Alignments for a candidate for fadA in Desulfallas geothermicus DSM 3669

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Desulfallas geothermicus DSM 3669

Align 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 (characterized)
to candidate WP_092482980.1 BM299_RS08135 thiolase family protein

Query= SwissProt::O32177
         (391 letters)



>NCBI__GCF_900115975.1:WP_092482980.1
          Length = 391

 Score =  446 bits (1146), Expect = e-130
 Identities = 231/390 (59%), Positives = 286/390 (73%), Gaps = 2/390 (0%)

Query: 1   MKEAVIVSGARTPVGKAKKGSLATVRPDDLGAICVKETLKRAGGYE-GNIDDLIIGCATP 59
           M+EAVIVS  RT VGKA +G+L   RP+ +GA  +KE L R  G +   IDD I+GC+ P
Sbjct: 1   MREAVIVSAVRTAVGKAPRGTLKKTRPEHMGAEVIKELLNRTPGLDPAEIDDFIVGCSFP 60

Query: 60  EAEQGLNMARNIGALAGLPYTVPAITVNRYCSSGLQSIAYAAEKIMLGAYDTAIAGGAES 119
           EAEQG+N+ R +   AGLP TV   TVNR+CSSGL+SIA  A ++M G  D  + GG ES
Sbjct: 61  EAEQGMNLGRMLVLKAGLPNTVSGATVNRFCSSGLESIAIGATRVMAGFADVYLCGGVES 120

Query: 120 MSQVPMMGHVTRPNLALAEKAPEYYMSMGHTAEQVAKKYGVSREDQDAFAVRSHQNAAKA 179
           MS VPM G+   P+  L E  PE YM MG TAE VA++YG++RE QD F+V SH  AA+A
Sbjct: 121 MSIVPMGGNKAMPDPELMEICPEAYMGMGLTAENVAEQYGITREMQDEFSVGSHAKAARA 180

Query: 180 LAEGKFKDEIVPVEVTVTEIGEDHKPMEKQFVFSQDEGVRPQTTADILSTLRPAFSVDGT 239
           + EG+FK++IVP+ VT T+     K  EK  VF  DEGVRP T+ + L+ LRP F   G+
Sbjct: 181 IQEGRFKEQIVPLTVT-TKTRAKGKLTEKSIVFDTDEGVRPGTSMETLAKLRPVFKTGGS 239

Query: 240 VTAGNSSQTSDGAAAVMLMDREKADALGLAPLVKFRSFAVGGVPPEVMGIGPVEAIPRAL 299
           VTAGNSSQTSDGAAAVM+M REKA++LGL PL  FRS+AVGG PPEVMGIGP  AIP+AL
Sbjct: 240 VTAGNSSQTSDGAAAVMIMSREKAESLGLKPLAVFRSYAVGGCPPEVMGIGPTVAIPKAL 299

Query: 300 KLAGLQLQDIGLFELNEAFASQAIQVIRELGIDEEKVNVNGGAIALGHPLGCTGTKLTLS 359
           KLAG+    + +FELNEAFA+QA+  I+ L +D  KVN NGGA+ALGHPLGCTG+KLT  
Sbjct: 300 KLAGITKDQVDVFELNEAFAAQALACIKVLELDPAKVNPNGGAVALGHPLGCTGSKLTTQ 359

Query: 360 LIHEMKRRNEQFGVVTMCIGGGMGAAGVFE 389
           L++EM+R N ++GVV+MCIGGGMGAA VFE
Sbjct: 360 LMYEMQRINARYGVVSMCIGGGMGAAAVFE 389


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: 475
Number of extensions: 21
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: 391
Length of database: 391
Length adjustment: 31
Effective length of query: 360
Effective length of database: 360
Effective search space:   129600
Effective search space used:   129600
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_092482980.1 BM299_RS08135 (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.10720.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.6e-145  470.8   1.5   1.8e-145  470.6   1.5    1.0  1  lcl|NCBI__GCF_900115975.1:WP_092482980.1  BM299_RS08135 thiolase family pr


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900115975.1:WP_092482980.1  BM299_RS08135 thiolase family protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  470.6   1.5  1.8e-145  1.8e-145       1     385 []       6     389 ..       6     389 .. 0.97

  Alignments for each domain:
  == domain 1  score: 470.6 bits;  conditional E-value: 1.8e-145
                                 TIGR01930   1 ivdavRtpig.klggslkelsaedLlaavikellera.gldpekidevilGnvlqageq.aniaReaal 66 
                                               iv+avRt++g + +g+lk++++e+++a+vikell+r+ gldp++id+ i+G++++++eq +n++R+ +l
  lcl|NCBI__GCF_900115975.1:WP_092482980.1   6 IVSAVRTAVGkAPRGTLKKTRPEHMGAEVIKELLNRTpGLDPAEIDDFIVGCSFPEAEQgMNLGRMLVL 74 
                                               8*********988******************************************************** PP

                                 TIGR01930  67 aaglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkak 135
                                               +aglp++v++ tvnr+C+Sgl+++a++a +++aG adv++ GGvEsmS vp++ +++    + +++ ++
  lcl|NCBI__GCF_900115975.1:WP_092482980.1  75 KAGLPNTVSGATVNRFCSSGLESIAIGATRVMAGFADVYLCGGVESMSIVPMGGNKA----MPDPELME 139
                                               ****************************************************98875....67776666 PP

                                 TIGR01930 136 ledqllkdlvktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk... 201
                                                         ++ + mg tAen+a++ygi+Re+qDe+++ Sh kaa+Ai+eg+fk++ivp++v +k   
  lcl|NCBI__GCF_900115975.1:WP_092482980.1 140 ICP-------EAYMGMGLTAENVAEQYGITREMQDEFSVGSHAKAARAIQEGRFKEQIVPLTVTTKtra 201
                                               666.......8899*************************************************99999* PP

                                 TIGR01930 202 .......kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgl 263
                                                      + v+++Deg+rp+t++e+LakL+p+fk+  gs vtAgNssq++DGAaa+++ms+e+a++lgl
  lcl|NCBI__GCF_900115975.1:WP_092482980.1 202 kgkltekSIVFDTDEGVRPGTSMETLAKLRPVFKT-GGS-VTAGNSSQTSDGAAAVMIMSREKAESLGL 268
                                               *****99999***********************96.797.***************************** PP

                                 TIGR01930 264 tplarivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekv 332
                                               +pla ++s+av g++pe+mg+gp+ Ai+kaLk ag++ +++d++E+nEAFAaq+la++k l+ ld++kv
  lcl|NCBI__GCF_900115975.1:WP_092482980.1 269 KPLAVFRSYAVGGCPPEVMGIGPTVAIPKALKLAGITKDQVDVFELNEAFAAQALACIKVLE-LDPAKV 336
                                               **************************************************************.99**** PP

                                 TIGR01930 333 NvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                               N nGGA+AlGHPlG++G+ ++++l++e+++ +++yG++++C+ggG+GaA+++e
  lcl|NCBI__GCF_900115975.1:WP_092482980.1 337 NPNGGAVALGHPLGCTGSKLTTQLMYEMQRINARYGVVSMCIGGGMGAAAVFE 389
                                               ***************************************************97 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 9.60
//
[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