GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Marinobacter adhaerens HP15

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate GFF832 HP15_811 acetyl-CoA synthetase

Query= SwissProt::Q8ZKF6
         (652 letters)



>FitnessBrowser__Marino:GFF832
          Length = 649

 Score =  968 bits (2502), Expect = 0.0
 Identities = 455/643 (70%), Positives = 535/643 (83%), Gaps = 1/643 (0%)

Query: 1   MSQTHKHAIPANIADRCLINPEQYETKYKQSINDPDTFWGEQGKILDWITPYQKVKNTSF 60
           M+    + +   +A + L+N EQYE  Y+QS+ DPDTFWGE GK L+WI PY KVKNT++
Sbjct: 1   MTGKQVYPVSPEVAKQALLNREQYEEMYRQSVEDPDTFWGEHGKRLEWIKPYTKVKNTTY 60

Query: 61  APGNVSIKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDTSQSKHISYRELHRDVCRF 120
              N+SIKW+EDG LN +ANCLDRHL++ GD+TAII+EGDD + S++++YRELH +  +F
Sbjct: 61  DYNNLSIKWFEDGQLNASANCLDRHLEKRGDQTAIIFEGDDPADSRNVTYRELHEETSKF 120

Query: 121 ANTLLDLGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSSS 180
           AN L  LG+KKGDVV IYMPM+ E AVAMLACARIGA+HSV+FGGFSPEA+  RI++  S
Sbjct: 121 ANVLKGLGVKKGDVVTIYMPMIVETAVAMLACARIGAIHSVVFGGFSPEALGARIVNGKS 180

Query: 181 RLVITADEGVRAGRSIPLKKNVDDALKNPNVTSVEHVIVLKRTG-SDIDWQEGRDLWWRD 239
           R V+TADEGVR GR IPLKKNVD ALKN +  +VE V+V+ RTG S++ W E RD  + D
Sbjct: 181 RFVVTADEGVRGGRKIPLKKNVDAALKNEDAANVEKVVVVTRTGNSEVPWNEARDERYED 240

Query: 240 LIEKASPEHQPEAMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAATTFKYVFDYHPGD 299
           L++ AS + QPE MNAEDPLF+LYTSGSTG PKGVLHTTGGY+VYA+ T +YVFDYH GD
Sbjct: 241 LMKSASADCQPEPMNAEDPLFMLYTSGSTGAPKGVLHTTGGYMVYASMTHEYVFDYHEGD 300

Query: 300 IYWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMCQVVDKHQVNILYTAPT 359
           +YWCTAD GWVTGHSY+LYGPLA GA T++FEGVPN+P  +RM QVVDKH+VNILYTAPT
Sbjct: 301 VYWCTADFGWVTGHSYILYGPLANGAITVLFEGVPNYPDSSRMGQVVDKHKVNILYTAPT 360

Query: 360 AIRALMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGKEKCPVVDTWWQTETG 419
           AIRALMAEG+  + GT R SL++LGSVGEPINPEAWEWY + IG  KCP+VDTWWQTETG
Sbjct: 361 AIRALMAEGESCMNGTTRESLKLLGSVGEPINPEAWEWYHRVIGNSKCPIVDTWWQTETG 420

Query: 420 GFMITPLPGAIELKAGSATRPFFGVQPALVDNEGHPQEGATEGNLVITDSWPGQARTLFG 479
           G +I+PLPGAI+LK GSAT PFFGVQPALVDN+G+  EG TEGNLVI DSWPGQ RT++G
Sbjct: 421 GILISPLPGAIDLKPGSATVPFFGVQPALVDNDGNILEGKTEGNLVILDSWPGQMRTIYG 480

Query: 480 DHERFEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAH 539
           DHERF QTYFST+K MYF+GDGARRDEDGYYWITGRVDDVLNVSGHRLGTAE+ESALV+H
Sbjct: 481 DHERFAQTYFSTYKGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEVESALVSH 540

Query: 540 PKIAEAAVVGIPHAIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWT 599
            K+AEAAVVG PH IKGQ IY YVTL HG+EPS EL  E+  WVRKEIGP+A+PDV+ W 
Sbjct: 541 EKVAEAAVVGYPHDIKGQGIYVYVTLVHGQEPSDELKKELVQWVRKEIGPIASPDVIQWA 600

Query: 600 DSLPKTRSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLL 642
             LPKTRSGKIMRRILRKIAA +   LGDTSTLADPGVV+ L+
Sbjct: 601 PGLPKTRSGKIMRRILRKIAANEHDQLGDTSTLADPGVVDDLI 643


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: 1485
Number of extensions: 64
Number of successful extensions: 2
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: 649
Length adjustment: 38
Effective length of query: 614
Effective length of database: 611
Effective search space:   375154
Effective search space used:   375154
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 GFF832 HP15_811 (acetyl-CoA synthetase)
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.3588.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
          0 1029.2   0.0          0 1029.0   0.0    1.0  1  lcl|FitnessBrowser__Marino:GFF832  HP15_811 acetyl-CoA synthetase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF832  HP15_811 acetyl-CoA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1029.0   0.0         0         0       3     627 ..      20     643 ..      18     645 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1029.0 bits;  conditional E-value: 0
                          TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdkva 75 
                                        + e+y+e+y++++edp++fw++++k +lew+kp++kv++++ +    ++kWfedg+ln+s+nc+drh+ekr d++a
  lcl|FitnessBrowser__Marino:GFF832  20 NREQYEEMYRQSVEDPDTFWGEHGK-RLEWIKPYTKVKNTTYDYnnlSIKWFEDGQLNASANCLDRHLEKRGDQTA 94 
                                        679**********************.5***********9986655579**************************** PP

                          TIGR02188  76 iiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsae 151
                                        ii+egd++  dsr++tY+el++e++++anvlk lGvkkgd v+iY+pmi+e+++amlacaRiGa+hsvvf+Gfs+e
  lcl|FitnessBrowser__Marino:GFF832  95 IIFEGDDPA-DSRNVTYRELHEETSKFANVLKGLGVKKGDVVTIYMPMIVETAVAMLACARIGAIHSVVFGGFSPE 169
                                        ********9.5***************************************************************** PP

                          TIGR02188 152 alaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDvwweelveke 226
                                        al  Riv+ ++++v+tadeg+Rgg++i+lkk+vd+al+++++ +vekv+vv rtg++ ++w+e rD  +e+l+++ 
  lcl|FitnessBrowser__Marino:GFF832 170 ALGARIVNGKSRFVVTADEGVRGGRKIPLKKNVDAALKNEDAaNVEKVVVVTRTGNSEVPWNEARDERYEDLMKS- 244
                                        ***************************************9999*************99****************6. PP

                          TIGR02188 227 asaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivyg 302
                                        asa+c+pe++++edplf+LYtsGstG PkGvlhttgGy+++a++t++yvfd++++d++wCtaD GWvtGhsYi+yg
  lcl|FitnessBrowser__Marino:GFF832 245 ASADCQPEPMNAEDPLFMLYTSGSTGAPKGVLHTTGGYMVYASMTHEYVFDYHEGDVYWCTADFGWVTGHSYILYG 320
                                        **************************************************************************** PP

                          TIGR02188 303 PLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpeaw 378
                                        PLanGa t+lfegvp+ypd+sr+ +v++k+kv+i+YtaPtaiRalm++ge+ ++ + ++sl++lgsvGepinpeaw
  lcl|FitnessBrowser__Marino:GFF832 321 PLANGAITVLFEGVPNYPDSSRMGQVVDKHKVNILYTAPTAIRALMAEGESCMNGTTRESLKLLGSVGEPINPEAW 396
                                        **************************************************************************** PP

                          TIGR02188 379 eWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkp 454
                                        eWy++v+G++kcpivdtwWqtetGgili+plpg a++lkpgsat+P+fG+++++vd++g+ +e ++e g Lvi ++
  lcl|FitnessBrowser__Marino:GFF832 397 EWYHRVIGNSKCPIVDTWWQTETGGILISPLPG-AIDLKPGSATVPFFGVQPALVDNDGNILEGKTE-GNLVILDS 470
                                        *********************************.6****************************8777.79****** PP

                          TIGR02188 455 wPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaea 530
                                        wP+++rtiygd+erf +tYf+++kg+yftGDgarrd+dGy+wi+GRvDdv+nvsGhrlgtae+esalvshe+vaea
  lcl|FitnessBrowser__Marino:GFF832 471 WPGQMRTIYGDHERFAQTYFSTYKGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEVESALVSHEKVAEA 546
                                        **************************************************************************** PP

                          TIGR02188 531 avvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiae 606
                                        avvg+p++ikg+ i+++v+l +g+e+++e l+kel ++vrkeigpia+pd i++++ lPktRsGkimRR+lrkia+
  lcl|FitnessBrowser__Marino:GFF832 547 AVVGYPHDIKGQGIYVYVTLVHGQEPSDE-LKKELVQWVRKEIGPIASPDVIQWAPGLPKTRSGKIMRRILRKIAA 621
                                        ****************************5.********************************************** PP

                          TIGR02188 607 ge.ellgdvstledpsvveelk 627
                                        +e ++lgd+stl+dp vv++l+
  lcl|FitnessBrowser__Marino:GFF832 622 NEhDQLGDTSTLADPGVVDDLI 643
                                        **9****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (649 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 12.19
//
[ok]

This GapMind analysis is from Sep 17 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