GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Sinorhizobium meliloti 1021

Align acetyl-CoA:acetyl-CoA C-acetyltransferase / acetyl-CoA:propanoyl-CoA 2-C-acetyltransferase (EC 2.3.1.9; EC 2.3.1.16) (characterized)
to candidate SMa1450 SMa1450 thiolase

Query= reanno::pseudo3_N2E3:AO353_25685
         (397 letters)



>FitnessBrowser__Smeli:SMa1450
          Length = 396

 Score =  555 bits (1431), Expect = e-163
 Identities = 276/389 (70%), Positives = 327/389 (84%)

Query: 6   DPIVIVSAVRTPMGGFQGELKSLSAPQLGAAAIRAAVERAGVAADAVEEVLFGCVLSAGL 65
           DP+VIV   RTP+G FQGELK LSA  LGAAAI  A++RAG+A DAV+EV+FGCVL+AG 
Sbjct: 5   DPVVIVGQARTPLGSFQGELKDLSAADLGAAAIVDALKRAGLAPDAVDEVMFGCVLTAGQ 64

Query: 66  GQAPARQAALGAGLDKSTRCTTLNKMCGSGMEAAILAHDMLLAGSADVVVAGGMESMSNA 125
           GQAPARQAALGAGL      TT+NKMCGSGM+AA+LAHD++ A SA +VVAGGMESM+NA
Sbjct: 65  GQAPARQAALGAGLPPGVGATTVNKMCGSGMKAAMLAHDLIKAESASIVVAGGMESMTNA 124

Query: 126 PYLLDRARSGYRMGHGKVLDHMFLDGLEDAYDKGRLMGTFAEDCAEANGFTREAQDEFAI 185
           PYLLDRAR GYR+GH KVLDHMFLDGLEDAYDKGRLMG+FAEDCAEA  FTR AQDE+AI
Sbjct: 125 PYLLDRARQGYRIGHQKVLDHMFLDGLEDAYDKGRLMGSFAEDCAEAYQFTRSAQDEYAI 184

Query: 186 ASTTRAQQAIKDGSFNAEIVPLQVIVGKEQKLITDDEQPPKAKLDKIASLKPAFRDGGTV 245
           AS  +AQ+A  DGSF  EIVPL +  GK ++ +  DEQP KA+LDKI  LKPAFRDGGT+
Sbjct: 185 ASLEKAQKASADGSFAEEIVPLSIASGKGERTVNLDEQPQKARLDKIPLLKPAFRDGGTI 244

Query: 246 TAANSSSISDGAAALLLMRRSEAEKRGLKPLAVIHGHAAFADTPGLFPVAPVGAIKKLLK 305
           TAAN+SSISDGAAAL+LMRRS A+K+G+ PLAVI GHA  AD P LFP AP+GAIK L +
Sbjct: 245 TAANASSISDGAAALVLMRRSAADKQGIGPLAVICGHATHADAPSLFPTAPIGAIKALCR 304

Query: 306 KTGWSLDEVELFEVNEAFAVVSLVTMTKLEIPHSKVNVHGGACALGHPIGASGARILVTL 365
           + GW + EV+LFE+NEAFAVV +  M +L +   KVNVHGGACALGHPIGASGAR++VTL
Sbjct: 305 RIGWDIGEVDLFEINEAFAVVPMAAMRELGLDAEKVNVHGGACALGHPIGASGARVIVTL 364

Query: 366 LSALRQKGLKRGVAAICIGGGEATAMAVE 394
           ++ALR++GL+RG+A++CIGGGEATA+AVE
Sbjct: 365 VNALRRRGLRRGIASVCIGGGEATAVAVE 393


Lambda     K      H
   0.318    0.133    0.378 

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: 546
Number of extensions: 17
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: 397
Length of database: 396
Length adjustment: 31
Effective length of query: 366
Effective length of database: 365
Effective search space:   133590
Effective search space used:   133590
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate SMa1450 SMa1450 (thiolase)
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.25653.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   5.9e-130  419.6   5.4   6.6e-130  419.4   5.4    1.0  1  lcl|FitnessBrowser__Smeli:SMa1450  SMa1450 thiolase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMa1450  SMa1450 thiolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  419.4   5.4  6.6e-130  6.6e-130       1     385 []       9     393 ..       9     393 .. 0.98

  Alignments for each domain:
  == domain 1  score: 419.4 bits;  conditional E-value: 6.6e-130
                          TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpesvpa 76 
                                        iv+ +Rtp g+++g lk+lsa+dL+aa+i  +l+ragl p+++dev++G+vl+ag+++++aR+aal aglp  v a
  lcl|FitnessBrowser__Smeli:SMa1450   9 IVGQARTPLGSFQGELKDLSAADLGAAAIVDALKRAGLAPDAVDEVMFGCVLTAGQGQAPARQAALGAGLPPGVGA 84 
                                        899************************************************************************* PP

                          TIGR01930  77 ltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl....vktk 148
                                        +tvn++C+Sg++A +la + ika  a++vvaGG+Esm+++p+ll+++  r+++++g++k+ d++  d+     +++
  lcl|FitnessBrowser__Smeli:SMa1450  85 TTVNKMCGSGMKAAMLAHDLIKAESASIVVAGGMESMTNAPYLLDRA--RQGYRIGHQKVLDHMFLDGledaYDKG 158
                                        *********************************************98..89***********99999999998899 PP

                          TIGR01930 149 lsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDegirpnttlekLak 222
                                          mg  Ae +a+ y+++R+ qDeya++S +ka+kA ++g f++eivp+++     +++v+ De+++ +  l+k+  
  lcl|FitnessBrowser__Smeli:SMa1450 159 RLMGSFAEDCAEAYQFTRSAQDEYAIASLEKAQKASADGSFAEEIVPLSIASGkgERTVNLDEQPQ-KARLDKIPL 233
                                        9************************************************99778999*******98.899****** PP

                          TIGR01930 223 LkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpvpAiekaLkkag 298
                                        Lkpaf++  g t+tA+N+s+++DGAaal+lm +++a++ g+ pla i ++a+ +  p+ ++++p+ Ai+++ ++ g
  lcl|FitnessBrowser__Smeli:SMa1450 234 LKPAFRD-GG-TITAANASSISDGAAALVLMRRSAADKQGIGPLAVICGHATHADAPSLFPTAPIGAIKALCRRIG 307
                                        *****96.67.7**************************************************************** PP

                          TIGR01930 299 lsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCv 374
                                        ++i ++dl+EinEAFA++ +a+++elg ld ekvNv+GGA AlGHP+GasGar+++tl+++L++rg ++G+a++C+
  lcl|FitnessBrowser__Smeli:SMa1450 308 WDIGEVDLFEINEAFAVVPMAAMRELG-LDAEKVNVHGGACALGHPIGASGARVIVTLVNALRRRGLRRGIASVCI 382
                                        ***************************.89********************************************** PP

                          TIGR01930 375 ggGqGaAvile 385
                                        ggG ++Av +e
  lcl|FitnessBrowser__Smeli:SMa1450 383 GGGEATAVAVE 393
                                        ********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (396 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: 00:00:00.01
# Mc/sec: 8.59
//
[ok]

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

Links

Downloads

Related tools

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:

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