Alignments for a candidate for aacS in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for aacS in Cupriavidus basilensis 4G11

Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate RR42_RS15595 RR42_RS15595 acetoacetyl-CoA synthetase

Query= BRENDA::D6EQU8
         (658 letters)



>FitnessBrowser__Cup4G11:RR42_RS15595
          Length = 678

 Score =  640 bits (1652), Expect = 0.0
 Identities = 315/666 (47%), Positives = 426/666 (63%), Gaps = 17/666 (2%)

Query: 4   ENPQPLWQPDAQRIAQARITRFQAWAAEHHGAPAEGGYAALHRWSVDELDTFWKAVTEWF 63
           E  Q  W P       +RI  F  W     G  A   Y AL +WSV +L+ FW A+  +F
Sbjct: 5   EEGQLRWTPSQAFRDGSRIAHFMRWLESERGL-AFADYGALWQWSVTDLEAFWDAIRAYF 63

Query: 64  DVRFSTPYARVLGDRTMPGAQWFPGATLNYAEHALRAAGTRP--DEPALLYVDETHEPAP 121
           D+RF TP  RVLG   MPGA+WF GA+LNY +   R AG+    +  A+ Y  E+     
Sbjct: 64  DLRFDTPAERVLGSAQMPGARWFEGASLNYVQQVFRHAGSGAARERTAIRYAGESIAVTD 123

Query: 122 VTWAELRRQVASLAAELRALGVRPGDRVSGYLPNIPQAVVALLATAAVGGVWTSCAPDFG 181
           ++W  L +QVASLA  LR +GV  GDRV+GYLPNIP  VVA LATA++G +W+ CAPD G
Sbjct: 124 LSWDVLEQQVASLAHALRGMGVARGDRVAGYLPNIPATVVAFLATASLGAIWSGCAPDMG 183

Query: 182 ARSVLDRFQQVEPVVLFTVDGYRYGGKEHDRRDTVAELRRELPTLRAVIHIPLLGTEA-- 239
             +V DRF+Q+EP VL  VDGYRYGGK +DR   +A+L   LP+L  ++ +P   T+A  
Sbjct: 184 QVAVSDRFRQIEPKVLIAVDGYRYGGKAYDRAPVLADLAAALPSLTDLVLVPGEHTDAHA 243

Query: 240 -PDGTL--------DWETLTAADAEPVYEQVPFDHPLWVLYSSGTTGLPKAIVQSQGGIL 290
            P+            W+ + A       E VPFDHPLW++YSSGTTG+PK IV   GGI+
Sbjct: 244 APNAIALPANVRRHAWQAVLAHRVPLAIESVPFDHPLWIVYSSGTTGMPKPIVHGHGGIV 303

Query: 291 VEHLKQLGLHCDLGPGDRFFWYTSTGWMMWNFLVSGLLTGTTIVLYDGSPGFPATDAQWR 350
           +E LK +  H +LGP D F WY+S+GW+MWN  ++GLL G+TI LYDG+P +P     WR
Sbjct: 304 IEQLKLMAFHNNLGPDDVFHWYSSSGWIMWNAQIAGLLLGSTIALYDGNPAWPDAGVLWR 363

Query: 351 IAERTGATLFGTSAAYVMACRKAGVHPARDLDLSAIQCVATTGSPLPPDGFRWLHDEFAA 410
             +    T FG  AA+  A  KAG+ PAR  DLS ++ + +TGSPLP + + W++   +A
Sbjct: 364 FVDAARVTAFGAGAAFFTAGMKAGIEPARVADLSRLRALGSTGSPLPAEAYDWIYRHVSA 423

Query: 411 GGADLWIASVSGGTDVCSCFAGAVPTLPVHIGELQAPGLGTDLQSWDPSGDPLTDEVGEL 470
              D+W+A +SGGTD    F    P LPV+ GE+Q   LG  ++++D +G+ L  EVGEL
Sbjct: 424 ---DIWLAPMSGGTDFAGSFVAGCPILPVYSGEMQCRCLGAKVEAFDEAGNALVGEVGEL 480

Query: 471 VVTNPMPSMPIRFWNDPDGSRYHDSYFDTYPGVWRHGDWITLTSRGSVVIHGRSDSTLNR 530
           V T PMPSMP+  W D +G RY DSYFDTYPGVWRHGDWI +T+ G  +I+GRSD+T+NR
Sbjct: 481 VCTAPMPSMPLFLWGDTNGQRYRDSYFDTYPGVWRHGDWIKITAHGGAIIYGRSDATINR 540

Query: 531 QGVRMGSADIYEAVERLPEIRESLVIGIEQPDGGYWMPLFVHLAPGATLDDALLDRIKRT 590
            G+RMG++++Y  VE LPE+ +S+V+ +E      +MPLFV L  G  LDDAL D ++  
Sbjct: 541 HGIRMGTSELYRVVEDLPEVLDSMVVDLEYLGRDSYMPLFVVLREGMVLDDALRDTMRAR 600

Query: 591 IRVNLSPRHVPDEVIEVPGIPHTLTGKRIEVPVKRLLQGTPLDKAVNPGSIDNLDLLHFY 650
           IR  LS RHVP+E+++VPG+P TL+GK++EVP+K+LL G   DK  N  ++ N + L +Y
Sbjct: 601 IRSALSSRHVPNEILQVPGVPRTLSGKKMEVPIKKLLLGHAPDKIANRDAMANPETLDWY 660

Query: 651 EELARK 656
              A +
Sbjct: 661 FAYAER 666


Lambda     K      H
   0.320    0.138    0.442 

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: 1482
Number of extensions: 71
Number of successful extensions: 4
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: 658
Length of database: 678
Length adjustment: 38
Effective length of query: 620
Effective length of database: 640
Effective search space:   396800
Effective search space used:   396800
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (25.4 bits)

Align candidate RR42_RS15595 RR42_RS15595 (acetoacetyl-CoA synthetase)
to HMM TIGR01217 (acetoacetate-CoA ligase (EC 6.2.1.16))

# 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/TIGR01217.hmm
# target sequence database:        /tmp/gapView.29045.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01217  [M=652]
Accession:   TIGR01217
Description: ac_ac_CoA_syn: acetoacetate-CoA ligase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   9.8e-240  783.0   0.0   1.2e-239  782.7   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS15595  RR42_RS15595 acetoacetyl-CoA syn


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS15595  RR42_RS15595 acetoacetyl-CoA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  782.7   0.0  1.2e-239  1.2e-239       2     647 ..       6     663 ..       5     667 .. 0.96

  Alignments for each domain:
  == domain 1  score: 782.7 bits;  conditional E-value: 1.2e-239
                                 TIGR01217   2 reqvlwepdaervkdarlarfraavgerfGaalgdydalyrwsvdeldafwkavwefsdvvfssaekev 70 
                                               + q  w+p +   + +r+a+f  +   + G+a++dy al++wsv++l+afw a+  ++d++f+++ ++v
  lcl|FitnessBrowser__Cup4G11:RR42_RS15595   6 EGQLRWTPSQAFRDGSRIAHFMRWLESERGLAFADYGALWQWSVTDLEAFWDAIRAYFDLRFDTPAERV 74 
                                               56888**************************************************************** PP

                                 TIGR01217  71 vddskmlaarffpgarlnyaenllrkkgs.....edallyvdeekesakvtfeelrrqvaslaaalral 134
                                               +++ +m++ar+f ga lny ++++r++gs      +a+ y +e   ++ ++++ l +qvasla alr +
  lcl|FitnessBrowser__Cup4G11:RR42_RS15595  75 LGSAQMPGARWFEGASLNYVQQVFRHAGSgaareRTAIRYAGESIAVTDLSWDVLEQQVASLAHALRGM 143
                                               ****************************988884445669999999*********************** PP

                                 TIGR01217 135 GvkkGdrvagylpnipeavaallatasvGaiwsscspdfGargvldrfsqiepkllfsvdgyvynGkeh 203
                                               Gv +Gdrvagylpnip +v+a+latas+Gaiws c+pd+G+ +v drf qiepk+l++vdgy+y+Gk  
  lcl|FitnessBrowser__Cup4G11:RR42_RS15595 144 GVARGDRVAGYLPNIPATVVAFLATASLGAIWSGCAPDMGQVAVSDRFRQIEPKVLIAVDGYRYGGKAY 212
                                               ********************************************************************* PP

                                 TIGR01217 204 drrekvrevakelpdlravvlipyvgdreklap...kvegaltledllaa.aqaaelvfeqlpfdhply 268
                                               dr   ++++a  lp+l   vl+p     ++ ap    +++ +  + + a  a+  +l  e +pfdhpl+
  lcl|FitnessBrowser__Cup4G11:RR42_RS15595 213 DRAPVLADLAAALPSLTDLVLVPGEHTDAHAAPnaiALPANVRRHAWQAVlAHRVPLAIESVPFDHPLW 281
                                               ***********************887666655532267888877777776566899************* PP

                                 TIGR01217 269 ilfssGttGvpkaivhsaGGtlvqhlkehvlhcdltdgdrllyyttvGwmmwnflvsglatGatlvlyd 337
                                               i++ssGttG+pk ivh  GG++++ lk +++h +l++ d++ +y++ Gw+mwn  ++gl+ G+t+ lyd
  lcl|FitnessBrowser__Cup4G11:RR42_RS15595 282 IVYSSGTTGMPKPIVHGHGGIVIEQLKLMAFHNNLGPDDVFHWYSSSGWIMWNAQIAGLLLGSTIALYD 350
                                               ********************************************************************* PP

                                 TIGR01217 338 GsplvpatnvlfdlaeregitvlGtsakyvsavrkkglkparthdlsalrlvastGsplkpegfeyvye 406
                                               G p  p++ vl++++++ ++t +G++a++ +a  k+g++par  dls lr++ stGspl++e+++++y+
  lcl|FitnessBrowser__Cup4G11:RR42_RS15595 351 GNPAWPDAGVLWRFVDAARVTAFGAGAAFFTAGMKAGIEPARVADLSRLRALGSTGSPLPAEAYDWIYR 419
                                               ********************************************************************* PP

                                 TIGR01217 407 eikadvllasisGGtdivscfvganpslpvykGeiqapglGlaveawdeeGkpvtgekGelvvtkplps 475
                                                + ad++la +sGGtd    fv + p lpvy Ge+q++ lG +vea+de G+++ ge+Gelv+t p+ps
  lcl|FitnessBrowser__Cup4G11:RR42_RS15595 420 HVSADIWLAPMSGGTDFAGSFVAGCPILPVYSGEMQCRCLGAKVEAFDEAGNALVGEVGELVCTAPMPS 488
                                               ********************************************************************* PP

                                 TIGR01217 476 mpvrfwndedGskyrkayfdkypgvwahGdyieltprGgivihGrsdatlnpnGvrlGsaeiynaverl 544
                                               mp+ +w d +G +yr++yfd+ypgvw+hGd+i++t++Gg +i+Grsdat+n++G+r+G++e+y +ve l
  lcl|FitnessBrowser__Cup4G11:RR42_RS15595 489 MPLFLWGDTNGQRYRDSYFDTYPGVWRHGDWIKITAHGGAIIYGRSDATINRHGIRMGTSELYRVVEDL 557
                                               ********************************************************************* PP

                                 TIGR01217 545 deveeslvigqeqedgeervvlfvklasGatldealvkeikdairaglsprhvpskiievagiprtlsG 613
                                               +ev +s+v+  e    + +++lfv l +G+ ld+al + ++ +ir++ls+rhvp++i++v+g+prtlsG
  lcl|FitnessBrowser__Cup4G11:RR42_RS15595 558 PEVLDSMVVDLEYLGRDSYMPLFVVLREGMVLDDALRDTMRARIRSALSSRHVPNEILQVPGVPRTLSG 626
                                               ********************************************************************* PP

                                 TIGR01217 614 kkvevavkdvvaGkpve...nkgalsnpealdlyeel 647
                                               kk+ev++k+++ G++ +   n++a++npe+ld y   
  lcl|FitnessBrowser__Cup4G11:RR42_RS15595 627 KKMEVPIKKLLLGHAPDkiaNRDAMANPETLDWYFAY 663
                                               *************9766666************99665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (652 nodes)
Target sequences:                          1  (678 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: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.05
# Mc/sec: 7.87
//
[ok]

This GapMind analysis is from Sep 17 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