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_009152103.1 SACMADRAFT_RS01985 acetoacetate--CoA ligase

Query= BRENDA::D6EQU8
         (658 letters)



>NCBI__GCF_000244955.1:WP_009152103.1
          Length = 659

 Score =  662 bits (1709), Expect = 0.0
 Identities = 333/648 (51%), Positives = 433/648 (66%), Gaps = 12/648 (1%)

Query: 6   PQPLWQPDAQRIAQARITRFQAWAAEHHGAPAEGGYAALHRWSVDELDTFWKAVTEWFDV 65
           P+ LW+P ++++ + RI  F+ W   +    A G Y  L  +SV +L  FW AV E+  V
Sbjct: 8   PEVLWRPTSEQVERTRIEDFRRWLGANRDVHA-GDYHELWSYSVRDLSGFWSAVAEYLGV 66

Query: 66  RFSTPYARVLGDRTMPGAQWFPGATLNYAEHALRA----AGTRPDEPALLYVDETHEPAP 121
           R+    A VL    MPGA+WF G TLNYAEHAL      A    ++PA+++  E      
Sbjct: 67  RWHQQPAEVLSGMEMPGARWFAGGTLNYAEHALSGGVAGAAKADNDPAVVFQREDGAEER 126

Query: 122 VTWAELRRQVASLAAELRALGVRPGDRVSGYLPNIPQAVVALLATAAVGGVWTSCAPDFG 181
           +++ +LR +VA+    LR+LGV  GDRV    PN PQ +VA LA A++G VW+SC+PDFG
Sbjct: 127 LSYGDLRARVAAARGALRSLGVGKGDRVVALAPNCPQTLVAFLAAASLGAVWSSCSPDFG 186

Query: 182 ARSVLDRFQQVEPVVLFTVDGYRYGGKEHDRRDTVAELRRELPTLRAVIHIPLLGTEAPD 241
            R+V DRF Q+EP VL  V+GYRY G+  D R TV ELR +LP L A + +   G     
Sbjct: 187 VRAVSDRFTQIEPKVLIAVNGYRYNGRSFDIRPTVEELRSKLPRLAATVLVGYEGGGTIP 246

Query: 242 GTLDWETLTAADAEPV--YEQVPFDHPLWVLYSSGTTGLPKAIVQSQGGILVEHLKQLGL 299
           GTLDWE L A  A     +E V FDHPLWVLYSSGTTGLPK IVQ  GGI+VEHLK L L
Sbjct: 247 GTLDWEALLAGHAGTALEFEPVEFDHPLWVLYSSGTTGLPKGIVQGHGGIIVEHLKILAL 306

Query: 300 HCDLGPGDRFFWYTSTGWMMWNFLVSGLLTGTTIVLYDGSPGFPATDAQWRIAERTGATL 359
           HCDLGPG+RFFW+T+TGWMMWNFLVSGLL GTTIVLYDGSP  P  +  WR+A++   T 
Sbjct: 307 HCDLGPGERFFWFTTTGWMMWNFLVSGLLVGTTIVLYDGSPAHPDLNTLWRLAQKHEVTY 366

Query: 360 FGTSAAYVMACRKAGVHPARDLDLSAIQCVATTGSPLPPDGFRWLHDEFAAGGADLWIAS 419
           FGTSA +V +C K  + PA + DLSA++ + +TG+PL  +GFRW+ +E    G  + I S
Sbjct: 367 FGTSAPFVQSCLKQRLRPAAEFDLSAMRALGSTGAPLSVEGFRWIAEEI---GEHVQICS 423

Query: 420 VSGGTDVCSCFAGAVPTLPVHIGELQAPGLGTDLQSWDPSGDPLTDEVGELVVTNPMPSM 479
           VSGGTD+C+ F GA P +PV +GEL    LG  ++++D +GDP+ D+VGEL++T PMPSM
Sbjct: 424 VSGGTDLCTAFVGASPDVPVWLGELSCRCLGAAVEAYDEAGDPVVDQVGELIITKPMPSM 483

Query: 480 PIRFWNDPDGSRYHDSYFDTYPGVWRHGDWITLTSRGSVVIHGRSDSTLNRQGVRMGSAD 539
           P+ FWNDPDG+R  ++YF+ YPG WRHGDWI +T RGS VI+GRSDSTLNR GVRMG+A+
Sbjct: 484 PVAFWNDPDGTRLREAYFEDYPGKWRHGDWIKITDRGSAVIYGRSDSTLNRGGVRMGTAE 543

Query: 540 IYEAVERLPEIRESLVIGIEQPDGGYWMPLFVHLAPGATLDDALLDRIKRTIRVNLSPRH 599
            Y  VE   E+ +SLVI     D G  +  F+ LA  A L+D +   ++  +R  LSPRH
Sbjct: 544 FYRVVEGFDEVLDSLVIDTSAGDEGQLL-CFLVLAQRAKLED-VEPTLRAELRKELSPRH 601

Query: 600 VPDEVIEVPGIPHTLTGKRIEVPVKRLLQGTPLDKAVNPGSIDNLDLL 647
           VPD  I V  +P TL GK+ EVPVK++L G   ++AV+  ++ N D L
Sbjct: 602 VPDRFIVVEQVPRTLNGKKCEVPVKKILSGVAPERAVSKDALANPDSL 649


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: 1511
Number of extensions: 80
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: 659
Length adjustment: 38
Effective length of query: 620
Effective length of database: 621
Effective search space:   385020
Effective search space used:   385020
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_009152103.1 SACMADRAFT_RS01985 (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.1063915.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.8e-247  808.6   0.0   2.3e-247  808.2   0.0    1.0  1  NCBI__GCF_000244955.1:WP_009152103.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000244955.1:WP_009152103.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  808.2   0.0  2.3e-247  2.3e-247       3     644 ..       8     652 ..       6     658 .. 0.97

  Alignments for each domain:
  == domain 1  score: 808.2 bits;  conditional E-value: 2.3e-247
                             TIGR01217   3 eqvlwepdaervkdarlarfraavgerfGaalgdydalyrwsvdeldafwkavwefsdvvfssaekevvddsk 75 
                                           ++vlw+p +e+v+++r++ fr + g +     gdy +l+++sv++l+ fw+av e+ +v+ +++ +ev+ + +
  NCBI__GCF_000244955.1:WP_009152103.1   8 PEVLWRPTSEQVERTRIEDFRRWLGANRDVHAGDYHELWSYSVRDLSGFWSAVAEYLGVRWHQQPAEVLSGME 80 
                                           689********************************************************************** PP

                             TIGR01217  76 mlaarffpgarlnyaenllr.......kkgsedallyvdeekesakvtfeelrrqvaslaaalralGvkkGdr 141
                                           m++ar+f g +lnyae++l        k+++++a++++ e+    ++++ +lr++va    alr+lGv+kGdr
  NCBI__GCF_000244955.1:WP_009152103.1  81 MPGARWFAGGTLNYAEHALSggvagaaKADNDPAVVFQREDGAEERLSYGDLRARVAAARGALRSLGVGKGDR 153
                                           ******************9644333336677****************************************** PP

                             TIGR01217 142 vagylpnipeavaallatasvGaiwsscspdfGargvldrfsqiepkllfsvdgyvynGkehdrrekvrevak 214
                                           v+++ pn p++++a+la+as+Ga+wsscspdfG+r+v drf+qiepk+l++v+gy+ynG+  d r +v+e++ 
  NCBI__GCF_000244955.1:WP_009152103.1 154 VVALAPNCPQTLVAFLAAASLGAVWSSCSPDFGVRAVSDRFTQIEPKVLIAVNGYRYNGRSFDIRPTVEELRS 226
                                           ************************************************************************* PP

                             TIGR01217 215 elpdlravvlipyvgdreklapkvegaltledllaaaqaaelvfeqlpfdhplyilfssGttGvpkaivhsaG 287
                                           +lp l+a+vl+ y g       +++g+l++e lla+   + l+fe + fdhpl++l+ssGttG+pk iv+  G
  NCBI__GCF_000244955.1:WP_009152103.1 227 KLPRLAATVLVGYEG-----GGTIPGTLDWEALLAGHAGTALEFEPVEFDHPLWVLYSSGTTGLPKGIVQGHG 294
                                           *************99.....5679************999********************************** PP

                             TIGR01217 288 GtlvqhlkehvlhcdltdgdrllyyttvGwmmwnflvsglatGatlvlydGsplvpatnvlfdlaeregitvl 360
                                           G++v+hlk ++lhcdl++g+r++++tt+Gwmmwnflvsgl++G+t+vlydGsp  p+ n l++la++  +t +
  NCBI__GCF_000244955.1:WP_009152103.1 295 GIIVEHLKILALHCDLGPGERFFWFTTTGWMMWNFLVSGLLVGTTIVLYDGSPAHPDLNTLWRLAQKHEVTYF 367
                                           ************************************************************************* PP

                             TIGR01217 361 GtsakyvsavrkkglkparthdlsalrlvastGsplkpegfeyvyeeikadvllasisGGtdivscfvganps 433
                                           Gtsa +v+ + k+ l+pa ++dlsa+r++ stG+pl+ egf+++ eei   v+++s+sGGtd+++ fvga p 
  NCBI__GCF_000244955.1:WP_009152103.1 368 GTSAPFVQSCLKQRLRPAAEFDLSAMRALGSTGAPLSVEGFRWIAEEIGEHVQICSVSGGTDLCTAFVGASPD 440
                                           ************************************************************************* PP

                             TIGR01217 434 lpvykGeiqapglGlaveawdeeGkpvtgekGelvvtkplpsmpvrfwndedGskyrkayfdkypgvwahGdy 506
                                           +pv+ Ge+ ++ lG avea+de G+pv +++Gel++tkp+psmpv fwnd+dG++ r+ayf+ ypg w+hGd+
  NCBI__GCF_000244955.1:WP_009152103.1 441 VPVWLGELSCRCLGAAVEAYDEAGDPVVDQVGELIITKPMPSMPVAFWNDPDGTRLREAYFEDYPGKWRHGDW 513
                                           ************************************************************************* PP

                             TIGR01217 507 ieltprGgivihGrsdatlnpnGvrlGsaeiynaverldeveeslvigqeqedgeervvlfvklasGatldea 579
                                           i++t rG+ vi+Grsd+tln++Gvr+G+ae y +ve +dev +slvi     d e ++  f+ la+ a+l+ +
  NCBI__GCF_000244955.1:WP_009152103.1 514 IKITDRGSAVIYGRSDSTLNRGGVRMGTAEFYRVVEGFDEVLDSLVIDTSAGD-EGQLLCFLVLAQRAKLE-D 584
                                           ****************************************************9.888999*********96.5 PP

                             TIGR01217 580 lvkeikdairaglsprhvpskiievagiprtlsGkkvevavkdvvaGkpve...nkgalsnpealdly 644
                                           +   ++  +r +lsprhvp++ i v+++prtl+Gkk ev+vk+++ G + e    k+al+np++l  +
  NCBI__GCF_000244955.1:WP_009152103.1 585 VEPTLRAELRKELSPRHVPDRFIVVEQVPRTLNGKKCEVPVKKILSGVAPEravSKDALANPDSLTPF 652
                                           7899*******************************************988878899********9755 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (652 nodes)
Target sequences:                          1  (659 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 29.68
//
[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