Alignments for a candidate for fadA in Sphingomonas histidinilytica UM2

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Sphingomonas histidinilytica UM2

Align 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 (characterized)
to candidate WP_079647015.1 B5X82_RS05000 thiolase family protein

Query= SwissProt::O32177
         (391 letters)



>NCBI__GCF_900167915.1:WP_079647015.1
          Length = 378

 Score =  342 bits (876), Expect = 1e-98
 Identities = 189/389 (48%), Positives = 245/389 (62%), Gaps = 13/389 (3%)

Query: 1   MKEAVIVSGARTPVGKAKKGSLATVRPDDLGAICVKETLKRAGGYEGNIDDLIIGCATPE 60
           M  AVI   AR+P   A KG LA VRPDDL A  ++  + ++G    +I+D+I+GCA PE
Sbjct: 1   MPNAVIAGYARSPFHLANKGELARVRPDDLAAQVIRGLIDKSGVKVEDIEDVILGCAFPE 60

Query: 61  AEQGLNMARNIGALAGLPYTVPAITVNRYCSSGLQSIAYAAEKIMLGAYDTAIAGGAESM 120
           AEQGLN+AR IG LA LP  V  +TVNR+C S + S+  AA +I +GA +  I  G ESM
Sbjct: 61  AEQGLNVARLIGLLADLPIKVGGMTVNRFCGSSMSSVHIAAGQIAIGAGEAFICAGVESM 120

Query: 121 SQVPMMGHVTRPNLALAEKAPEYYMSMGHTAEQVAKKYGVSREDQDAFAVRSHQNAAKAL 180
           S+VPMMG+   P+  LA+K P  YMSMG TAE VA +Y V R  Q+AFAV S + A  A 
Sbjct: 121 SRVPMMGYNPLPSPDLAKKRPGAYMSMGETAENVASQYQVPRAAQEAFAVESQKKAGAAR 180

Query: 181 AEGKFKDEIVPVEVTVTEIGEDHKPMEKQFVFSQDEGVRPQTTADILSTLRPAFSVDGTV 240
             G+ KDEIVP+      +  D  P             RP TTA+ L++L+PAF  +GTV
Sbjct: 181 EAGRLKDEIVPIRTRKGVVDVDGTP-------------RPDTTAEALASLKPAFDQNGTV 227

Query: 241 TAGNSSQTSDGAAAVMLMDREKADALGLAPLVKFRSFAVGGVPPEVMGIGPVEAIPRALK 300
           TAG SS  +DGAAAV++   + A A GL  L + +S AV G  PE+MGIGPV+A  +AL+
Sbjct: 228 TAGTSSPLTDGAAAVLVTSEDYAKANGLTILARIKSVAVSGCEPEIMGIGPVQATRKALE 287

Query: 301 LAGLQLQDIGLFELNEAFASQAIQVIRELGIDEEKVNVNGGAIALGHPLGCTGTKLTLSL 360
            AGL + D+ + E+NEAFASQAI    ELG   E VN++GGAIA+GHPLG TG ++    
Sbjct: 288 RAGLVVGDLDIVEINEAFASQAIACSNELGFKLETVNLDGGAIAIGHPLGATGARIVGKA 347

Query: 361 IHEMKRRNEQFGVVTMCIGGGMGAAGVFE 389
              +KR   ++ + T CIGGG G A V E
Sbjct: 348 AALLKREGGKYALATQCIGGGQGIATVLE 376


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: 393
Number of extensions: 12
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: 378
Length adjustment: 30
Effective length of query: 361
Effective length of database: 348
Effective search space:   125628
Effective search space used:   125628
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_079647015.1 B5X82_RS05000 (thiolase family protein)
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.3682057.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.9e-135  436.6   4.5   4.7e-135  436.4   4.5    1.0  1  NCBI__GCF_900167915.1:WP_079647015.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900167915.1:WP_079647015.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  436.4   4.5  4.7e-135  4.7e-135       1     385 []       6     376 ..       6     376 .. 0.97

  Alignments for each domain:
  == domain 1  score: 436.4 bits;  conditional E-value: 4.7e-135
                             TIGR01930   1 ivdavRtpig.klggslkelsaedLlaavikelleragldpekidevilGnvlqageq.aniaReaalaaglp 71 
                                           i +++R+p+  + +g l+ ++++dL+a+vi++l++++g++ e+i++vilG++++++eq  n+aR + l a+lp
  NCBI__GCF_900167915.1:WP_079647015.1   6 IAGYARSPFHlANKGELARVRPDDLAAQVIRGLIDKSGVKVEDIEDVILGCAFPEAEQgLNVARLIGLLADLP 78 
                                           67899*****977************************************************************ PP

                             TIGR01930  72 esvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl 144
                                            +v ++tvnr+C+S++ +v++aa +i+ G+ ++++ +GvEsmSrvp++  +       +++ ak++       
  NCBI__GCF_900167915.1:WP_079647015.1  79 IKVGGMTVNRFCGSSMSSVHIAAGQIAIGAGEAFICAGVESMSRVPMMGYNP----LPSPDLAKKRP------ 141
                                           ***********************************************98886....66776677777...... PP

                             TIGR01930 145 vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgkkkvvskDegirpnttl 217
                                             + +smgetAen+a +y++ R  q+++a++S++ka +A e+g++kdeivp++ ++   vv+ D ++rp+tt+
  NCBI__GCF_900167915.1:WP_079647015.1 142 -GAYMSMGETAENVASQYQVPRAAQEAFAVESQKKAGAAREAGRLKDEIVPIRTRK--GVVDVDGTPRPDTTA 211
                                           .6789**********************************************98876..799************ PP

                             TIGR01930 218 ekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpvpAi 290
                                           e+La+Lkpaf+ ++g tvtAg ss+l+DGAaa+l++se+ ak+ glt+lari s+av+g++pe+mg+gpv+A+
  NCBI__GCF_900167915.1:WP_079647015.1 212 EALASLKPAFD-QNG-TVTAGTSSPLTDGAAAVLVTSEDYAKANGLTILARIKSVAVSGCEPEIMGIGPVQAT 282
                                           **********9.59*.6******************************************************** PP

                             TIGR01930 291 ekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeLker 363
                                           +kaL++agl + d+d+vEinEAFA+q++a+ +elg  +le vN  GGAiA+GHPlGa+Gariv + +  Lk++
  NCBI__GCF_900167915.1:WP_079647015.1 283 RKALERAGLVVGDLDIVEINEAFASQAIACSNELG-FKLETVNLDGGAIAIGHPLGATGARIVGKAAALLKRE 354
                                           ***********************************.77*********************************** PP

                             TIGR01930 364 gkkyGlatlCvggGqGaAvile 385
                                           g+ky+lat C+ggGqG+A++le
  NCBI__GCF_900167915.1:WP_079647015.1 355 GGKYALATQCIGGGQGIATVLE 376
                                           ********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (378 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 27.55
//
[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 2024 update 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