Alignments for a candidate for aacS in Saccharomonospora marina XMU15

GapMind for catabolism of small carbon sources

Alignments for a candidate for aacS in Saccharomonospora marina XMU15

Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_157617261.1 SACMADRAFT_RS15460 acetoacetate--CoA ligase

Query= BRENDA::D6EQU8
         (658 letters)



>NCBI__GCF_000244955.1:WP_157617261.1
          Length = 663

 Score =  648 bits (1671), Expect = 0.0
 Identities = 324/655 (49%), Positives = 420/655 (64%), Gaps = 12/655 (1%)

Query: 9   LWQPDAQRIAQARITRFQAWAAEHHGAPAEGGYAALHRWSVDELDTFWKAVTEWFDVRFS 68
           LW+PD     +  +T +  W     G      YAAL  WSV +L  FW+++ ++F VR S
Sbjct: 13  LWEPDQAWRDRTHLTAYLRWLERERGLRF-ADYAALWEWSVSDLPAFWQSIWDYFGVRAS 71

Query: 69  TPYARVLGDRTMPGAQWFPGATLNYAEHALRAAGTRPDEPALLYVDETHEPAPVTWAELR 128
            P   VL DR+MPGA+WFPGA LNYAEHAL  +G      A+L+  E      ++W +  
Sbjct: 72  APARCVLADRSMPGARWFPGAELNYAEHAL--SGEHRGGAAVLWAGEHTPLGAMSWQQFA 129

Query: 129 RQVASLAAELRALGVRPGDRVSGYLPNIPQAVVALLATAAVGGVWTSCAPDFGARSVLDR 188
             V  LA  LR LGVRPGDRV  YLPNIP  ++A+LAT ++G VW +C+PDFGA   LDR
Sbjct: 130 GAVRVLATRLRELGVRPGDRVVAYLPNIPHTLIAMLATTSIGAVWAACSPDFGATGALDR 189

Query: 189 FQQVEPVVLFTVDGYRYGGKEHDRRDTVAELRRELPTLRAVIHIPLLGTE--APDGTLDW 246
           F Q+EP VLF VDGYRYGG E DRRD V  L R LP LR V+ +  L  +   P  TLDW
Sbjct: 190 FGQLEPTVLFAVDGYRYGGVERDRRDEVRALARALPGLRHVVSVRYLYPDQPVPADTLDW 249

Query: 247 ETLT----AADAEPVYEQVPFDHPLWVLYSSGTTGLPKAIVQSQGGILVEHLKQLGLHCD 302
           E L         E  +EQVPFDHPLW+L+SSGTTG PKAIV   GGIL+E LK    H D
Sbjct: 250 ERLLDHPGVGAEEFSFEQVPFDHPLWILFSSGTTGPPKAIVHGHGGILLEQLKLHHFHMD 309

Query: 303 LGPGDRFFWYTSTGWMMWNFLVSGLLTGTTIVLYDGSPGFPATDAQWRIAERTGATLFGT 362
           L  GDR F+Y++TGWMMWNFL S LL G   VLYDGSP  P  D  WR+AE    + FG 
Sbjct: 310 LHEGDRLFFYSTTGWMMWNFLASSLLAGAVPVLYDGSPTHPDVDVLWRLAEEAEVSCFGA 369

Query: 363 SAAYVMACRKAGVHPARDLDLSAIQCVATTGSPLPPDGFRWLHDEFAAGGADLWIASVSG 422
           S +YV    +AG+ P    +L+A++ V   GSP+  +   W +         LW+A+ SG
Sbjct: 370 SPSYVDLIDRAGLAPGERFELTALRTVVPAGSPVSAECTAWFYRNVKRR---LWVATGSG 426

Query: 423 GTDVCSCFAGAVPTLPVHIGELQAPGLGTDLQSWDPSGDPLTDEVGELVVTNPMPSMPIR 482
           GTD C+ F G VPTLPV  GE+QA  LG    ++D SG P+T +VGELV+T P+PSMP+R
Sbjct: 427 GTDCCTGFVGGVPTLPVRAGEIQARSLGVAAHAFDDSGRPVTGQVGELVLTEPLPSMPVR 486

Query: 483 FWNDPDGSRYHDSYFDTYPGVWRHGDWITLTSRGSVVIHGRSDSTLNRQGVRMGSADIYE 542
           FW D DGSRY  SYF+ +PGVWRHGD+  +  RG   + GRSD+TLNR GVR+G+A+IY 
Sbjct: 487 FWGDDDGSRYRASYFEHFPGVWRHGDFFLVNERGGCFVLGRSDATLNRHGVRIGTAEIYR 546

Query: 543 AVERLPEIRESLVIGIEQPDGGYWMPLFVHLAPGATLDDALLDRIKRTIRVNLSPRHVPD 602
           A++ L EI  +LV+ + +P GG+ MPLFV L  G  LDDAL  +I   +R   +PRHVPD
Sbjct: 547 ALDELAEIDNALVVNLHRPGGGFHMPLFVTLTEGTVLDDALRAKINDQLRHTRTPRHVPD 606

Query: 603 EVIEVPGIPHTLTGKRIEVPVKRLLQGTPLDKAVNPGSIDNLDLLHFYEELARKR 657
           E++ VP IP T++GK++E+PV+R+LQG P+++  +  ++ +   L  + E AR +
Sbjct: 607 EIVAVPAIPMTISGKKLEIPVRRILQGEPVEQVADRSALADPSALDAFVEYARNQ 661


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: 1634
Number of extensions: 96
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: 663
Length adjustment: 38
Effective length of query: 620
Effective length of database: 625
Effective search space:   387500
Effective search space used:   387500
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_157617261.1 SACMADRAFT_RS15460 (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.3629266.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.4e-248  809.6   0.0     1e-247  809.4   0.0    1.0  1  NCBI__GCF_000244955.1:WP_157617261.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000244955.1:WP_157617261.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  809.4   0.0    1e-247    1e-247       5     650 ..      12     660 ..       8     662 .. 0.98

  Alignments for each domain:
  == domain 1  score: 809.4 bits;  conditional E-value: 1e-247
                             TIGR01217   5 vlwepdaervkdarlarfraavgerfGaalgdydalyrwsvdeldafwkavwefsdvvfssaekevvddskml 77 
                                            lwepd+   ++++l+ +  +   + G+ ++dy+al++wsv++l afw+++w++++v++s++   v+ d+ m+
  NCBI__GCF_000244955.1:WP_157617261.1  12 LLWEPDQAWRDRTHLTAYLRWLERERGLRFADYAALWEWSVSDLPAFWQSIWDYFGVRASAPARCVLADRSMP 84 
                                           79*********************************************************************** PP

                             TIGR01217  78 aarffpgarlnyaenllrkkgs.edallyvdeekesakvtfeelrrqvaslaaalralGvkkGdrvagylpni 149
                                           +ar+fpga lnyae++l  +   + a+l+ +e+     ++++++   v  la+ lr+lGv++Gdrv++ylpni
  NCBI__GCF_000244955.1:WP_157617261.1  85 GARWFPGAELNYAEHALSGEHRgGAAVLWAGEHTPLGAMSWQQFAGAVRVLATRLRELGVRPGDRVVAYLPNI 157
                                           *****************988774778888888889999*********************************** PP

                             TIGR01217 150 peavaallatasvGaiwsscspdfGargvldrfsqiepkllfsvdgyvynGkehdrrekvrevakelpdlrav 222
                                           p+++ a+lat+s+Ga+w++cspdfGa g ldrf+q+ep +lf+vdgy+y+G e+drr++vr++a+ lp lr+v
  NCBI__GCF_000244955.1:WP_157617261.1 158 PHTLIAMLATTSIGAVWAACSPDFGATGALDRFGQLEPTVLFAVDGYRYGGVERDRRDEVRALARALPGLRHV 230
                                           ************************************************************************* PP

                             TIGR01217 223 vlipyvgdreklapkvegaltledllaa..aqaaelvfeqlpfdhplyilfssGttGvpkaivhsaGGtlvqh 293
                                           v + y+ + + +     ++l++e ll    + a e  feq+pfdhpl+ilfssGttG pkaivh  GG+l++ 
  NCBI__GCF_000244955.1:WP_157617261.1 231 VSVRYLYPDQPVPA---DTLDWERLLDHpgVGAEEFSFEQVPFDHPLWILFSSGTTGPPKAIVHGHGGILLEQ 300
                                           *******7766655...89******98666999**************************************** PP

                             TIGR01217 294 lkehvlhcdltdgdrllyyttvGwmmwnflvsglatGatlvlydGsplvpatnvlfdlaeregitvlGtsaky 366
                                           lk h++h dl++gdrl++y+t+Gwmmwnfl+s+l++Ga  vlydGsp+ p+ +vl++lae   ++ +G+s  y
  NCBI__GCF_000244955.1:WP_157617261.1 301 LKLHHFHMDLHEGDRLFFYSTTGWMMWNFLASSLLAGAVPVLYDGSPTHPDVDVLWRLAEEAEVSCFGASPSY 373
                                           ************************************************************************* PP

                             TIGR01217 367 vsavrkkglkparthdlsalrlvastGsplkpegfeyvyeeikadvllasisGGtdivscfvganpslpvykG 439
                                           v+ + ++gl p + ++l+alr+v+ +Gsp+++e   + y+++k  +++a+ sGGtd ++ fvg++p+lpv  G
  NCBI__GCF_000244955.1:WP_157617261.1 374 VDLIDRAGLAPGERFELTALRTVVPAGSPVSAECTAWFYRNVKRRLWVATGSGGTDCCTGFVGGVPTLPVRAG 446
                                           ************************************************************************* PP

                             TIGR01217 440 eiqapglGlaveawdeeGkpvtgekGelvvtkplpsmpvrfwndedGskyrkayfdkypgvwahGdyieltpr 512
                                           eiqa++lG+a +a+d++G+pvtg++Gelv t+plpsmpvrfw d+dGs+yr++yf+++pgvw+hGd+  ++ r
  NCBI__GCF_000244955.1:WP_157617261.1 447 EIQARSLGVAAHAFDDSGRPVTGQVGELVLTEPLPSMPVRFWGDDDGSRYRASYFEHFPGVWRHGDFFLVNER 519
                                           ************************************************************************* PP

                             TIGR01217 513 GgivihGrsdatlnpnGvrlGsaeiynaverldeveeslvigqeqedgeervvlfvklasGatldealvkeik 585
                                           Gg  ++Grsdatln++Gvr+G+aeiy a+++l e++++lv+  +++ g+ +++lfv l++G+ ld+al  +i+
  NCBI__GCF_000244955.1:WP_157617261.1 520 GGCFVLGRSDATLNRHGVRIGTAEIYRALDELAEIDNALVVNLHRPGGGFHMPLFVTLTEGTVLDDALRAKIN 592
                                           ************************************************************************* PP

                             TIGR01217 586 dairaglsprhvpskiievagiprtlsGkkvevavkdvvaGkpve...nkgalsnpealdlyeeleel 650
                                           d++r   +prhvp++i++v+ ip t+sGkk+e++v+++++G+pve   ++ al++p ald + e ++ 
  NCBI__GCF_000244955.1:WP_157617261.1 593 DQLRHTRTPRHVPDEIVAVPAIPMTISGKKLEIPVRRILQGEPVEqvaDRSALADPSALDAFVEYARN 660
                                           ********************************************98889*************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (652 nodes)
Target sequences:                          1  (663 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: 32.37
//
[ok]

This GapMind analysis is from Sep 24 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