GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Cupriavidus basilensis 4G11

Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Beta-ketothiolase; EC 2.3.1.9 (characterized)
to candidate RR42_RS26090 RR42_RS26090 acetyl-CoA acetyltransferase

Query= SwissProt::P14611
         (393 letters)



>FitnessBrowser__Cup4G11:RR42_RS26090
          Length = 391

 Score =  600 bits (1547), Expect = e-176
 Identities = 304/392 (77%), Positives = 340/392 (86%), Gaps = 1/392 (0%)

Query: 1   MTDVVIVSAARTAVGKFGGSLAKIPAPELGAVVIKAALERAGVKPEQVSEVIMGQVLTAG 60
           M DVVIV+AARTAVGKFGGSLAK+PAPELGA VIKA LER+G+KPE V EV++GQVLTAG
Sbjct: 1   MEDVVIVAAARTAVGKFGGSLAKVPAPELGATVIKALLERSGLKPEMVDEVLLGQVLTAG 60

Query: 61  SGQNPARQAAIKAGLPAMVPAMTINKVCGSGLKAVMLAANAIMAGDAEIVVAGGQENMSA 120
            GQNPARQAAIKAGLP  VPAMTI KVCGSGLKAV LAA AI  GDA+IV+AGGQENMSA
Sbjct: 61  GGQNPARQAAIKAGLPNTVPAMTIGKVCGSGLKAVHLAAQAIKCGDADIVIAGGQENMSA 120

Query: 121 APHVLPGSRDGFRMGDAKLVDTMIVDGLWDVYNQYHMGITAENVAKEYGITREAQDEFAV 180
           +PHVL GSRDG RMGD KL DTMIVDGLWD +NQYHMG TAENVAK Y I+RE QD FA 
Sbjct: 121 SPHVLAGSRDGQRMGDWKLTDTMIVDGLWDAFNQYHMGTTAENVAKAYHISREQQDAFAA 180

Query: 181 GSQNKAEAAQKAGKFDEEIVPVLIPQRKGDPVAFKTDEFVRQGATLDSMSGLKPAFDKAG 240
            SQ KAE AQK G+F +EIVPV I  +KG  V F TDEF++ G T D+++GL+PAFDKAG
Sbjct: 181 ASQQKAELAQKTGRFKDEIVPVSIVSKKG-TVVFDTDEFIKHGTTADALAGLRPAFDKAG 239

Query: 241 TVTAANASGLNDGAAAVVVMSAAKAKELGLTPLATIKSYANAGVDPKVMGMGPVPASKRA 300
           +VTA NASGLNDGAAAV++MSA+KA+ELGLTPLA I SYA+AG+DP +MGMGPVPAS+R 
Sbjct: 240 SVTAGNASGLNDGAAAVLMMSASKARELGLTPLARIASYASAGLDPAIMGMGPVPASQRC 299

Query: 301 LSRAEWTPQDLDLMEINEAFAAQALAVHQQMGWDTSKVNVNGGAIAIGHPIGASGCRILV 360
           L +A W+  DLDLMEINEAFAAQA AV+Q+M WD SK+NVNGGAIAIGHPIGASGCRILV
Sbjct: 300 LHKAGWSINDLDLMEINEAFAAQACAVNQEMDWDASKINVNGGAIAIGHPIGASGCRILV 359

Query: 361 TLLHEMKRRDAKKGLASLCIGGGMGVALAVER 392
           TLLHEM RRDA++GLASLCIGGGMGVALAVER
Sbjct: 360 TLLHEMARRDARRGLASLCIGGGMGVALAVER 391


Lambda     K      H
   0.315    0.131    0.369 

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: 552
Number of extensions: 18
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: 393
Length of database: 391
Length adjustment: 31
Effective length of query: 362
Effective length of database: 360
Effective search space:   130320
Effective search space used:   130320
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 RR42_RS26090 RR42_RS26090 (acetyl-CoA acetyltransferase)
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.12268.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.9e-156  504.7   9.2   8.9e-156  504.6   9.2    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS26090  RR42_RS26090 acetyl-CoA acetyltr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS26090  RR42_RS26090 acetyl-CoA acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  504.6   9.2  8.9e-156  8.9e-156       1     385 []       6     390 ..       6     390 .. 0.99

  Alignments for each domain:
  == domain 1  score: 504.6 bits;  conditional E-value: 8.9e-156
                                 TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaag 69 
                                               iv+a+Rt++gk+ggsl++++a +L+a+vik+ller+gl+pe +dev lG+vl+ag ++n+aR+aa++ag
  lcl|FitnessBrowser__Cup4G11:RR42_RS26090   6 IVAAARTAVGKFGGSLAKVPAPELGATVIKALLERSGLKPEMVDEVLLGQVLTAGGGQNPARQAAIKAG 74 
                                               8******************************************************************** PP

                                 TIGR01930  70 lpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakled 138
                                               lp++vpa+t+ +vC+Sgl+Av+laaq+ik+G+ad+v+aGG E+mS +p++l  s  r++ ++g+ kl d
  lcl|FitnessBrowser__Cup4G11:RR42_RS26090  75 LPNTVPAMTIGKVCGSGLKAVHLAAQAIKCGDADIVIAGGQENMSASPHVLAGS--RDGQRMGDWKLTD 141
                                               ***************************************************998..8************ PP

                                 TIGR01930 139 qllkdl...vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..k 202
                                               +++ d+   + ++++mg+tAen+ak y+isRe+qD++a++S+qka+ A++ g+fkdeivpv++  k  +
  lcl|FitnessBrowser__Cup4G11:RR42_RS26090 142 TMIVDGlwdAFNQYHMGTTAENVAKAYHISREQQDAFAAASQQKAELAQKTGRFKDEIVPVSIVSKkgT 210
                                               *****9***99****************************************************999999 PP

                                 TIGR01930 203 kvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivs 271
                                               +v+++De i+ +tt+++La+L+paf++ +gs vtAgN+s+lnDGAaa+l+ms ++a+elgltplari s
  lcl|FitnessBrowser__Cup4G11:RR42_RS26090 211 VVFDTDEFIKHGTTADALAGLRPAFDK-AGS-VTAGNASGLNDGAAAVLMMSASKARELGLTPLARIAS 277
                                               *************************95.9*7.************************************* PP

                                 TIGR01930 272 aavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiA 340
                                               +a ag+dp++mg+gpvpA++++L+kag+si+d+dl+EinEAFAaq+ av++e++  d +k+NvnGGAiA
  lcl|FitnessBrowser__Cup4G11:RR42_RS26090 278 YASAGLDPAIMGMGPVPASQRCLHKAGWSINDLDLMEINEAFAAQACAVNQEMD-WDASKINVNGGAIA 345
                                               ******************************************************.88************ PP

                                 TIGR01930 341 lGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                               +GHP+GasG+ri++tll+e+++r++++Gla+lC+ggG+G+A+ +e
  lcl|FitnessBrowser__Cup4G11:RR42_RS26090 346 IGHPIGASGCRILVTLLHEMARRDARRGLASLCIGGGMGVALAVE 390
                                               *****************************************9886 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 11.82
//
[ok]

This GapMind analysis is from Sep 17 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:

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