Alignments for a candidate for fadA in Cupriavidus basilensis 4G11

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.2105955.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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 24.36
//
[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:

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