Alignments for a candidate for fadA in Sinorhizobium meliloti 1021

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.605.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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.87
//
[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)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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