GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Rhodanobacter denitrificans 2APBS1

Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate WP_015446959.1 R2APBS1_RS03900 3-oxoadipyl-CoA thiolase

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



>NCBI__GCF_000230695.2:WP_015446959.1
          Length = 400

 Score =  493 bits (1268), Expect = e-144
 Identities = 246/399 (61%), Positives = 304/399 (76%)

Query: 1   MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60
           M   ++ DA RTP GR GGALAGVRADDLAA+P+ AL+  +P + W  +DEV  GCANQA
Sbjct: 1   MTSAWLVDATRTPFGRLGGALAGVRADDLAALPIAALMARHPTLDWAALDEVILGCANQA 60

Query: 61  GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120
           GEDNRNVARMA LLAGLP+S+P VT+NRLCASG++AIG A RAIA GE EL +AGGVESM
Sbjct: 61  GEDNRNVARMATLLAGLPQSVPAVTVNRLCASGLEAIGQAARAIACGEAELVVAGGVESM 120

Query: 121 SRAPFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRAD 180
           SRAP+V+ KA+  Y+R  +LEDTT+GWR +NP M++ YG+DSM +TA+N+A ++ + R  
Sbjct: 121 SRAPYVLAKADVAYARGQQLEDTTLGWRLVNPRMQAGYGIDSMTQTAENLAREHGIDRDS 180

Query: 181 QDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETIVERDEHLRPETTLEALTKLKPV 240
           QDA+ALRSQQ+ A AQA G+ AEEI  V   H K   +V+ DEH R +TT   L  LKP+
Sbjct: 181 QDAYALRSQQRTAHAQAQGWLAEEITAVHAPHGKESLVVQVDEHPRADTTAAKLAALKPL 240

Query: 241 NGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPVP 300
            G   ++TAGNASG+NDGAAA++LAS  A+ ++GL P AR++GMA+ GVAPRVMGIGPVP
Sbjct: 241 LGAGSSITAGNASGLNDGAAAVLLASEAALARYGLQPLARIVGMAAAGVAPRVMGIGPVP 300

Query: 301 AVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLGM 360
           A+ KL  R G+  SDFD IE+NEAFA+Q LA  R LG+ DDA  VN NGGAIALGHPLG 
Sbjct: 301 AIHKLLARTGLGASDFDRIEINEAFAAQVLACTRSLGLPDDAEHVNANGGAIALGHPLGA 360

Query: 361 SGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIER 399
           SGARL LTA   L +    + L ++CVGVGQGLALA+ER
Sbjct: 361 SGARLALTAAFALRRHRQHRALVSLCVGVGQGLALALER 399


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: 479
Number of extensions: 11
Number of successful extensions: 1
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: 400
Length adjustment: 31
Effective length of query: 369
Effective length of database: 369
Effective search space:   136161
Effective search space used:   136161
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_015446959.1 R2APBS1_RS03900 (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.2001012.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.5e-134  434.7   8.8   1.6e-134  434.6   8.8    1.0  1  NCBI__GCF_000230695.2:WP_015446959.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000230695.2:WP_015446959.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  434.6   8.8  1.6e-134  1.6e-134       2     385 .]       7     398 ..       6     398 .. 0.93

  Alignments for each domain:
  == domain 1  score: 434.6 bits;  conditional E-value: 1.6e-134
                             TIGR01930   2 vdavRtpigklggslkelsaedLlaavikellera.gldpekidevilGnvlqageq.aniaReaalaaglpe 72 
                                           vda+Rtp+g+lgg+l+ ++a+dL+a  i +l++r   ld +++devilG++ qage+  n+aR+a+l aglp+
  NCBI__GCF_000230695.2:WP_015446959.1   7 VDATRTPFGRLGGALAGVRADDLAALPIAALMARHpTLDWAALDEVILGCANQAGEDnRNVARMATLLAGLPQ 79 
                                           9********************************************************9*************** PP

                             TIGR01930  73 svpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl. 144
                                           svpa+tvnr+CaSgl+A+ +aa++i++Gea++vvaGGvEsmSr+p++l ++   + ++ ++ ++       + 
  NCBI__GCF_000230695.2:WP_015446959.1  80 SVPAVTVNRLCASGLEAIGQAARAIACGEAELVVAGGVESMSRAPYVLAKADV-AYARGQQLEDTTL----Gw 147
                                           **********************************************9999732.2233333333332....12 PP

                             TIGR01930 145 .........vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvs 206
                                                     +   sm++tAenla+++gi R++qD+yalrS+q++a+A+++g +++ei+ v+ ++   + vv+
  NCBI__GCF_000230695.2:WP_015446959.1 148 rlvnprmqaGYGIDSMTQTAENLAREHGIDRDSQDAYALRSQQRTAHAQAQGWLAEEITAVHAPHGkeSLVVQ 220
                                           345778776455669**********************************************99877889999* PP

                             TIGR01930 207 kDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdp 279
                                            De++r++tt++kLa Lkp +   +gs +tAgN+s+lnDGAaa+ll+se++++++gl+plariv++a agv p
  NCBI__GCF_000230695.2:WP_015446959.1 221 VDEHPRADTTAAKLAALKPLLG--AGSSITAGNASGLNDGAAAVLLASEAALARYGLQPLARIVGMAAAGVAP 291
                                           *********************8..5778********************************************* PP

                             TIGR01930 280 eemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsld.lekvNvnGGAiAlGHPlGasGar 351
                                           ++mg+gpvpAi+k+L+++gl +sd+d +EinEAFAaqvla+++ lg+ d  e vN nGGAiAlGHPlGasGar
  NCBI__GCF_000230695.2:WP_015446959.1 292 RVMGIGPVPAIHKLLARTGLGASDFDRIEINEAFAAQVLACTRSLGLPDdAEHVNANGGAIALGHPLGASGAR 364
                                           **********************************************85569********************** PP

                             TIGR01930 352 ivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                           + lt + +L++++++++l++lCvg GqG A+ le
  NCBI__GCF_000230695.2:WP_015446959.1 365 LALTAAFALRRHRQHRALVSLCVGVGQGLALALE 398
                                           ******************************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (400 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: 29.31
//
[ok]

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

Links

Downloads

Related tools

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:

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:

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:

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:

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