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

GapMind for catabolism of small carbon sources

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

Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate CA265_RS06590 CA265_RS06590 acetyl-CoA acetyltransferase

Query= BRENDA::P45359
         (392 letters)



>FitnessBrowser__Pedo557:CA265_RS06590
          Length = 391

 Score =  395 bits (1015), Expect = e-114
 Identities = 210/392 (53%), Positives = 272/392 (69%), Gaps = 3/392 (0%)

Query: 1   MKEVVIASAVRTAIGSYGKSLKDVPAVDLGATAIKEAVKKAGIKPEDVNEVILGNVLQAG 60
           MKEVVI SAVRT IGS+G SL    A  LG  AIK A++KAG+KPE + EV +GNVL A 
Sbjct: 1   MKEVVIVSAVRTPIGSFGGSLAQFSATQLGGFAIKAAIEKAGLKPEQIQEVYMGNVLSAN 60

Query: 61  LGQNPARQASFKAGLPVEIPAMTINKVCGSGLRTVSLAAQIIKAGDADVIIAGGMENMSR 120
           LGQ PA QA+  AGLP ++PA TINKVC SG + + LAAQ I  GD ++I+AGGME+MS 
Sbjct: 61  LGQAPATQAAKFAGLP-DLPATTINKVCASGTKAIMLAAQSIANGDNEIIVAGGMESMSN 119

Query: 121 APYLANNARWGYRMGNAKFVDEMITDGLWDAFNDYHMGITAENIAERWNISREEQDEFAL 180
            PY  + AR GYR+G+ +  D ++ DGLWD +NDYHMG  AE  A   NI+RE QD FA+
Sbjct: 120 VPYYLDKARNGYRLGHGQITDGLVKDGLWDVYNDYHMGSAAELCATECNINREAQDNFAI 179

Query: 181 ASQKKAEEAIKSGQFKDEIVPVVIKGRKGE-TVVDTDEHPRFGSTIEGLAKLKPAFKKDG 239
           +S K+A+ A  SG+F +EIV + +K RKG+ T+VDTD+ P      + +  LKP FKKDG
Sbjct: 180 SSYKRAQAAQTSGKFANEIVAIEVKDRKGDITLVDTDDEPT-AVKFDKIPSLKPVFKKDG 238

Query: 240 TVTAGNASGLNDCAAVLVIMSAEKAKELGVKPLAKIVSYGSAGVDPAIMGYGPFYATKAA 299
           TVTA NAS LND AA LV+MSA+KAKELG+ PLAKI+ Y  A   P      P  A   A
Sbjct: 239 TVTAANASTLNDGAAALVLMSADKAKELGLTPLAKILGYADAQQAPEWFTTAPSKAIPLA 298

Query: 300 IEKAGWTVDELDLIESNEAFAAQSLAVAKDLKFDMNKVNVNGGAIALGHPIGASGARILV 359
           + KA   ++++D  E NEAFA  S+A  + L  + N+VNVNGGA++LGHP+GASGARI+V
Sbjct: 299 LHKANVNINDVDFFEINEAFAVVSIANNQLLALNDNQVNVNGGAVSLGHPLGASGARIVV 358

Query: 360 TLVHAMQKRDAKKGLATLCIGGGQGTAILLEK 391
           TL+  + + D K G+A +C GGG  +A+++ K
Sbjct: 359 TLLSVLAQNDGKIGVAGICNGGGGASALVIGK 390


Lambda     K      H
   0.315    0.132    0.375 

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: 454
Number of extensions: 11
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: 392
Length of database: 391
Length adjustment: 31
Effective length of query: 361
Effective length of database: 360
Effective search space:   129960
Effective search space used:   129960
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_RS06590 CA265_RS06590 (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.1285.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-134  434.7   6.2   1.7e-134  434.5   6.2    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS06590  CA265_RS06590 acetyl-CoA acetylt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS06590  CA265_RS06590 acetyl-CoA acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  434.5   6.2  1.7e-134  1.7e-134       1     384 [.       6     388 ..       6     389 .. 0.98

  Alignments for each domain:
  == domain 1  score: 434.5 bits;  conditional E-value: 1.7e-134
                                  TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaa 68 
                                                iv+avRtpig++ggsl+++sa +L+  +ik+++e+agl+pe+i ev++Gnvl+a+ ++++a +aa  a
  lcl|FitnessBrowser__Pedo557:CA265_RS06590   6 IVSAVRTPIGSFGGSLAQFSATQLGGFAIKAAIEKAGLKPEQIQEVYMGNVLSANLGQAPATQAAKFA 73 
                                                8******************************************************************* PP

                                  TIGR01930  69 glpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakl 136
                                                glp+ +pa+t+n+vCaSg +A++laaq+i+ G+++++vaGG+EsmS+vp++l+++  r++++lg+ + 
  lcl|FitnessBrowser__Pedo557:CA265_RS06590  74 GLPD-LPATTINKVCASGTKAIMLAAQSIANGDNEIIVAGGMESMSNVPYYLDKA--RNGYRLGHGQI 138
                                                ***9.************************************************98..89********* PP

                                  TIGR01930 137 edqllkdl...vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk 201
                                                 d l+kd+   v+++++mg  Ae +a++ +i+Re qD++a++S+++a++A+ +gkf++eiv +evk++
  lcl|FitnessBrowser__Pedo557:CA265_RS06590 139 TDGLVKDGlwdVYNDYHMGSAAELCATECNINREAQDNFAISSYKRAQAAQTSGKFANEIVAIEVKDR 206
                                                ***********99*****************************************************99 PP

                                  TIGR01930 202 ...kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltpl 266
                                                    + v++D+++   ++ +k+ +Lkp+fk+ +g tvtA+N+s lnDGAaal+lms ++akelgltpl
  lcl|FitnessBrowser__Pedo557:CA265_RS06590 207 kgdITLVDTDDEPT-AVKFDKIPSLKPVFKK-DG-TVTAANASTLNDGAAALVLMSADKAKELGLTPL 271
                                                99767778888887.8*************95.9*.6******************************** PP

                                  TIGR01930 267 arivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNv 334
                                                a+i ++a a   pe ++++p +Ai+ aL+ka+++i+d+d++EinEAFA++ +a+++ l+ l++++vNv
  lcl|FitnessBrowser__Pedo557:CA265_RS06590 272 AKILGYADAQQAPEWFTTAPSKAIPLALHKANVNINDVDFFEINEAFAVVSIANNQLLA-LNDNQVNV 338
                                                ***********************************************************.889***** PP

                                  TIGR01930 335 nGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvil 384
                                                nGGA++lGHPlGasGariv+tll+ L+++++k+G+a +C+ggG ++A+++
  lcl|FitnessBrowser__Pedo557:CA265_RS06590 339 NGGAVSLGHPLGASGARIVVTLLSVLAQNDGKIGVAGICNGGGGASALVI 388
                                                ***********************************************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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.65
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
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Protein sequences (fasta format)
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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