Alignments for a candidate for fadA in Methylomicrobium alcaliphilum 20Z

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Methylomicrobium alcaliphilum 20Z

Align 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 (characterized)
to candidate WP_014146962.1 MEALZ_RS02230 acetyl-CoA C-acyltransferase

Query= SwissProt::O32177
         (391 letters)



>NCBI__GCF_000968535.2:WP_014146962.1
          Length = 380

 Score =  329 bits (844), Expect = 7e-95
 Identities = 185/389 (47%), Positives = 243/389 (62%), Gaps = 12/389 (3%)

Query: 1   MKEAVIVSGARTPVGKAKKGSLATVRPDDLGAICVKETLKRAGGYEGNIDDLIIGCATPE 60
           M   VI   AR+P   A KG LA VRPDDL A  VK  + + G     I+DLI+GCA PE
Sbjct: 1   MNNVVIAGYARSPFTPAGKGELAHVRPDDLAAQVVKALIDKCGVDPNAIEDLILGCAFPE 60

Query: 61  AEQGLNMARNIGALAGLPYTVPAITVNRYCSSGLQSIAYAAEKIMLGAYDTAIAGGAESM 120
            EQGLN+AR +  LA LP +V  +TVNR+C S +Q+I  AA  I + A +  I  G ESM
Sbjct: 61  GEQGLNLARLVVHLAELPISVAGMTVNRFCGSSMQAIHIAAGAIQMNAGEVFICAGVESM 120

Query: 121 SQVPMMGHVTRPNLALAEKAPEYYMSMGHTAEQVAKKYGVSREDQDAFAVRSHQNAAKAL 180
           S+VPM G  T P+  L +  PE YMSMG TAE +A++Y ++R DQ+ FA+ S +    A 
Sbjct: 121 SRVPMGGFNTLPHPGLYKNHPEAYMSMGETAENLARRYSIARRDQENFALTSQRKTQHAR 180

Query: 181 AEGKFKDEIVPVEVTVTEIGEDHKPMEKQFVFSQDEGVRPQTTADILSTLRPAFSVDGTV 240
             G F DEIVP+   +T  G+            QD   RP +TA+ L+ L+PAF  +G+V
Sbjct: 181 QSGGFADEIVPI---LTHRGDR---------IDQDGCPRPDSTAEGLAGLKPAFLENGSV 228

Query: 241 TAGNSSQTSDGAAAVMLMDREKADALGLAPLVKFRSFAVGGVPPEVMGIGPVEAIPRALK 300
           TA  SS  +DGAAAV++     ADA GL  L + +S AV    PE+MGIGPV A  +AL+
Sbjct: 229 TAATSSPLTDGAAAVLVCSEAYADAHGLPKLARIKSIAVSACQPEIMGIGPVAATHKALQ 288

Query: 301 LAGLQLQDIGLFELNEAFASQAIQVIRELGIDEEKVNVNGGAIALGHPLGCTGTKLTLSL 360
            AGL L+DI L ELNEAFA+QA+ V++EL I  EK+N++GGAIALGHPLG TG ++T   
Sbjct: 289 RAGLTLEDIDLVELNEAFAAQALAVLQELPIPIEKLNLDGGAIALGHPLGATGARITGKA 348

Query: 361 IHEMKRRNEQFGVVTMCIGGGMGAAGVFE 389
              + R  +++ + T CIGGG G A + E
Sbjct: 349 ASLLHRERKRYALATQCIGGGQGIATILE 377


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: 380
Number of extensions: 10
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: 380
Length adjustment: 30
Effective length of query: 361
Effective length of database: 350
Effective search space:   126350
Effective search space used:   126350
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 WP_014146962.1 MEALZ_RS02230 (acetyl-CoA C-acyltransferase)
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.9622.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.4e-134  434.8   0.7   1.7e-134  434.5   0.7    1.0  1  lcl|NCBI__GCF_000968535.2:WP_014146962.1  MEALZ_RS02230 acetyl-CoA C-acylt


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000968535.2:WP_014146962.1  MEALZ_RS02230 acetyl-CoA C-acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  434.5   0.7  1.7e-134  1.7e-134       1     385 []       6     377 ..       6     377 .. 0.98

  Alignments for each domain:
  == domain 1  score: 434.5 bits;  conditional E-value: 1.7e-134
                                 TIGR01930   1 ivdavRtpig.klggslkelsaedLlaavikelleragldpekidevilGnvlqageq.aniaReaala 67 
                                               i +++R+p++ + +g l++++++dL+a+v+k+l+++ g+dp++i+++ilG+++++geq  n+aR ++  
  lcl|NCBI__GCF_000968535.2:WP_014146962.1   6 IAGYARSPFTpAGKGELAHVRPDDLAAQVVKALIDKCGVDPNAIEDLILGCAFPEGEQgLNLARLVVHL 74 
                                               67899*****9779******************************************************* PP

                                 TIGR01930  68 aglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakl 136
                                               a+lp sv+++tvnr+C+S++qA+++aa +i++ + +v++ +GvEsmSrvp++  +       ++g +k+
  lcl|NCBI__GCF_000968535.2:WP_014146962.1  75 AELPISVAGMTVNRFCGSSMQAIHIAAGAIQMNAGEVFICAGVESMSRVPMGGFNT----LPHPGLYKN 139
                                               ***************************************************88875....789999999 PP

                                 TIGR01930 137 edqllkdlvktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgkkkvv 205
                                               +        ++ +smgetAenla++y+i R++q+++al S++k+++A ++g f+deivp+  ++  + +
  lcl|NCBI__GCF_000968535.2:WP_014146962.1 140 HP-------EAYMSMGETAENLARRYSIARRDQENFALTSQRKTQHARQSGGFADEIVPILTHR-GDRI 200
                                               99.......8899**********************************************97776.7999 PP

                                 TIGR01930 206 skDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaav 274
                                               ++D ++rp++t+e La+Lkpaf e +gs vtA+ ss+l+DGAaa+l+ se+ a+++gl  lari s+av
  lcl|NCBI__GCF_000968535.2:WP_014146962.1 201 DQDGCPRPDSTAEGLAGLKPAFLE-NGS-VTAATSSPLTDGAAAVLVCSEAYADAHGLPKLARIKSIAV 267
                                               **********************96.9*7.**************************************** PP

                                 TIGR01930 275 agvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGH 343
                                               ++++pe+mg+gpv A++kaL++agl+++didlvE+nEAFAaq+lav +el  +  ek+N  GGAiAlGH
  lcl|NCBI__GCF_000968535.2:WP_014146962.1 268 SACQPEIMGIGPVAATHKALQRAGLTLEDIDLVELNEAFAAQALAVLQELP-IPIEKLNLDGGAIALGH 335
                                               ***************************************************.88*************** PP

                                 TIGR01930 344 PlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                               PlGa+Gari+ + ++ L++++k+y+lat C+ggGqG+A+ile
  lcl|NCBI__GCF_000968535.2:WP_014146962.1 336 PLGATGARITGKAASLLHRERKRYALATQCIGGGQGIATILE 377
                                               ****************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (380 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.19
//
[ok]

This GapMind analysis is from Sep 24 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