Alignments for a candidate for aacS in Sulfuritalea hydrogenivorans DSM 22779

GapMind for catabolism of small carbon sources

Alignments for a candidate for aacS in Sulfuritalea hydrogenivorans DSM 22779

Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_041096347.1 SUTH_RS00825 acetoacetate--CoA ligase

Query= BRENDA::D6EQU8
         (658 letters)



>NCBI__GCF_000828635.1:WP_041096347.1
          Length = 652

 Score =  661 bits (1706), Expect = 0.0
 Identities = 319/655 (48%), Positives = 433/655 (66%), Gaps = 15/655 (2%)

Query: 8   PLWQPDAQRIAQARITRFQAWAAEHHGAPAEGGYAALHRWSVDELDTFWKAVTEWFDVRF 67
           P W+P A  I+ A+IT F  W A   G      Y AL RWSV++L+ FW AV ++F +  
Sbjct: 4   PAWRPSAATISAAKITAFSNWLAAERGLKF-ADYDALWRWSVEDLEGFWGAVWDYFAIPA 62

Query: 68  STPYARVLGDRTMPGAQWFPGATLNYAEHALRAAGTRPDEPALLYVDETHEPAPVTWAEL 127
           +TP  RVL D  MPGAQWFPG T+NY E   R     P+ PA++  +E      + W EL
Sbjct: 63  ATPRTRVLADARMPGAQWFPGVTMNYVEQVFRHV--TPNRPAVISRNEAGVDRELGWPEL 120

Query: 128 RRQVASLAAELRALGVRPGDRVSGYLPNIPQAVVALLATAAVGGVWTSCAPDFGARSVLD 187
           RRQV +LAA LR +GV  GDRV  YLPNIP+ VVA LA A++G +W++C+PD G  +VLD
Sbjct: 121 RRQVGALAASLRGMGVGRGDRVVAYLPNIPETVVAFLAVASLGAIWSACSPDMGRIAVLD 180

Query: 188 RFQQVEPVVLFTVDGYRYGGKEHDRRDTVAELRRELPTLRAVIHIPLLGTEAPDGTL--- 244
           RF+Q+ P VL  VDGY+YGGK +DRR+ + EL  ELP++  ++ +P    +A        
Sbjct: 181 RFRQIAPKVLIAVDGYQYGGKSYDRRELIHELLAELPSIDHMVLLPSFDEQADPAEFASC 240

Query: 245 -DWETLTAADAEPVYEQVPFDHPLWVLYSSGTTGLPKAIVQSQGGILVEHLKQLGLHCDL 303
             W   TA       E +  DHPLWV+YSSGTTGLPK IV S GGI++EH+K    H DL
Sbjct: 241 TGWAAATAGS-----EPLQVDHPLWVVYSSGTTGLPKPIVHSHGGIVIEHVKLGAFHLDL 295

Query: 304 GPGDRFFWYTSTGWMMWNFLVSGLLTGTTIVLYDGSPGFPATDAQWRIAERTGATLFGTS 363
           GP DR+ WY+S+GW+MWN  + GLL G+TI +YDG+PG+P  +A WR       T FG  
Sbjct: 296 GPEDRYHWYSSSGWIMWNCQLIGLLMGSTICIYDGNPGWPDWNALWRFVGEKRVTFFGAG 355

Query: 364 AAYVMACRKAGVHPARDLDLSAIQCVATTGSPLPPDGFRWLHDEFAAGGADLWIASVSGG 423
           AA+ ++C KA V P    DLSA++ V +TGSPLP +G++W++D       D+WI  +SGG
Sbjct: 356 AAFFLSCLKAHVEPNEVADLSALRVVGSTGSPLPEEGYQWIYDHVRP---DIWINPISGG 412

Query: 424 TDVCSCFAGAVPTLPVHIGELQAPGLGTDLQSWDPSGDPLTDEVGELVVTNPMPSMPIRF 483
           TD   CF G V TLPV++GE+Q   LG  +++W+ +G  L DEVGELV + PMPSMP++F
Sbjct: 413 TDFAGCFVGGVATLPVYLGEMQCRCLGAKVEAWNEAGKALIDEVGELVCSAPMPSMPLKF 472

Query: 484 WNDPDGSRYHDSYFDTYPGVWRHGDWITLTSRGSVVIHGRSDSTLNRQGVRMGSADIYEA 543
           WNDP+  RY +SYFD YPGVWRHGDW+ +T  G  +I+GRSD+T+NR G+RMG++++Y A
Sbjct: 473 WNDPEDRRYRESYFDMYPGVWRHGDWLRITPHGGAIIYGRSDATINRHGIRMGTSELYRA 532

Query: 544 VERLPEIRESLVIGIEQPDGGYWMPLFVHLAPGATLDDALLDRIKRTIRVNLSPRHVPDE 603
           VE LPE+ +SLV+ +E      +MPLFV L PG  L   L   ++  I+V LS RHVP+E
Sbjct: 533 VEELPEVLDSLVVDLEFLGRESYMPLFVVLRPGHELTKQLEATLRERIKVALSARHVPNE 592

Query: 604 VIEVPGIPHTLTGKRIEVPVKRLLQGTPLDKAVNPGSIDNLDLLHFYEELARKRS 658
           + +V  +P TL+GK++E+PVK+LL G  LDK  NP ++ N   L ++ + A +R+
Sbjct: 593 IFQVAEVPRTLSGKKMELPVKKLLLGHALDKIANPDAMANPASLQWFVDFAMRRA 647


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: 1481
Number of extensions: 83
Number of successful extensions: 5
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: 652
Length adjustment: 38
Effective length of query: 620
Effective length of database: 614
Effective search space:   380680
Effective search space used:   380680
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 WP_041096347.1 SUTH_RS00825 (acetoacetate--CoA ligase)
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.459344.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.4e-243  793.8   0.0   6.2e-243  793.6   0.0    1.0  1  NCBI__GCF_000828635.1:WP_041096347.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000828635.1:WP_041096347.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  793.6   0.0  6.2e-243  6.2e-243       5     650 ..       4     645 ..       1     647 [. 0.97

  Alignments for each domain:
  == domain 1  score: 793.6 bits;  conditional E-value: 6.2e-243
                             TIGR01217   5 vlwepdaervkdarlarfraavgerfGaalgdydalyrwsvdeldafwkavwefsdvvfssaekevvddskml 77 
                                           + w+p a  +  a+++ f ++ + + G+ ++dydal+rwsv++l+ fw avw+++ + + ++  +v+ d +m+
  NCBI__GCF_000828635.1:WP_041096347.1   4 PAWRPSAATISAAKITAFSNWLAAERGLKFADYDALWRWSVEDLEGFWGAVWDYFAIPAATPRTRVLADARMP 76 
                                           68*********************************************************************** PP

                             TIGR01217  78 aarffpgarlnyaenllrkkgs.edallyvdeekesakvtfeelrrqvaslaaalralGvkkGdrvagylpni 149
                                           +a++fpg ++ny e+++r+     +a++ ++e  +  ++ + elrrqv  laa+lr +Gv++Gdrv++ylpni
  NCBI__GCF_000828635.1:WP_041096347.1  77 GAQWFPGVTMNYVEQVFRHVTPnRPAVISRNEAGVDRELGWPELRRQVGALAASLRGMGVGRGDRVVAYLPNI 149
                                           ******************976527899999999**************************************** PP

                             TIGR01217 150 peavaallatasvGaiwsscspdfGargvldrfsqiepkllfsvdgyvynGkehdrrekvrevakelpdlrav 222
                                           pe+v+a+la as+Gaiws+cspd+G  +vldrf qi+pk+l++vdgy+y+Gk  drre ++e+  elp++ ++
  NCBI__GCF_000828635.1:WP_041096347.1 150 PETVVAFLAVASLGAIWSACSPDMGRIAVLDRFRQIAPKVLIAVDGYQYGGKSYDRRELIHELLAELPSIDHM 222
                                           ************************************************************************* PP

                             TIGR01217 223 vlipyvgdreklap.kvegaltledllaaaqaaelvfeqlpfdhplyilfssGttGvpkaivhsaGGtlvqhl 294
                                           vl+p   +  + +p +  ++  ++  +a+        e l  dhpl++++ssGttG+pk ivhs GG++++h+
  NCBI__GCF_000828635.1:WP_041096347.1 223 VLLPSFDE--QADPaEFASCTGWAAATAG-------SEPLQVDHPLWVVYSSGTTGLPKPIVHSHGGIVIEHV 286
                                           ****9984..4455246666666666665.......688999******************************* PP

                             TIGR01217 295 kehvlhcdltdgdrllyyttvGwmmwnflvsglatGatlvlydGsplvpatnvlfdlaeregitvlGtsakyv 367
                                           k  ++h dl++ dr+ +y++ Gw+mwn    gl++G+t+++ydG p+ p+ n+l++++  +++t +G++a++ 
  NCBI__GCF_000828635.1:WP_041096347.1 287 KLGAFHLDLGPEDRYHWYSSSGWIMWNCQLIGLLMGSTICIYDGNPGWPDWNALWRFVGEKRVTFFGAGAAFF 359
                                           ************************************************************************* PP

                             TIGR01217 368 savrkkglkparthdlsalrlvastGsplkpegfeyvyeeikadvllasisGGtdivscfvganpslpvykGe 440
                                             + k+ ++p +  dlsalr+v stGspl+ eg++++y+ +++d+++  isGGtd   cfvg++++lpvy Ge
  NCBI__GCF_000828635.1:WP_041096347.1 360 LSCLKAHVEPNEVADLSALRVVGSTGSPLPEEGYQWIYDHVRPDIWINPISGGTDFAGCFVGGVATLPVYLGE 432
                                           ************************************************************************* PP

                             TIGR01217 441 iqapglGlaveawdeeGkpvtgekGelvvtkplpsmpvrfwndedGskyrkayfdkypgvwahGdyieltprG 513
                                           +q++ lG +veaw+e Gk++ +e+Gelv++ p+psmp++fwnd++  +yr++yfd ypgvw+hGd+ ++tp+G
  NCBI__GCF_000828635.1:WP_041096347.1 433 MQCRCLGAKVEAWNEAGKALIDEVGELVCSAPMPSMPLKFWNDPEDRRYRESYFDMYPGVWRHGDWLRITPHG 505
                                           ************************************************************************* PP

                             TIGR01217 514 givihGrsdatlnpnGvrlGsaeiynaverldeveeslvigqeqedgeervvlfvklasGatldealvkeikd 586
                                           g +i+Grsdat+n++G+r+G++e+y ave+l+ev +slv+  e    e +++lfv l +G++l+++l   +++
  NCBI__GCF_000828635.1:WP_041096347.1 506 GAIIYGRSDATINRHGIRMGTSELYRAVEELPEVLDSLVVDLEFLGRESYMPLFVVLRPGHELTKQLEATLRE 578
                                           ************************************************************************* PP

                             TIGR01217 587 airaglsprhvpskiievagiprtlsGkkvevavkdvvaGkpve...nkgalsnpealdlyeeleel 650
                                           +i+++ls+rhvp++i +va++prtlsGkk+e++vk+++ G++++   n++a++np +l+ + +++ +
  NCBI__GCF_000828635.1:WP_041096347.1 579 RIKVALSARHVPNEIFQVAEVPRTLSGKKMELPVKKLLLGHALDkiaNPDAMANPASLQWFVDFAMR 645
                                           ******************************************99999**************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (652 nodes)
Target sequences:                          1  (652 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: 36.11
//
[ok]

This GapMind analysis is from Sep 24 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