Alignments for a candidate for fadA in Sulfuritalea hydrogenivorans DSM 22779

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Sulfuritalea hydrogenivorans DSM 22779

Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate WP_041100093.1 SUTH_RS13985 3-oxoadipyl-CoA thiolase

Query= metacyc::MONOMER-3207
         (400 letters)



>NCBI__GCF_000828635.1:WP_041100093.1
          Length = 402

 Score =  556 bits (1434), Expect = e-163
 Identities = 277/397 (69%), Positives = 326/397 (82%), Gaps = 1/397 (0%)

Query: 5   FICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQAGEDN 64
           FICDA+RTPIGR+GG L+G+R DDL A+P++AL+  N  V W++VDEV +GCANQAGEDN
Sbjct: 6   FICDAVRTPIGRYGGTLSGIRTDDLGALPIRALMARNGKVDWERVDEVIYGCANQAGEDN 65

Query: 65  RNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESMSRAP 124
           RNVARMA LLAGLP ++ G T+NRLC SGMDA+GTA RAI +GE  L IAGGVESMSRAP
Sbjct: 66  RNVARMAGLLAGLPVAVAGATINRLCGSGMDAVGTAARAIKTGETALMIAGGVESMSRAP 125

Query: 125 FVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRADQDAF 184
           FVM KA+S +SR+  + DTTIGWRF+N LMK QYGVDSMPETADNVA D+ + RA+QDAF
Sbjct: 126 FVMPKADSAFSRSNAVYDTTIGWRFVNKLMKQQYGVDSMPETADNVAADFCIGRAEQDAF 185

Query: 185 ALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGET-IVERDEHLRPETTLEALTKLKPVNGP 243
           ALRSQQ+ AAAQA G F +EI PV IA KKGE+ I + DEH RP+TTLE L KLK +NGP
Sbjct: 186 ALRSQQRWAAAQAKGLFKDEIAPVEIAQKKGESKIFDTDEHPRPDTTLEQLAKLKGINGP 245

Query: 244 DKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPVPAVR 303
           D TVTAGNASGVNDGA AL+LAS  A K HGLTPRARV+ MA+ GVAPR+MG GP PAV+
Sbjct: 246 DLTVTAGNASGVNDGACALLLASEAAAKAHGLTPRARVVAMATAGVAPRIMGFGPAPAVK 305

Query: 304 KLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLGMSGA 363
           KL    G+ +   DVIELNEAFA+QGLAV R+LG+ADD  +VNP GGAIA+GHPLGMSGA
Sbjct: 306 KLLALTGLRLEQMDVIELNEAFAAQGLAVTRDLGLADDDARVNPYGGAIAIGHPLGMSGA 365

Query: 364 RLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400
           RLV TA++QL ++GGR  L TMC+GVGQG+A+ IERV
Sbjct: 366 RLVTTAMYQLHRTGGRYALCTMCIGVGQGIAMVIERV 402


Lambda     K      H
   0.318    0.134    0.383 

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: 515
Number of extensions: 11
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: 400
Length of database: 402
Length adjustment: 31
Effective length of query: 369
Effective length of database: 371
Effective search space:   136899
Effective search space used:   136899
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 WP_041100093.1 SUTH_RS13985 (3-oxoadipyl-CoA 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.4579.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.5e-139  449.3   3.9   6.2e-139  449.1   3.9    1.0  1  lcl|NCBI__GCF_000828635.1:WP_041100093.1  SUTH_RS13985 3-oxoadipyl-CoA thi


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000828635.1:WP_041100093.1  SUTH_RS13985 3-oxoadipyl-CoA thiolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  449.1   3.9  6.2e-139  6.2e-139       1     385 []       7     400 ..       7     400 .. 0.94

  Alignments for each domain:
  == domain 1  score: 449.1 bits;  conditional E-value: 6.2e-139
                                 TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikellera.gldpekidevilGnvlqageq.aniaReaala 67 
                                               i davRtpig++gg+l+ ++ +dL+a  i++l++r+ ++d e++devi+G++ qage+  n+aR+a l 
  lcl|NCBI__GCF_000828635.1:WP_041100093.1   7 ICDAVRTPIGRYGGTLSGIRTDDLGALPIRALMARNgKVDWERVDEVIYGCANQAGEDnRNVARMAGLL 75 
                                               789*******99**********************************************9********** PP

                                 TIGR01930  68 aglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakl 136
                                               aglp  v++ t+nr+C+Sg++Av +aa++ik+Ge  +++aGGvEsmSr+p++++++    s+  +++ +
  lcl|NCBI__GCF_000828635.1:WP_041100093.1  76 AGLPVAVAGATINRLCGSGMDAVGTAARAIKTGETALMIAGGVESMSRAPFVMPKAD---SAFSRSNAV 141
                                               ****************************************************99973...333333444 PP

                                 TIGR01930 137 edqllkdl...........vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeiv 194
                                               +d++   +           ++   sm etA+n+a+++ i R eqD++alrS+q+ a+A+++g fkdei 
  lcl|NCBI__GCF_000828635.1:WP_041100093.1 142 YDTT---IgwrfvnklmkqQYGVDSMPETADNVAADFCIGRAEQDAFALRSQQRWAAAQAKGLFKDEIA 207
                                               4422...123356777787777789******************************************** PP

                                 TIGR01930 195 pvevkgk...kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevake 260
                                               pve+ +k   +k++++De++rp+ttle+LakLk +   ++  tvtAgN+s++nDGA+alll+se++ak+
  lcl|NCBI__GCF_000828635.1:WP_041100093.1 208 PVEIAQKkgeSKIFDTDEHPRPDTTLEQLAKLKGING-PDL-TVTAGNASGVNDGACALLLASEAAAKA 274
                                               ****9999*99*************************9.599.6************************** PP

                                 TIGR01930 261 lgltplarivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsld. 328
                                               +gltp ar+v++a+agv p++mg+gp+pA++k+L+ +gl+++++d++E+nEAFAaq lav+++lg+ d 
  lcl|NCBI__GCF_000828635.1:WP_041100093.1 275 HGLTPRARVVAMATAGVAPRIMGFGPAPAVKKLLALTGLRLEQMDVIELNEAFAAQGLAVTRDLGLADd 343
                                               *****************************************************************8667 PP

                                 TIGR01930 329 lekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                               +++vN +GGAiA+GHPlG+sGar+v+t +++L++ g++y+l t+C+g GqG+A+++e
  lcl|NCBI__GCF_000828635.1:WP_041100093.1 344 DARVNPYGGAIAIGHPLGMSGARLVTTAMYQLHRTGGRYALCTMCIGVGQGIAMVIE 400
                                               9******************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (402 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: 10.48
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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