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 subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate WP_079648236.1 B5X82_RS11200 3-oxoadipyl-CoA thiolase

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



>NCBI__GCF_900167915.1:WP_079648236.1
          Length = 402

 Score =  560 bits (1444), Expect = e-164
 Identities = 278/402 (69%), Positives = 337/402 (83%), Gaps = 2/402 (0%)

Query: 1   MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60
           M + FICDA+RTPIGR+GG L+GVRADDL A+P++ALIE NP +    ++EVF+GCANQ+
Sbjct: 1   MAEAFICDAVRTPIGRYGGILSGVRADDLGALPIRALIERNPGLDPASIEEVFYGCANQS 60

Query: 61  GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120
           GEDNRNVARM+LLLAGLP ++PGVTLNRLCASG++A+G A RAI +GEM+LAIAGGVESM
Sbjct: 61  GEDNRNVARMSLLLAGLPTAVPGVTLNRLCASGLEAVGAAARAIRTGEMDLAIAGGVESM 120

Query: 121 SRAPFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRAD 180
           +RAP V+GKA   + R+ KLEDTT+GWRF+NP + + +G ++MP TA+N+A+D+ +SRAD
Sbjct: 121 TRAPLVIGKAGGAFGRDQKLEDTTMGWRFVNPALDALHGTETMPRTAENLAEDHGISRAD 180

Query: 181 QDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHK-KGETI-VERDEHLRPETTLEALTKLK 238
           QDAFALRSQQ+A AAQA GF AEEI+PV +  K +GET  V+ DEH R +TTLE L KLK
Sbjct: 181 QDAFALRSQQRAVAAQANGFHAEEIIPVTVPGKRRGETSQVDTDEHPRADTTLETLGKLK 240

Query: 239 PVNGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGP 298
           P+ GP  TVTAGNASG+NDGAAA+I+A   A +  GLTPRAR+LGMAS GV PRVMGIGP
Sbjct: 241 PLFGPAGTVTAGNASGINDGAAAMIVAGEAAARAAGLTPRARILGMASAGVDPRVMGIGP 300

Query: 299 VPAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPL 358
           VPA RKL  RLG+++  FD IELNEAFASQ LAVLR LG+ DDAPQVNPNGGAIALGHPL
Sbjct: 301 VPATRKLLARLGLSIDAFDAIELNEAFASQSLAVLRGLGLPDDAPQVNPNGGAIALGHPL 360

Query: 359 GMSGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400
           GMSGAR+  + +HQLE++GGR GLAT+CVGVG GLALA+ERV
Sbjct: 361 GMSGARIAASLVHQLERTGGRLGLATLCVGVGMGLALAVERV 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: 601
Number of extensions: 24
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: 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_079648236.1 B5X82_RS11200 (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.3198091.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.1e-140  452.4   0.9   6.9e-140  452.3   0.9    1.0  1  NCBI__GCF_900167915.1:WP_079648236.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900167915.1:WP_079648236.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  452.3   0.9  6.9e-140  6.9e-140       1     385 []       6     400 ..       6     400 .. 0.94

  Alignments for each domain:
  == domain 1  score: 452.3 bits;  conditional E-value: 6.9e-140
                             TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikellera.gldpekidevilGnvlqageq.aniaReaalaaglp 71 
                                           i davRtpig++gg l+ ++a+dL+a  i++l+er+ gldp+ i+ev +G++ q+ge+  n+aR+ +l aglp
  NCBI__GCF_900167915.1:WP_079648236.1   6 ICDAVRTPIGRYGGILSGVRADDLGALPIRALIERNpGLDPASIEEVFYGCANQSGEDnRNVARMSLLLAGLP 78 
                                           789*******99**********************************************9************** PP

                             TIGR01930  72 esvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl 144
                                           + vp++t+nr+CaSgl+Av  aa++i++Ge+d+++aGGvEsm+r+p+++ ++     +  +++kled+++  +
  NCBI__GCF_900167915.1:WP_079648236.1  79 TAVPGVTLNRLCASGLEAVGAAARAIRTGEMDLAIAGGVESMTRAPLVIGKAGG---AFGRDQKLEDTTM--G 146
                                           *************************************************99743...3333334444222..1 PP

                             TIGR01930 145 ..........vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk....kk 203
                                                      +   +m  tAenla+++gisR +qD++alrS+q+a +A+++g+ ++ei+pv+v+gk    + 
  NCBI__GCF_900167915.1:WP_079648236.1 147 wrfvnpaldaLHGTETMPRTAENLAEDHGISRADQDAFALRSQQRAVAAQANGFHAEEIIPVTVPGKrrgeTS 219
                                           345678899978899***************************************************9***999 PP

                             TIGR01930 204 vvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavag 276
                                           +v++De++r++ttle+L+kLkp f  ++g tvtAgN+s++nDGAaa++++ e++a++ gltp ari ++a ag
  NCBI__GCF_900167915.1:WP_079648236.1 220 QVDTDEHPRADTTLETLGKLKPLFG-PAG-TVTAGNASGINDGAAAMIVAGEAAARAAGLTPRARILGMASAG 290
                                           99**********************9.59*.6****************************************** PP

                             TIGR01930 277 vdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsld.lekvNvnGGAiAlGHPlGas 348
                                           vdp++mg+gpvpA++k+L++ glsi+ +d++E+nEAFA+q lav + lg+ d   +vN nGGAiAlGHPlG+s
  NCBI__GCF_900167915.1:WP_079648236.1 291 VDPRVMGIGPVPATRKLLARLGLSIDAFDAIELNEAFASQSLAVLRGLGLPDdAPQVNPNGGAIALGHPLGMS 363
                                           *************************************************855689****************** PP

                             TIGR01930 349 GarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                           Gari ++l+++L++ g+++GlatlCvg G+G A+ +e
  NCBI__GCF_900167915.1:WP_079648236.1 364 GARIAASLVHQLERTGGRLGLATLCVGVGMGLALAVE 400
                                           *********************************9886 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 25.90
//
[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