Alignments for a candidate for acs in Croceitalea dokdonensis DOKDO 023

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Croceitalea dokdonensis DOKDO 023

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_054557960.1 I595_RS03385 acetate--CoA ligase

Query= SwissProt::P27550
         (652 letters)



>NCBI__GCF_001306415.1:WP_054557960.1
          Length = 635

 Score =  680 bits (1754), Expect = 0.0
 Identities = 339/628 (53%), Positives = 438/628 (69%), Gaps = 9/628 (1%)

Query: 22  QQYEAMYQQSINVPDTFWGEQGKI-LDWIKPYQKVKNTSFAPGNVSIKWYEDGTLNLAAN 80
           ++Y  +Y++S+  P+ FW E  +    W K +  V    F+   V  KW+    LN+  N
Sbjct: 10  EEYYQVYRKSVRHPENFWEEIAEEHFVWRKKWNSVLEWDFSKPEV--KWFNGAQLNITEN 67

Query: 81  CLDRHLQENGDRTAIIWEGDD-ASQSKHISYKELHRDVCRFANTLLELGIKKGDVVAIYM 139
           C+DRHL   G +TAI++E ++   +++HI+YKELH  VC+ AN L E GIKKGD V IY+
Sbjct: 68  CIDRHLHIRGHKTAILFEPNNPGEEARHITYKELHEQVCKMANVLSEKGIKKGDRVIIYL 127

Query: 140 PMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITSDEGVRAGRSIPLK 199
           PM+PE A+++LACARIGAVHSV+F GFS  A++ R+ D  +++VITSD   R  ++I LK
Sbjct: 128 PMIPELAISLLACARIGAVHSVVFAGFSSTALSTRVNDCGAKMVITSDGSFRGAKTIDLK 187

Query: 200 KNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVEQASDQHQAEEMNAEDPL 259
             VD+ALK      V+ V+V KR    I  + GRD W   L++ A   +  E M AEDPL
Sbjct: 188 GIVDEALKE--CPEVKTVLVAKRIHSDISMKAGRDEWLAPLMDAAYGDYPPEIMEAEDPL 245

Query: 260 FILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTADVGWVTGHSYLLYG 319
           F+LYTSGSTGKPKG+LHTTGGY+VY A TFK VF Y   D+YWCTAD+GW+TGHSY++YG
Sbjct: 246 FVLYTSGSTGKPKGMLHTTGGYMVYTAYTFKNVFQYREDDVYWCTADIGWITGHSYIVYG 305

Query: 320 PLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMAEGDKAIEGTDRSS 379
           PLA GATT+MFEGVP++P   R  ++VDKH+V   YTAPTAIRAL  E    +   D SS
Sbjct: 306 PLANGATTVMFEGVPSYPDFGRFWEIVDKHKVTQFYTAPTAIRALAKENLDFVTTYDLSS 365

Query: 380 LRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITPLPGATELKAGSATR 439
           L++LG+VGEPIN EAW WY   +G +KCP+VDTWWQTETGG +I+P+P +T  K   AT 
Sbjct: 366 LKVLGTVGEPINEEAWHWYNDHVGEKKCPIVDTWWQTETGGILISPIPFSTPTKPTYATL 425

Query: 440 PFFGVQPALVDNEGNPLEG-ATEGSLVITDSWPGQARTLFGDHERFEQTYFSTFKNMYFS 498
           P  GVQPAL+D  G  + G   +G L I   WP  ART++GDH+R++ TYF+ FKNMYF+
Sbjct: 426 PLPGVQPALMDENGQEITGNQVDGRLCIKFPWPSMARTIWGDHKRYKDTYFTAFKNMYFT 485

Query: 499 GDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAVVGIPHNIKGQA 558
           GDGA RDE GYY ITGRVDDV+ VSGH LGTA IE A+  HP +AE+AVVG PH+IKG A
Sbjct: 486 GDGALRDEVGYYRITGRVDDVIIVSGHNLGTAPIEDAINEHPAVAESAVVGFPHDIKGNA 545

Query: 559 IYAYVTLNHGEE--PSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRSGKIMRRILR 616
           +Y YV L    E      L  E+   + + IGP+A  + + + + LPKTRSGKIMRRILR
Sbjct: 546 LYGYVMLKETGESRDRDNLKKEINQMITEHIGPIAKLNKIQFVNGLPKTRSGKIMRRILR 605

Query: 617 KIAAGDTSNLGDTSTLADPGVVEKLLEE 644
           KIA+ DTSNLGDTSTL +P VV ++++E
Sbjct: 606 KIASKDTSNLGDTSTLLNPEVVSEIIKE 633


Lambda     K      H
   0.317    0.135    0.421 

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: 1260
Number of extensions: 64
Number of successful extensions: 6
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: 652
Length of database: 635
Length adjustment: 38
Effective length of query: 614
Effective length of database: 597
Effective search space:   366558
Effective search space used:   366558
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)

Align candidate WP_054557960.1 I595_RS03385 (acetate--CoA ligase)
to HMM TIGR02188 (acs: acetate--CoA ligase (EC 6.2.1.1))

# 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/TIGR02188.hmm
# target sequence database:        /tmp/gapView.3723585.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02188  [M=629]
Accession:   TIGR02188
Description: Ac_CoA_lig_AcsA: acetate--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-295  967.1   0.1   2.1e-295  966.9   0.1    1.0  1  NCBI__GCF_001306415.1:WP_054557960.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001306415.1:WP_054557960.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  966.9   0.1  2.1e-295  2.1e-295       2     628 ..       7     632 ..       6     633 .. 0.98

  Alignments for each domain:
  == domain 1  score: 966.9 bits;  conditional E-value: 2.1e-295
                             TIGR02188   2 aeleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep.kvkWfedgelnvsyncvdrhvekrkdk 73 
                                           ++leey ++y++++++pe+fw++ a+e++ w k++++vl++++++ +vkWf++++ln++ nc+drh++ r +k
  NCBI__GCF_001306415.1:WP_054557960.1   7 KHLEEYYQVYRKSVRHPENFWEEIAEEHFVWRKKWNSVLEWDFSKpEVKWFNGAQLNITENCIDRHLHIRGHK 79 
                                           6899**************************************9988*************************** PP

                             TIGR02188  74 vaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfa 146
                                           +ai +e +++ge++r++tY+el+++vc++anvl e G+kkgdrv+iYlpmipe++i +lacaRiGavhsvvfa
  NCBI__GCF_001306415.1:WP_054557960.1  80 TAILFEPNNPGEEARHITYKELHEQVCKMANVLSEKGIKKGDRVIIYLPMIPELAISLLACARIGAVHSVVFA 152
                                           ************************************************************************* PP

                             TIGR02188 147 GfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvww 219
                                           Gfs+ al +R++d+ ak+vit+d+++Rg k+i+lk ivdeal++++ +v++vlv kr+ ++++ +k grD w+
  NCBI__GCF_001306415.1:WP_054557960.1 153 GFSSTALSTRVNDCGAKMVITSDGSFRGAKTIDLKGIVDEALKECP-EVKTVLVAKRIHSDIS-MKAGRDEWL 223
                                           *********************************************9.7*************76.********* PP

                             TIGR02188 220 eelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGW 292
                                             l++  a  + +pe +++edplf+LYtsGstGkPkG+lhttgGy++++a+t+k vf+++++d++wCtaD+GW
  NCBI__GCF_001306415.1:WP_054557960.1 224 APLMDA-AYGDYPPEIMEAEDPLFVLYTSGSTGKPKGMLHTTGGYMVYTAYTFKNVFQYREDDVYWCTADIGW 295
                                           *****6.9999************************************************************** PP

                             TIGR02188 293 vtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrv 365
                                           +tGhsYivygPLanGatt++fegvp+ypd +rfwe+++k+kvt+fYtaPtaiRal k+  ++v+ +dlssl+v
  NCBI__GCF_001306415.1:WP_054557960.1 296 ITGHSYIVYGPLANGATTVMFEGVPSYPDFGRFWEIVDKHKVTQFYTAPTAIRALAKENLDFVTTYDLSSLKV 368
                                           ************************************************************************* PP

                             TIGR02188 366 lgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegk 438
                                           lg+vGepin eaw+Wy+++vG++kcpivdtwWqtetGgili+p+p   t++kp  atlPl+G++++++de+g+
  NCBI__GCF_001306415.1:WP_054557960.1 369 LGTVGEPINEEAWHWYNDHVGEKKCPIVDTWWQTETGGILISPIPF-STPTKPTYATLPLPGVQPALMDENGQ 440
                                           **********************************************.6************************* PP

                             TIGR02188 439 eveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhr 511
                                           e++ ++ +g L+ik pwPsm+rti+gd++r+ +tYf+++k++yftGDga rd+ Gy+ i+GRvDdvi vsGh+
  NCBI__GCF_001306415.1:WP_054557960.1 441 EITGNQVDGRLCIKFPWPSMARTIWGDHKRYKDTYFTAFKNMYFTGDGALRDEVGYYRITGRVDDVIIVSGHN 513
                                           ***88888***************************************************************** PP

                             TIGR02188 512 lgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedee.elekelkklvrkeigpiakpdkil 583
                                           lgta ie+a+ +h+avae+avvg+p++ikg+a++ +v+lke+ e+ ++ +l+ke++++++++igpiak +ki+
  NCBI__GCF_001306415.1:WP_054557960.1 514 LGTAPIEDAINEHPAVAESAVVGFPHDIKGNALYGYVMLKETGESRDRdNLKKEINQMITEHIGPIAKLNKIQ 586
                                           ****************************************9877554449*********************** PP

                             TIGR02188 584 vveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
                                           +v+ lPktRsGkimRR+lrkia+++ ++lgd+stl +p+vv e+++
  NCBI__GCF_001306415.1:WP_054557960.1 587 FVNGLPKTRSGKIMRRILRKIASKDtSNLGDTSTLLNPEVVSEIIK 632
                                           ***********************9999****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (635 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: 21.12
//
[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