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.3748945.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: 00:00:00.02
# Mc/sec: 20.49
//
[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:

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:

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:

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:

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