Alignments for a candidate for aacS in Marinobacter guineae M3B

GapMind for catabolism of small carbon sources

Alignments for a candidate for aacS in Marinobacter guineae M3B

Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_099618202.1 CLH62_RS11015 acetoacetate--CoA ligase

Query= BRENDA::D6EQU8
         (658 letters)



>NCBI__GCF_002744735.1:WP_099618202.1
          Length = 662

 Score =  565 bits (1455), Expect = e-165
 Identities = 290/659 (44%), Positives = 408/659 (61%), Gaps = 14/659 (2%)

Query: 3   TENPQPLWQPDAQRIAQARITRFQAWAAEHHGAPAEGGYAALHRWSVDELDTFWKAVTEW 62
           TE    +W P    +  +R+  F+AW  E  G      Y ALH+WS+DELDTFW+ V ++
Sbjct: 4   TEQSPVVWSPSEDTLKNSRMGLFKAWL-EQQGFGPFADYHALHQWSIDELDTFWQKVWDY 62

Query: 63  FDVRFSTPYARVLGDRTMPGAQWFPGATLNYAEHALRAA-GTRPDEPALLYVDETHEPAP 121
             +   TP  ++LG R MPGA+WFPG  LN+A + LR A G   +  A++   ET     
Sbjct: 63  CGLVCHTPADQILGKRDMPGAEWFPGMKLNFAANLLRLADGEHANREAVVAYCETRPVLR 122

Query: 122 VTWAELRRQVASLAAELRALGVRPGDRVSGYLPNIPQAVVALLATAAVGGVWTSCAPDFG 181
            ++A+L+    +L A LR+  +R GDRV+G + N  +A+V +LA  ++G VW+S +PDFG
Sbjct: 123 RSYAQLKADAGALEAFLRSKDIRQGDRVAGVVTNGYEALVGMLAATSLGAVWSSASPDFG 182

Query: 182 ARSVLDRFQQVEPVVLFTVDGYRYGGKEHDRRDTVAELRRELPTLRAVIHIPLLGTEAP- 240
             ++LDRF Q+EP  L  V+GY YGGK   R+   AEL   LPTL+ V+ +  L  EAP 
Sbjct: 183 VGAILDRFGQIEPSALIVVNGYGYGGKAFARQQDFAELIAGLPTLKTVVSVQQLPDEAPI 242

Query: 241 --DGTLDWETLTA--ADAEPVYEQVPFDHPLWVLYSSGTTGLPKAIVQSQGGILVEHLKQ 296
             D    WE   A  A   P +  +P DHP+++LYSSGTTG PK IV    G+LV H K+
Sbjct: 243 PGDLVTTWEDALAFGAGTAPSFTPLPPDHPVYILYSSGTTGKPKCIVHGNAGLLVNHAKE 302

Query: 297 LGLHCDLGPGDRFFWYTSTGWMMWNFLVSGLLTGTTIVLYDGSPGFPATDAQWRIAERTG 356
           L LH D+GP DRF ++T+ GWMMWN+  S LLTG  ++  DGSPG+P+    W       
Sbjct: 303 LMLHGDVGPDDRFLYFTTCGWMMWNWQASALLTGAAVITVDGSPGYPSLSFLWDTVAGEK 362

Query: 357 ATLFGTSAAYVMACRKAGVHPARDLDLSAIQCVATTGSPLPPDGFRWLHDEFAAGGADLW 416
            T FGTSA ++  CRKA + PA+  D S ++ V +TGSPL P+ + W++ +   G  +  
Sbjct: 363 VTHFGTSARFIAGCRKAELEPAKTRDQSKLRIVFSTGSPLLPEDYDWMYTD---GAPNAL 419

Query: 417 IASVSGGTDVCSCFAGAVPTLPVHIGELQAPGLGTDLQSWDPSGDPLTDEVGELVVTNPM 476
           + S++GGTD+C CF GA P LPV  GE+Q   LG D  ++   G+P+++  GELV   P+
Sbjct: 420 LGSIAGGTDICGCFVGATPLLPVRRGEIQCRFLGVDAVAYGDDGEPVSEGRGELVCRQPL 479

Query: 477 PSMPIRFWNDPDGSRYHDSYFDTYPGVWRHGDWITLTSRGSVVIHGRSDSTLNRQGVRMG 536
           PSMP+ FW DP+G RY D+YF+T+PGVW HGD+I  T  G  +I+GRSD+TLN  GVR+G
Sbjct: 480 PSMPVCFWEDPNGERYRDAYFNTFPGVWAHGDFIEFTEHGGAIIYGRSDATLNPGGVRIG 539

Query: 537 SADIYEAVERLPEIRESLVIGIEQPDGGYWMPLFVHLAPGATLDDALLDRIKRTIRVNLS 596
           +A+IY  VE + E+++SLV+G  Q DG   + L V  A G  + D L  ++K  IR   S
Sbjct: 540 TAEIYRQVETVAEVKDSLVVG-RQIDGDVEVVLLVVPAEGQEVTDDLRKQLKSRIREGAS 598

Query: 597 PRHVPDEVIEVPGIPHTLTGKRIEVPVKRLLQGTPLDKAVNPGSIDNLDLL-HFYEELA 654
           PRHVP  +++V  IP+T +GK++E+ V RL+ G+   KA N  ++ N + L H  E LA
Sbjct: 599 PRHVPKHIVQVNDIPYTRSGKKVELAVARLINGS--KKADNRDALGNPEALDHIRERLA 655


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: 1458
Number of extensions: 81
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: 662
Length adjustment: 38
Effective length of query: 620
Effective length of database: 624
Effective search space:   386880
Effective search space used:   386880
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_099618202.1 CLH62_RS11015 (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.1943694.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.1e-239  782.8   0.0   1.5e-239  782.4   0.0    1.0  1  NCBI__GCF_002744735.1:WP_099618202.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002744735.1:WP_099618202.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  782.4   0.0  1.5e-239  1.5e-239       3     646 ..       7     652 ..       5     655 .. 0.96

  Alignments for each domain:
  == domain 1  score: 782.4 bits;  conditional E-value: 1.5e-239
                             TIGR01217   3 eqvlwepdaervkdarlarfraavgerfGaalgdydalyrwsvdeldafwkavwefsdvvfssaekevvddsk 75 
                                             v+w p ++  k++r+  f+a+  ++    ++dy al++ws+deld+fw++vw+++++v++++ +++++++ 
  NCBI__GCF_002744735.1:WP_099618202.1   7 SPVVWSPSEDTLKNSRMGLFKAWLEQQGFGPFADYHALHQWSIDELDTFWQKVWDYCGLVCHTPADQILGKRD 79 
                                           5689*******************97776569****************************************** PP

                             TIGR01217  76 mlaarffpgarlnyaenllrkkgs....edallyvdeekesakvtfeelrrqvaslaaalralGvkkGdrvag 144
                                           m++a++fpg +ln+a nllr ++      +a++   e++ + + ++++l++    l+a lr+  +++Gdrvag
  NCBI__GCF_002744735.1:WP_099618202.1  80 MPGAEWFPGMKLNFAANLLRLADGehanREAVVAYCETRPVLRRSYAQLKADAGALEAFLRSKDIRQGDRVAG 152
                                           ********************887644544566667788999999***************************** PP

                             TIGR01217 145 ylpnipeavaallatasvGaiwsscspdfGargvldrfsqiepkllfsvdgyvynGkehdrrekvrevakelp 217
                                           ++ n  ea++ +la++s+Ga+wss+spdfG+ ++ldrf+qiep  l++v+gy y+Gk   r++  +e+  +lp
  NCBI__GCF_002744735.1:WP_099618202.1 153 VVTNGYEALVGMLAATSLGAVWSSASPDFGVGAILDRFGQIEPSALIVVNGYGYGGKAFARQQDFAELIAGLP 225
                                           ************************************************************************* PP

                             TIGR01217 218 dlravvlipyvgdreklapkvegaltledllaaaqaaelvfeqlpfdhplyilfssGttGvpkaivhsaGGtl 290
                                           +l++vv +  + d++ +    +   t+ed la    + + f  lp dhp+yil+ssGttG pk+ivh + G+l
  NCBI__GCF_002744735.1:WP_099618202.1 226 TLKTVVSVQQLPDEAPIPG--DLVTTWEDALAFGAGTAPSFTPLPPDHPVYILYSSGTTGKPKCIVHGNAGLL 296
                                           *********9996665555..66679******988999*********************************** PP

                             TIGR01217 291 vqhlkehvlhcdltdgdrllyyttvGwmmwnflvsglatGatlvlydGsplvpatnvlfdlaeregitvlGts 363
                                           v+h ke+ lh+d+++ dr+ly+tt+Gwmmwn+ +s+l+tGa+++  dGsp+ p+   l+d ++ e++t +Gts
  NCBI__GCF_002744735.1:WP_099618202.1 297 VNHAKELMLHGDVGPDDRFLYFTTCGWMMWNWQASALLTGAAVITVDGSPGYPSLSFLWDTVAGEKVTHFGTS 369
                                           ************************************************************************* PP

                             TIGR01217 364 akyvsavrkkglkparthdlsalrlvastGsplkpegfeyvyeeikadvllasisGGtdivscfvganpslpv 436
                                           a+++  +rk++l+pa+t d s lr+v stGspl pe ++++y   +++ ll+si+GGtdi+ cfvga+p+lpv
  NCBI__GCF_002744735.1:WP_099618202.1 370 ARFIAGCRKAELEPAKTRDQSKLRIVFSTGSPLLPEDYDWMYTDGAPNALLGSIAGGTDICGCFVGATPLLPV 442
                                           ************************************************************************* PP

                             TIGR01217 437 ykGeiqapglGlaveawdeeGkpvtgekGelvvtkplpsmpvrfwndedGskyrkayfdkypgvwahGdyiel 509
                                            +Geiq++ lG++  a+ ++G+pv + +Gelv+ +plpsmpv fw+d++G +yr+ayf+++pgvwahGd+ie+
  NCBI__GCF_002744735.1:WP_099618202.1 443 RRGEIQCRFLGVDAVAYGDDGEPVSEGRGELVCRQPLPSMPVCFWEDPNGERYRDAYFNTFPGVWAHGDFIEF 515
                                           ************************************************************************* PP

                             TIGR01217 510 tprGgivihGrsdatlnpnGvrlGsaeiynaverldeveeslvigqeqedgeervvlfvklasGatldealvk 582
                                           t +Gg +i+Grsdatlnp+Gvr+G+aeiy +ve + ev++slv+g+ q dg++ vvl+v  a+G++++++l k
  NCBI__GCF_002744735.1:WP_099618202.1 516 TEHGGAIIYGRSDATLNPGGVRIGTAEIYRQVETVAEVKDSLVVGR-QIDGDVEVVLLVVPAEGQEVTDDLRK 587
                                           *********************************************7.5799********************** PP

                             TIGR01217 583 eikdairaglsprhvpskiievagiprtlsGkkvevavkdvvaG.kpvenkgalsnpealdlyee 646
                                           ++k++ir g+sprhvp++i++v++ip+t sGkkve+av ++++G k  +n++al npeald  +e
  NCBI__GCF_002744735.1:WP_099618202.1 588 QLKSRIREGASPRHVPKHIVQVNDIPYTRSGKKVELAVARLINGsKKADNRDALGNPEALDHIRE 652
                                           *******************************************945678***********98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (652 nodes)
Target sequences:                          1  (662 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: 22.76
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

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