GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Arenitalea lutea P7-3-5

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_019387228.1 P735_RS0106600 acetate--CoA ligase

Query= SwissProt::Q8ZKF6
         (652 letters)



>NCBI__GCF_000283015.1:WP_019387228.1
          Length = 635

 Score =  690 bits (1780), Expect = 0.0
 Identities = 343/627 (54%), Positives = 447/627 (71%), Gaps = 9/627 (1%)

Query: 22  EQYETKYKQSINDPDTFWGEQGKI-LDWITPYQKVKNTSFAPGNVSIKWYEDGTLNLAAN 80
           E+Y   Y++S+ +P+TFW E  +    W   +  V +  F    V  KW+E   LN+  N
Sbjct: 10  EEYYQVYRKSVRNPETFWEEIAEEHFMWRKKWDNVLSWDFTKPEV--KWFEGAKLNITEN 67

Query: 81  CLDRHLQENGDRTAIIWEGDDTSQ-SKHISYRELHRDVCRFANTLLDLGIKKGDVVAIYM 139
           C+DRHL   GD+TAII+E +   + ++HISYRELH  VCRFAN L + G+ KGD V IY+
Sbjct: 68  CIDRHLYTRGDKTAIIFEPNSPEEKAQHISYRELHEKVCRFANVLKNNGVGKGDRVCIYL 127

Query: 140 PMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSSSRLVITADEGVRAGRSIPLK 199
           PM+PE AV++LACARIGA+HSV+F GFS  A+A RI D   ++VIT+D   R  ++I LK
Sbjct: 128 PMIPELAVSVLACARIGAIHSVVFAGFSSTALATRINDCDCKMVITSDGSYRGSKTIDLK 187

Query: 200 KNVDDALKNPNVTSVEHVIVLKRTGSDIDWQEGRDLWWRDLIEKASPEHQPEAMNAEDPL 259
             VDDAL++     V+ V+V KR  S+I+ +  RD W + L+++A  + +PE M+AEDPL
Sbjct: 188 GIVDDALED--CPGVDTVLVAKRINSEINMKADRDKWLQPLLDEAHHDCEPEIMDAEDPL 245

Query: 260 FILYTSGSTGKPKGVLHTTGGYLVYAATTFKYVFDYHPGDIYWCTADVGWVTGHSYLLYG 319
           FILYTSGSTGKPKG++H+T GY+VY A TFK VF Y   D+YWCTAD+GW+TGHSY++YG
Sbjct: 246 FILYTSGSTGKPKGMVHSTAGYMVYTAYTFKNVFQYREQDVYWCTADIGWITGHSYIVYG 305

Query: 320 PLACGATTLMFEGVPNWPTPARMCQVVDKHQVNILYTAPTAIRALMAEGDKAIEGTDRSS 379
           PL  GATT+MFEGVP++P   R  ++V KH+VN  YTAPTAIRAL  EG + +E  D SS
Sbjct: 306 PLCNGATTVMFEGVPSYPDFGRFWEIVAKHKVNQFYTAPTAIRALAKEGVEHLEKHDLSS 365

Query: 380 LRILGSVGEPINPEAWEWYWKKIGKEKCPVVDTWWQTETGGFMITPLPGAIELKAGSATR 439
           L++LG+VGEPIN EAW WY   +GK+K P+VDTWWQTETGG MITP+  A   K   AT 
Sbjct: 366 LKVLGTVGEPINEEAWHWYDDNVGKKKSPIVDTWWQTETGGIMITPIAFATPTKPTYATL 425

Query: 440 PFFGVQPALVDNEGHPQEG-ATEGNLVITDSWPGQARTLFGDHERFEQTYFSTFKNMYFS 498
           PF GVQPAL+D  G   +G   +G L I   WP  ART++G+H+R++ TYFS ++N YF+
Sbjct: 426 PFIGVQPALMDEHGQEIKGNQVDGRLCIKFPWPSMARTIWGNHQRYKDTYFSAYENKYFT 485

Query: 499 GDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAVVGIPHAIKGQA 558
           GDGA RDE GYY ITGRVDDV+ VSGH LGTA IE A+  HP +AE+A+VG PH IKG A
Sbjct: 486 GDGALRDEVGYYRITGRVDDVIIVSGHNLGTAPIEDAINEHPAVAESAIVGFPHDIKGNA 545

Query: 559 IYAYVTLNHGEEPSP--ELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRSGKIMRRILR 616
           +Y YVTL    E      L  E+   + ++IGP+A  D + +T+ LPKTRSGKIMRRILR
Sbjct: 546 LYGYVTLKETGESRDHNNLRKEINQIITEQIGPIAKLDKIQFTNGLPKTRSGKIMRRILR 605

Query: 617 KIAAGDTSNLGDTSTLADPGVVEKLLE 643
           KIA+ +TSNLGDTSTL +P VV+++++
Sbjct: 606 KIASNETSNLGDTSTLLNPEVVQEIMD 632


Lambda     K      H
   0.317    0.135    0.423 

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: 1281
Number of extensions: 61
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_019387228.1 P735_RS0106600 (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.2849018.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.3e-297  974.1   0.4   1.5e-297  973.9   0.4    1.0  1  NCBI__GCF_000283015.1:WP_019387228.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000283015.1:WP_019387228.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  973.9   0.4  1.5e-297  1.5e-297       2     628 ..       7     632 ..       6     633 .. 0.98

  Alignments for each domain:
  == domain 1  score: 973.9 bits;  conditional E-value: 1.5e-297
                             TIGR02188   2 aeleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep.kvkWfedgelnvsyncvdrhvekrkdk 73 
                                           ++leey ++y++++++pe+fw++ a+e++ w k++++vl++++++ +vkWfe+++ln++ nc+drh+ +r dk
  NCBI__GCF_000283015.1:WP_019387228.1   7 KHLEEYYQVYRKSVRNPETFWEEIAEEHFMWRKKWDNVLSWDFTKpEVKWFEGAKLNITENCIDRHLYTRGDK 79 
                                           6899**************************************9988*************************** PP

                             TIGR02188  74 vaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfa 146
                                           +aii+e ++++e++++++Y+el+++vcr+anvlk+ Gv kgdrv+iYlpmipe+++ +lacaRiGa+hsvvfa
  NCBI__GCF_000283015.1:WP_019387228.1  80 TAIIFEPNSPEEKAQHISYRELHEKVCRFANVLKNNGVGKGDRVCIYLPMIPELAVSVLACARIGAIHSVVFA 152
                                           ************************************************************************* PP

                             TIGR02188 147 GfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvww 219
                                           Gfs+ ala+Ri+d+++k+vit+d+++Rg k+i+lk ivd+ale+++  v++vlv kr+++e++ +k +rD+w+
  NCBI__GCF_000283015.1:WP_019387228.1 153 GFSSTALATRINDCDCKMVITSDGSYRGSKTIDLKGIVDDALEDCP-GVDTVLVAKRINSEIN-MKADRDKWL 223
                                           *********************************************9.6*************66.********* PP

                             TIGR02188 220 eelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGW 292
                                           + l+++ a+++cepe +d+edplfiLYtsGstGkPkG++h+t+Gy++++a+t+k vf+++++d++wCtaD+GW
  NCBI__GCF_000283015.1:WP_019387228.1 224 QPLLDE-AHHDCEPEIMDAEDPLFILYTSGSTGKPKGMVHSTAGYMVYTAYTFKNVFQYREQDVYWCTADIGW 295
                                           *****6.****************************************************************** PP

                             TIGR02188 293 vtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrv 365
                                           +tGhsYivygPL+nGatt++fegvp+ypd +rfwe++ k+kv++fYtaPtaiRal k+g e+++khdlssl+v
  NCBI__GCF_000283015.1:WP_019387228.1 296 ITGHSYIVYGPLCNGATTVMFEGVPSYPDFGRFWEIVAKHKVNQFYTAPTAIRALAKEGVEHLEKHDLSSLKV 368
                                           ************************************************************************* PP

                             TIGR02188 366 lgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegk 438
                                           lg+vGepin eaw+Wy ++vGk+k+pivdtwWqtetGgi+itp++  at++kp  atlP++G++++++de+g+
  NCBI__GCF_000283015.1:WP_019387228.1 369 LGTVGEPINEEAWHWYDDNVGKKKSPIVDTWWQTETGGIMITPIAF-ATPTKPTYATLPFIGVQPALMDEHGQ 440
                                           *********************************************9.6************************* PP

                             TIGR02188 439 eveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhr 511
                                           e++ ++ +g L+ik pwPsm+rti+g+++r+ +tYf+++++ yftGDga rd+ Gy+ i+GRvDdvi vsGh+
  NCBI__GCF_000283015.1:WP_019387228.1 441 EIKGNQVDGRLCIKFPWPSMARTIWGNHQRYKDTYFSAYENKYFTGDGALRDEVGYYRITGRVDDVIIVSGHN 513
                                           ***88888***************************************************************** PP

                             TIGR02188 512 lgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegve.edeeelekelkklvrkeigpiakpdkil 583
                                           lgta ie+a+ +h+avae+a+vg+p++ikg+a++ +v+lke+ e  d+++l+ke++++++++igpiak dki+
  NCBI__GCF_000283015.1:WP_019387228.1 514 LGTAPIEDAINEHPAVAESAIVGFPHDIKGNALYGYVTLKETGEsRDHNNLRKEINQIITEQIGPIAKLDKIQ 586
                                           ****************************************9877245569*********************** PP

                             TIGR02188 584 vveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
                                           +++ lPktRsGkimRR+lrkia++e ++lgd+stl +p+vv+e+++
  NCBI__GCF_000283015.1:WP_019387228.1 587 FTNGLPKTRSGKIMRRILRKIASNEtSNLGDTSTLLNPEVVQEIMD 632
                                           *************************99****************976 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 22.81
//
[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