 361
           AGL+ +DI L ELNEAFASQ++ VIR L ++ + +NVNGGAIALGHPLGCTG KLT+ ++
Sbjct: 302 AGLKKEDIDLIELNEAFASQSLAVIRTLDLNPDVINVNGGAIALGHPLGCTGAKLTVQIM 361

Query: 362 HEMKRRNEQFGVVTMCIGGGMGAAGVFEL 390
           +E+KR+N+++G+VTMC+G G GAAG+FEL
Sbjct: 362 NELKRQNKKYGMVTMCVGTGQGAAGIFEL 390


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: 404
Number of extensions: 14
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: 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 CA265_RS17585 CA265_RS17585 (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.13961.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   1.8e-138  447.6   0.5   2.1e-138  447.4   0.5    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS17585  CA265_RS17585 acetyl-CoA acetylt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS17585  CA265_RS17585 acetyl-CoA acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  447.4   0.5  2.1e-138  2.1e-138       1     385 []       5     389 ..       5     389 .. 0.95

  Alignments for each domain:
  == domain 1  score: 447.4 bits;  conditional E-value: 2.1e-138
                                  TIGR01930   1 ivdavRtpig.klggslkelsaedLlaavikellera.gldpekidevilGnvlqageq.aniaReaa 65 
                                                i++++Rt++g + +g+++ ++a+dL+a+vi++l++ + +ld+e+id+vi+Gn+++++eq  ni+R++ 
  lcl|FitnessBrowser__Pedo557:CA265_RS17585   5 IIAGYRTAVGkAPRGVFRFTRADDLAAEVIRALVASVpNLDNEQIDDVIVGNATPEAEQgLNIGRMIS 72 
                                                89********988******************************************************9 PP

                                  TIGR01930  66 laaglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgk 133
                                                l     ++vp++tvnr+CaSgl+++a+a++kikaG+ad+++aGGvE mS +p++        +l +++
  lcl|FitnessBrowser__Pedo557:CA265_RS17585  73 LMGLDTDKVPGVTVNRYCASGLDTIATAVAKIKAGMADCIIAGGVEVMSGMPFGGW------KLVPNA 134
                                                98777899********************************************8544......455533 PP

                                  TIGR01930 134 akledqllkdlvktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk 201
                                                   ++      ++    mg tAe +ak+y++sRe+qD+++l+Sh+ka +Ai++g++kd i+p++v+++
  lcl|FitnessBrowser__Pedo557:CA265_RS17585 135 EVAKN-----NPDWYWGMGLTAEAVAKEYNVSREDQDAFSLKSHEKAIHAIKNGHLKDGILPITVNEN 197
                                                32222.....457789**************************************************99 PP

                                  TIGR01930 202 ...........kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseeva 258
                                                           + vv++Deg+r++ttl+kLakLkp+f+   gs vtAgNssq++DGAa++l++se+++
  lcl|FitnessBrowser__Pedo557:CA265_RS17585 198 yldanlkkktrSYVVDTDEGPRADTTLDKLAKLKPVFDA-VGS-VTAGNSSQTSDGAAFVLVVSEKKM 263
                                                *******99998999**********************96.797.************************ PP

                                  TIGR01930 259 kelgltplarivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgs 326
                                                kel+ +p+ar+vs+++agv+p++mg+gp++Ai+kaLk+agl+ +didl+E+nEAFA+q lav++ l+ 
  lcl|FitnessBrowser__Pedo557:CA265_RS17585 264 KELNAEPIARLVSYGIAGVPPRIMGIGPIEAIPKALKQAGLKKEDIDLIELNEAFASQSLAVIRTLD- 330
                                                *******************************************************************. PP

                                  TIGR01930 327 ldlekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                                l+++ +NvnGGAiAlGHPlG++Ga +++++++eLk+++kkyG++t+Cvg+GqGaA i+e
  lcl|FitnessBrowser__Pedo557:CA265_RS17585 331 LNPDVINVNGGAIALGHPLGCTGAKLTVQIMNELKRQNKKYGMVTMCVGTGQGAAGIFE 389
                                                88******************************************************997 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.04
# Mc/sec: 3.10
//
[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 preprint 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