Alignments for a candidate for aacS in Amycolatopsis halophila YIM 93223

GapMind for catabolism of small carbon sources

Alignments for a candidate for aacS in Amycolatopsis halophila YIM 93223

Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_034268252.1 AMYHA_RS04515 acetoacetate--CoA ligase

Query= BRENDA::D6EQU8
         (658 letters)



>NCBI__GCF_000504245.1:WP_034268252.1
          Length = 674

 Score =  648 bits (1671), Expect = 0.0
 Identities = 335/649 (51%), Positives = 427/649 (65%), Gaps = 15/649 (2%)

Query: 6   PQPLWQPDAQRIAQARITRFQAWAAEHHGAPAEGGYAALHRWSVDELDTFWKAVTEWFDV 65
           P+ LW+P A  +A   I RF+ W  +         Y  L  WSV ELD FW A  E+  V
Sbjct: 12  PEVLWRPAADHVADTAIERFRQWLRDAKDVQVND-YDELWEWSVTELDAFWSAAAEFCGV 70

Query: 66  RF-STPYARVLGDRTMPGAQWFPGATLNYAEHALRA----AGTRPDEPALLYVDETHEPA 120
           R+   P A   G+R MP   WFPG TLNYAEHAL      A  R D+ A+++  E     
Sbjct: 71  RWHERPTAITEGER-MPDVHWFPGGTLNYAEHALSGGVAGAEKRDDDLAVIFHREDGSTE 129

Query: 121 PVTWAELRRQVASLAAELRALGVRPGDRVSGYLPNIPQAVVALLATAAVGGVWTSCAPDF 180
            +T+ +LR QVA+  A L +LGV  GDRV    PN PQ ++A LA A++G VW+SC+PDF
Sbjct: 130 QLTYGQLRSQVAAARAALSSLGVGMGDRVVALAPNCPQTLIAFLAAASLGAVWSSCSPDF 189

Query: 181 GARSVLDRFQQVEPVVLFTVDGYRYGGKEHDRRDTVAELRRELPTLRAVIHIPLLGTEAP 240
           G R++ DRF Q+EP VL  V+GY YGG+  D   TV ELR E+P+L   + I    T   
Sbjct: 190 GVRAIADRFTQIEPKVLVAVNGYMYGGRTFDITGTVRELRAEMPSLAGTVLIDYADTGGV 249

Query: 241 DGTLDWETLTAA-DAEPV-YEQVPFDHPLWVLYSSGTTGLPKAIVQSQGGILVEHLKQLG 298
           D T DW+ L A  D  P+ ++ VPF+HPLWVLYSSGTTGLPK IVQ  GGI +EHLK L 
Sbjct: 250 DDTHDWDALLAQHDGAPLAFDPVPFEHPLWVLYSSGTTGLPKGIVQGHGGITLEHLKSLS 309

Query: 299 LHCDLGPGDRFFWYTSTGWMMWNFLVSGLLTGTTIVLYDGSPGFPATDAQWRIAERTGAT 358
           L  DLGPG+RFFW+T+TGWMMWNFL+SGLL G+T+VLYDGSPG+P   A WR+AE+   T
Sbjct: 310 LQMDLGPGERFFWFTTTGWMMWNFLISGLLVGSTVVLYDGSPGYPDLGALWRLAEQHRIT 369

Query: 359 LFGTSAAYVMACRKAGVHPARDLDLSAIQCVATTGSPLPPDGFRWLHDEFAAG--GADLW 416
            FG SA ++  C K  + P  + DLSA++ V +TG+PL  +GFRW+ DE      G  + 
Sbjct: 370 YFGVSAPFIQQCFKQRLSPTTEHDLSALRAVGSTGAPLSVEGFRWIIDELGRDEHGRPVQ 429

Query: 417 IASVSGGTDVCSCFAGAVPTLPVHIGELQAPGLGTDLQSWDPSGDPLTDEVGELVVTNPM 476
           I SVSGGTDVC+ F GA P +PV +GEL    LG  + ++D  G+ + ++VGELV+T PM
Sbjct: 430 ICSVSGGTDVCTAFVGASPDVPVWLGELSCRALGAAVAAFDEDGNEVVEQVGELVITKPM 489

Query: 477 PSMPIRFWNDPDGSRYHDSYFDTYPGVWRHGDWITLTSRGSVVIHGRSDSTLNRQGVRMG 536
           PSMP+ FWND DG+R   +YF+ YPGVWRHGDWI +TSRGS VI+GRSDSTLNR GVRMG
Sbjct: 490 PSMPVFFWNDADGARLRSAYFEEYPGVWRHGDWIRITSRGSSVIYGRSDSTLNRGGVRMG 549

Query: 537 SADIYEAVERLPEIRESLVIGIEQ--PDGGYWMPLFVHLAPGATLDDALLDRIKRTIRVN 594
           +A+ Y  VE   EI +SLVI   +   D G  +  FV LAPGA+L D   D +++ +R  
Sbjct: 550 TAEFYRVVEGRDEIADSLVIDTTRVGEDEGKLL-CFVVLAPGASLADVEPD-LRKELRSA 607

Query: 595 LSPRHVPDEVIEVPGIPHTLTGKRIEVPVKRLLQGTPLDKAVNPGSIDN 643
           LSPRHVPDE IEV  +P TL GK+ EVPVK++L G   +KAV+  ++ N
Sbjct: 608 LSPRHVPDEFIEVSDVPRTLNGKKCEVPVKKILSGVRPEKAVSADALAN 656


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: 1618
Number of extensions: 88
Number of successful extensions: 7
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: 674
Length adjustment: 38
Effective length of query: 620
Effective length of database: 636
Effective search space:   394320
Effective search space used:   394320
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_034268252.1 AMYHA_RS04515 (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.1485937.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.2e-242  789.9   0.0     1e-241  789.5   0.0    1.0  1  NCBI__GCF_000504245.1:WP_034268252.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000504245.1:WP_034268252.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  789.5   0.0    1e-241    1e-241       3     644 ..      12     663 ..      10     667 .. 0.96

  Alignments for each domain:
  == domain 1  score: 789.5 bits;  conditional E-value: 1e-241
                             TIGR01217   3 eqvlwepdaervkdarlarfraavgerfGaalgdydalyrwsvdeldafwkavwefsdvvfssaekevvddsk 75 
                                           ++vlw+p a+ v+d+ ++rfr++  ++    + dyd+l++wsv+eldafw+a  ef++v+ ++   ++ ++++
  NCBI__GCF_000504245.1:WP_034268252.1  12 PEVLWRPAADHVADTAIERFRQWLRDAKDVQVNDYDELWEWSVTELDAFWSAAAEFCGVRWHERPTAITEGER 84 
                                           789********************************************************************** PP

                             TIGR01217  76 mlaarffpgarlnyaenllrkkgs.......edallyvdeekesakvtfeelrrqvaslaaalralGvkkGdr 141
                                           m++ ++fpg +lnyae++l    +       + a+++  e+  + ++t+ +lr qva   aal +lGv+ Gdr
  NCBI__GCF_000504245.1:WP_034268252.1  85 MPDVHWFPGGTLNYAEHALSGGVAgaekrddDLAVIFHREDGSTEQLTYGQLRSQVAAARAALSSLGVGMGDR 157
                                           ******************97422222445547799************************************** PP

                             TIGR01217 142 vagylpnipeavaallatasvGaiwsscspdfGargvldrfsqiepkllfsvdgyvynGkehdrrekvrevak 214
                                           v+++ pn p+++ a+la+as+Ga+wsscspdfG+r++ drf+qiepk+l++v+gy+y+G+  d + +vre++ 
  NCBI__GCF_000504245.1:WP_034268252.1 158 VVALAPNCPQTLIAFLAAASLGAVWSSCSPDFGVRAIADRFTQIEPKVLVAVNGYMYGGRTFDITGTVRELRA 230
                                           ************************************************************************* PP

                             TIGR01217 215 elpdlravvlipyvgdreklapkvegaltledllaaaqaaelvfeqlpfdhplyilfssGttGvpkaivhsaG 287
                                           e+p+l+ +vli y+         v+++ +++ lla  + a+l f+ +pf+hpl++l+ssGttG+pk iv+  G
  NCBI__GCF_000504245.1:WP_034268252.1 231 EMPSLAGTVLIDYAD-----TGGVDDTHDWDALLAQHDGAPLAFDPVPFEHPLWVLYSSGTTGLPKGIVQGHG 298
                                           *************98.....3457999********************************************** PP

                             TIGR01217 288 GtlvqhlkehvlhcdltdgdrllyyttvGwmmwnflvsglatGatlvlydGsplvpatnvlfdlaeregitvl 360
                                           G+ ++hlk ++l  dl++g+r++++tt+Gwmmwnfl+sgl++G+t+vlydGsp+ p+  +l++lae+ +it +
  NCBI__GCF_000504245.1:WP_034268252.1 299 GITLEHLKSLSLQMDLGPGERFFWFTTTGWMMWNFLISGLLVGSTVVLYDGSPGYPDLGALWRLAEQHRITYF 371
                                           ************************************************************************* PP

                             TIGR01217 361 GtsakyvsavrkkglkparthdlsalrlvastGsplkpegfeyvyeeika.....dvllasisGGtdivscfv 428
                                           G sa +++ + k+ l p+ +hdlsalr+v stG+pl+ egf+++ +e+        v+++s+sGGtd+++ fv
  NCBI__GCF_000504245.1:WP_034268252.1 372 GVSAPFIQQCFKQRLSPTTEHDLSALRAVGSTGAPLSVEGFRWIIDELGRdehgrPVQICSVSGGTDVCTAFV 444
                                           ***********************************************988666667***************** PP

                             TIGR01217 429 ganpslpvykGeiqapglGlaveawdeeGkpvtgekGelvvtkplpsmpvrfwndedGskyrkayfdkypgvw 501
                                           ga p +pv+ Ge+ +++lG av a+de+G+ v +++Gelv+tkp+psmpv fwnd dG++ r+ayf++ypgvw
  NCBI__GCF_000504245.1:WP_034268252.1 445 GASPDVPVWLGELSCRALGAAVAAFDEDGNEVVEQVGELVITKPMPSMPVFFWNDADGARLRSAYFEEYPGVW 517
                                           ************************************************************************* PP

                             TIGR01217 502 ahGdyieltprGgivihGrsdatlnpnGvrlGsaeiynaverldeveeslvigqeqe.dgeervvlfvklasG 573
                                           +hGd+i++t+rG+ vi+Grsd+tln++Gvr+G+ae y +ve  de+++slvi   +  + e ++  fv la+G
  NCBI__GCF_000504245.1:WP_034268252.1 518 RHGDWIRITSRGSSVIYGRSDSTLNRGGVRMGTAEFYRVVEGRDEIADSLVIDTTRVgEDEGKLLCFVVLAPG 590
                                           ****************************************************98764133778999******* PP

                             TIGR01217 574 atldealvkeikdairaglsprhvpskiievagiprtlsGkkvevavkdvvaGkpve...nkgalsnpealdl 643
                                           a l + +  ++++ +r++lsprhvp++ iev+++prtl+Gkk ev+vk+++ G   e     +al+np+al+ 
  NCBI__GCF_000504245.1:WP_034268252.1 591 ASLAD-VEPDLRKELRSALSPRHVPDEFIEVSDVPRTLNGKKCEVPVKKILSGVRPEkavSADALANPKALEP 662
                                           ***86.67889******************************************66554667899*****9985 PP

                             TIGR01217 644 y 644
                                           +
  NCBI__GCF_000504245.1:WP_034268252.1 663 F 663
                                           5 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (652 nodes)
Target sequences:                          1  (674 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: 35.15
//
[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