Alignments for a candidate for fadA in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Pseudomonas fluorescens GW456-L13

Align 3-oxo-acyl CoA thiolase (EC 2.3.1.16) (characterized)
to candidate PfGW456L13_3394 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)

Query= metacyc::G185E-7833-MONOMER
         (386 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3394
          Length = 391

 Score =  331 bits (849), Expect = 2e-95
 Identities = 187/400 (46%), Positives = 253/400 (63%), Gaps = 24/400 (6%)

Query: 1   MTEAYVIDAVRTAVGKRGGALAGIHPVDLGALAWRGLLDRTDIDPAAVDDVIAGCVDAIG 60
           M +  ++DAVRT +GK  G+L+G+    LG+L    LL+R D+ P  VDDVI G V  IG
Sbjct: 1   MKDIVIVDAVRTPIGKFRGSLSGVRADHLGSLVISRLLERVDVSPTLVDDVIFGNVTQIG 60

Query: 61  GQAGNIARLSWLAAGYPEEVPGVTVDRQCGSSQQAISFGAQAIMSGTADVIVAGGVQNMS 120
            Q+ NIAR + L AG+P  V G+T+DR+CGS + A+     AI +G AD++VAGG +NMS
Sbjct: 61  EQSANIARTALLGAGWPVTVAGLTIDRKCGSGEVAVHMAVGAIAAGAADIVVAGGAENMS 120

Query: 121 QIPISSAMTV-GEQFGFTSPTNESKQWLHRYGDQEISQFRGSELIAEKWNLSREEMERYS 179
           ++P+ S   + G  FG          W+     +  SQ   +E +A+KW LSR+ ++ ++
Sbjct: 121 RVPMGSNREIHGAAFG----------WMAAQRYELTSQGEAAERMADKWALSRDALDDFA 170

Query: 180 LTSHERAFAAIRAGHFENEIITVETE----------SGPFRVDEG-PRESSLEKMAGLQP 228
             SH+RA AA  AG+F+NE I V  E          +G  R DE   R++S EK++ L+ 
Sbjct: 171 FASHQRAAAACDAGYFDNETIPVVVEELREKELSEPAGVLRHDETIRRDTSREKLSTLKT 230

Query: 229 LV--EGGRLTAAMASQISDGASAVLLASERAVKDHGLRPRARIHHISARAADPVFMLTGP 286
               + GR+TA  +SQISDGA+A+LL S    K  GL+ RAR+   +   +DP  MLTGP
Sbjct: 231 SFRPDTGRITAGNSSQISDGAAALLLMSADTAKKLGLKARARVVAFTTVGSDPTLMLTGP 290

Query: 287 IPATRYALDKTGLAIDDIDTVEINEAFAPVVMAWLKEIKADPAKVNPNGGAIALGHPLGA 346
           I AT+  L K GL+I+DID  E+NEAFA V +AW++E     +K+N NGGAIALGHPLGA
Sbjct: 291 IAATQKVLAKAGLSINDIDLFEVNEAFASVPLAWMQETGVPHSKLNVNGGAIALGHPLGA 350

Query: 347 TGAKLFTTMLGELERIGGRYGLQTMCEGGGTANVTIIERL 386
           +GA+L TTML ELER GGRYGLQ +C  GG    TIIERL
Sbjct: 351 SGARLMTTMLNELERRGGRYGLQAICCAGGMGTATIIERL 390


Lambda     K      H
   0.317    0.134    0.389 

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: 432
Number of extensions: 20
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: 386
Length of database: 391
Length adjustment: 30
Effective length of query: 356
Effective length of database: 361
Effective search space:   128516
Effective search space used:   128516
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 PfGW456L13_3394 (3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9))
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.6222.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
   1.5e-143  464.3   3.4   1.7e-143  464.1   3.4    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3394  3-ketoacyl-CoA thiolase (EC 2.3.


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3394  3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltran
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  464.1   3.4  1.7e-143  1.7e-143       1     385 []       6     388 ..       6     388 .. 0.97

  Alignments for each domain:
  == domain 1  score: 464.1 bits;  conditional E-value: 1.7e-143
                                               TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqag 55 
                                                             ivdavRtpigk++gsl+ ++a++L++ vi++ller++++p  +d+vi+Gnv+q g
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3394   6 IVDAVRTPIGKFRGSLSGVRADHLGSLVISRLLERVDVSPTLVDDVIFGNVTQIG 60 
                                                             9****************************************************** PP

                                               TIGR01930  56 eq.aniaReaalaaglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGG 109
                                                             eq aniaR+a+l ag p +v++lt++r C+Sg  Av++a+ +i+aG+ad+vvaGG
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3394  61 EQsANIARTALLGAGWPVTVAGLTIDRKCGSGEVAVHMAVGAIAAGAADIVVAGG 115
                                                             ******************************************************* PP

                                               TIGR01930 110 vEsmSrvpillkaslrreslklgkakledqllkdlvktklsmgetAenlakkygi 164
                                                             +E+mSrvp+++++++  +++ +g +  +        ++  s+ge Ae++a+k+++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3394 116 AENMSRVPMGSNREI--HGAAFGWMAAQR-------YELTSQGEAAERMADKWAL 161
                                                             ************985..566665565555.......56889************** PP

                                               TIGR01930 165 sReeqDeyalrShqkaakAieegkfkdeivpvevkgk........kkvvskDegi 211
                                                             sR+ +D++a +Shq+aa+A ++g+f++e +pv+v++         + v+ +De+i
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3394 162 SRDALDDFAFASHQRAAAACDAGYFDNETIPVVVEELrekelsepAGVLRHDETI 216
                                                             ********************************998768999*9999999****** PP

                                               TIGR01930 212 rpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltpl 266
                                                             r++t+ ekL++Lk+ f++  g+ +tAgNssq++DGAaalllms ++ak+lgl+  
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3394 217 RRDTSREKLSTLKTSFRPDTGR-ITAGNSSQISDGAAALLLMSADTAKKLGLKAR 270
                                                             ******************99*6.******************************** PP

                                               TIGR01930 267 arivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlave 321
                                                             ar+v+++++g+dp+ m++gp+ A++k+L+kaglsi+didl+E+nEAFA++ la++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3394 271 ARVVAFTTVGSDPTLMLTGPIAATQKVLAKAGLSINDIDLFEVNEAFASVPLAWM 325
                                                             ******************************************************* PP

                                               TIGR01930 322 kelgsldlekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvgg 376
                                                             +e+g   ++k+NvnGGAiAlGHPlGasGar+++t+l+eL++rg++yGl+++C +g
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3394 326 QETG-VPHSKLNVNGGAIALGHPLGASGARLMTTMLNELERRGGRYGLQAICCAG 379
                                                             ****.77************************************************ PP

                                               TIGR01930 377 GqGaAvile 385
                                                             G+G+A+i+e
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3394 380 GMGTATIIE 388
                                                             *******97 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 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 8.78
//
[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:

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 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