GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Sphingobium czechense LL01

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_066607468.1 V473_RS15130 acetate--CoA ligase

Query= SwissProt::Q8ZKF6
         (652 letters)



>NCBI__GCF_001046645.1:WP_066607468.1
          Length = 647

 Score =  848 bits (2190), Expect = 0.0
 Identities = 406/642 (63%), Positives = 492/642 (76%), Gaps = 5/642 (0%)

Query: 9   IPANIADRCLINPEQYETKYKQSINDPDTFWGEQGKILDWITPYQKVKNTSFAPGNVSIK 68
           +P + A   L++    +  Y +SI D D +W E+ + LDWIT   K   +SFA G+  +K
Sbjct: 8   VPESWAKGALMDRAARDADYARSIEDSDAYWLERAQRLDWITVPTKCNESSFAEGDFGVK 67

Query: 69  WYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDT-SQSKHISYRELHRDVCRFANTLLDL 127
           W+ DG LN++ANC+DRHL +  D+TAI+WE D   +Q +  SY +LH +VCR AN L   
Sbjct: 68  WFADGVLNVSANCIDRHLAQRADQTAILWEPDSPDAQPRRYSYAQLHEEVCRLANVLKAA 127

Query: 128 GIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSSSRLVITAD 187
           G KKGD + IYMPM+PEAA A+LACARIGAVHSV+FGGFSP+A+AGRI D  S +VITAD
Sbjct: 128 GAKKGDRITIYMPMIPEAAFALLACARIGAVHSVVFGGFSPDALAGRIQDCDSNIVITAD 187

Query: 188 EGVRAGRSIPLKKNVDDALKNPNVTSVEHVIVLKRTGSDIDWQEGRDLWWRDLIEKASPE 247
           EG R G+++PLK NVD AL +    SV+ VIV+K TG  +  Q+GRDLW  +   K SP+
Sbjct: 188 EGRRGGKAVPLKVNVDAALVH--CPSVKKVIVVKATGGTVTMQDGRDLWLHEEAAKTSPD 245

Query: 248 HQPEAMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAATTFKYVFDYHPGDIYWCTADV 307
             PE MNAEDPLFILYTSGSTGKPKGVLHTTGGYL++AA T +  FDY PGDIYWC AD+
Sbjct: 246 CPPEPMNAEDPLFILYTSGSTGKPKGVLHTTGGYLLWAALTHELCFDYRPGDIYWCAADI 305

Query: 308 GWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMCQVVDKHQVNILYTAPTAIRALMAE 367
           GWVTGHSY++YGPLA GATTLM+EGVPNWPTP+R+ +VVD+HQV  ++TAPTA+RALM E
Sbjct: 306 GWVTGHSYIVYGPLANGATTLMYEGVPNWPTPSRIWEVVDRHQVQTIFTAPTALRALMKE 365

Query: 368 GDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGKEKCPVVDTWWQTETGGFMITPLP 427
           GD  +  T R+SLR+LG+VGEPINPEAW WY + +G+ +CP++DTWWQTETGG MI P P
Sbjct: 366 GDGFVHSTSRASLRLLGTVGEPINPEAWRWYHEVVGEGRCPIIDTWWQTETGGAMIAPTP 425

Query: 428 GAIELKAGSATRPFFGVQPALVDNEGHPQEGATEGNLVITDSWPGQARTLFGDHERFEQT 487
           GA +LK GSAT P  GV P +VD EGH  +GA EGNLVI  SWPGQ RT++GDH+RF QT
Sbjct: 426 GATDLKPGSATFPMPGVAPQIVDAEGHVLDGAAEGNLVIAQSWPGQMRTVWGDHDRFFQT 485

Query: 488 YFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAV 547
           YF+TF   Y +GDGARRD DGYYWITGRVDDV+NVSGHR+GTAE+ESALV H  +AEAAV
Sbjct: 486 YFTTFPGKYTTGDGARRDGDGYYWITGRVDDVINVSGHRMGTAEVESALVLHESVAEAAV 545

Query: 548 VGIPHAIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRS 607
           VG PH IKGQ IYAYVTLN GEE + +L   +  WVR EIGP+ATPD + +   LPKTRS
Sbjct: 546 VGFPHDIKGQGIYAYVTLNSGEEATDDLRKTLVKWVRTEIGPIATPDAIQFAPGLPKTRS 605

Query: 608 GKIMRRILRKIAAGDTS--NLGDTSTLADPGVVEKLLEEKQA 647
           GKIMRRILRKIA GD S   LGDTSTLADP VV+ L+  +Q+
Sbjct: 606 GKIMRRILRKIAEGDVSAQALGDTSTLADPSVVDNLIANRQS 647


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: 1468
Number of extensions: 63
Number of successful extensions: 4
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: 647
Length adjustment: 38
Effective length of query: 614
Effective length of database: 609
Effective search space:   373926
Effective search space used:   373926
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_066607468.1 V473_RS15130 (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.2463448.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.4e-300  982.3   0.0     5e-300  982.1   0.0    1.0  1  NCBI__GCF_001046645.1:WP_066607468.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001046645.1:WP_066607468.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  982.1   0.0    5e-300    5e-300       8     628 ..      24     643 ..      17     644 .. 0.98

  Alignments for each domain:
  == domain 1  score: 982.1 bits;  conditional E-value: 5e-300
                             TIGR02188   8 kelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdkvaii 77 
                                            + y+++ied +++w + a+ +l+w++  +k  ++s+++    vkWf+dg lnvs+nc+drh+++r+d++ai 
  NCBI__GCF_001046645.1:WP_066607468.1  24 DADYARSIEDSDAYWLERAQ-RLDWITVPTKCNESSFAEgdfGVKWFADGVLNVSANCIDRHLAQRADQTAIL 95 
                                           566899**************.5***************9988789***************************** PP

                             TIGR02188  78 wegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsa 150
                                           we d+++ + r+++Ya+l++evcrlanvlk++G kkgdr++iY+pmipea++a+lacaRiGavhsvvf+Gfs+
  NCBI__GCF_001046645.1:WP_066607468.1  96 WEPDSPDAQPRRYSYAQLHEEVCRLANVLKAAGAKKGDRITIYMPMIPEAAFALLACARIGAVHSVVFGGFSP 168
                                           ******999**************************************************************** PP

                             TIGR02188 151 ealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwweelv 223
                                           +ala Ri+d+++++vitadeg Rggk+++lk +vd+al +++ sv+kv+vvk tg  v+ +++grD+w++e+ 
  NCBI__GCF_001046645.1:WP_066607468.1 169 DALAGRIQDCDSNIVITADEGRRGGKAVPLKVNVDAALVHCP-SVKKVIVVKATGGTVT-MQDGRDLWLHEEA 239
                                           *****************************************9.7*************76.************* PP

                             TIGR02188 224 ekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGh 296
                                           +k +s +c+pe++++edplfiLYtsGstGkPkGvlhttgGyll+aalt+++ fd++++di+wC+aD+GWvtGh
  NCBI__GCF_001046645.1:WP_066607468.1 240 AK-TSPDCPPEPMNAEDPLFILYTSGSTGKPKGVLHTTGGYLLWAALTHELCFDYRPGDIYWCAADIGWVTGH 311
                                           *7.********************************************************************** PP

                             TIGR02188 297 sYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsv 369
                                           sYivygPLanGattl++egvp++p++sr+wev+++++v++ +taPta+Ralmk+g+ +v+++++ slr+lg+v
  NCBI__GCF_001046645.1:WP_066607468.1 312 SYIVYGPLANGATTLMYEGVPNWPTPSRIWEVVDRHQVQTIFTAPTALRALMKEGDGFVHSTSRASLRLLGTV 384
                                           ************************************************************************* PP

                             TIGR02188 370 GepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkevee 442
                                           Gepinpeaw+Wy+evvG+++cpi+dtwWqtetGg++i+p pg at+lkpgsat P++G+ +++vd eg+ ++ 
  NCBI__GCF_001046645.1:WP_066607468.1 385 GEPINPEAWRWYHEVVGEGRCPIIDTWWQTETGGAMIAPTPG-ATDLKPGSATFPMPGVAPQIVDAEGHVLDG 456
                                           ******************************************.6****************************8 PP

                             TIGR02188 443 eeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgta 515
                                            +e g Lvi ++wP+++rt++gd++rf++tYf++++g y tGDgarrd dGy+wi+GRvDdvinvsGhr+gta
  NCBI__GCF_001046645.1:WP_066607468.1 457 AAE-GNLVIAQSWPGQMRTVWGDHDRFFQTYFTTFPGKYTTGDGARRDGDGYYWITGRVDDVINVSGHRMGTA 528
                                           777.79******************************************************************* PP

                             TIGR02188 516 eiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvveel 588
                                           e+esalv he+vaeaavvg+p++ikg+ i+a+v+l++g+e++++ l+k+l k+vr+eigpia+pd i++++ l
  NCBI__GCF_001046645.1:WP_066607468.1 529 EVESALVLHESVAEAAVVGFPHDIKGQGIYAYVTLNSGEEATDD-LRKTLVKWVRTEIGPIATPDAIQFAPGL 600
                                           ****************************************9995.**************************** PP

                             TIGR02188 589 PktRsGkimRRllrkiaege...ellgdvstledpsvveelke 628
                                           PktRsGkimRR+lrkiaeg+   ++lgd+stl+dpsvv++l++
  NCBI__GCF_001046645.1:WP_066607468.1 601 PKTRSGKIMRRILRKIAEGDvsaQALGDTSTLADPSVVDNLIA 643
                                           ******************98766789*************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (647 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: 00:00:00.03
# Mc/sec: 12.46
//
[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