GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Magnetospirillum magneticum AMB-1

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_011386526.1 AMB_RS21140 acetate--CoA ligase

Query= SwissProt::P27550
         (652 letters)



>NCBI__GCF_000009985.1:WP_011386526.1
          Length = 645

 Score =  937 bits (2422), Expect = 0.0
 Identities = 439/646 (67%), Positives = 538/646 (83%), Gaps = 6/646 (0%)

Query: 1   MSQIHKHTIPANIADRCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSF 60
           MS+++   +PA  A   LI+  +Y   Y++S+  PD FWGE GK +DWIKP+ KVKN S+
Sbjct: 1   MSEVYP--VPAETAKNALIDNDKYNEWYERSVKDPDGFWGEHGKRIDWIKPFTKVKNVSY 58

Query: 61  APGNVSIKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRF 120
           + G+VSIKW+EDGTLN++ANCLDRHL +  D+TAIIWEGDD ++S HI+Y +LH  VCR 
Sbjct: 59  S-GDVSIKWFEDGTLNVSANCLDRHLAKRRDQTAIIWEGDDPNESAHITYGDLHERVCRL 117

Query: 121 ANTLLELGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNS 180
           AN + +LG+KKGD V IY+PM+PEAAVAMLACAR+GAVHS++FGGFSP+A+AGRI D +S
Sbjct: 118 ANAMTDLGVKKGDRVTIYLPMIPEAAVAMLACARVGAVHSIVFGGFSPDALAGRIQDCDS 177

Query: 181 RLVITSDEGVRAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDL 240
            L+IT+DEG+R GR +PLK NVD AL+     S + V+V+KRTGG I    GRD W+HDL
Sbjct: 178 SLLITADEGLRGGRKVPLKANVDKALET--CWSCKSVIVVKRTGGDIHMVTGRDHWYHDL 235

Query: 241 VEQASDQHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDI 300
           V +A+  H   EM+AEDPLF+LYTSGSTGKPKGV+HTTGGYLVYA++T +YVFDYH GDI
Sbjct: 236 VAKAAPTHTPVEMSAEDPLFLLYTSGSTGKPKGVVHTTGGYLVYASMTHQYVFDYHEGDI 295

Query: 301 YWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTA 360
           YWCTADVGWVTGHSY++YGPLA GA TLMFEG+PN+PT +R   VVDKH+VNI YTAPTA
Sbjct: 296 YWCTADVGWVTGHSYIVYGPLANGAITLMFEGIPNYPTVSRFWDVVDKHKVNIFYTAPTA 355

Query: 361 IRALMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGG 420
           IR+LM EG++ ++ T R+SLR+LGSVGEPINPEAW WY + +G+ +CP+VDTWWQTETGG
Sbjct: 356 IRSLMREGEEPVKKTSRASLRLLGSVGEPINPEAWTWYHRVVGDGRCPIVDTWWQTETGG 415

Query: 421 FMITPLPGATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITD-SWPGQARTLFG 479
            +ITPLPGAT LK GSATRPFFGV+P +VD EG  LEGA EG+L + +  WPGQ RTL+G
Sbjct: 416 ILITPLPGATALKPGSATRPFFGVKPVMVDAEGKTLEGAVEGNLCLAEPGWPGQMRTLWG 475

Query: 480 DHERFEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAH 539
           DHERF+Q+YF+T++ MYF+GDGARRDEDGYYWITGRVDDV+NVSGHR+GTAE+ESALVAH
Sbjct: 476 DHERFKQSYFATYQGMYFTGDGARRDEDGYYWITGRVDDVINVSGHRMGTAEVESALVAH 535

Query: 540 PKIAEAAVVGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWT 599
           PK+AEAAVVG PH+IKGQ IYAYVTL  GEEPS +L  E+ NWVRKEIGP+A+PD++ W+
Sbjct: 536 PKVAEAAVVGYPHDIKGQGIYAYVTLVAGEEPSEDLRKELVNWVRKEIGPIASPDLIQWS 595

Query: 600 DSLPKTRSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEK 645
             LPKTRSGKIMRRILRKIA  D  +LGDTSTLADPGVV+ L++ +
Sbjct: 596 PGLPKTRSGKIMRRILRKIAENDFGSLGDTSTLADPGVVDDLIDSR 641


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: 1505
Number of extensions: 59
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: 645
Length adjustment: 38
Effective length of query: 614
Effective length of database: 607
Effective search space:   372698
Effective search space used:   372698
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_011386526.1 AMB_RS21140 (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.999.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 1034.0   0.0          0 1033.8   0.0    1.0  1  lcl|NCBI__GCF_000009985.1:WP_011386526.1  AMB_RS21140 acetate--CoA ligase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_011386526.1  AMB_RS21140 acetate--CoA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1033.8   0.0         0         0       3     628 ..      18     639 ..      16     640 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1033.8 bits;  conditional E-value: 0
                                 TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep..kvkWfedgelnvsyncvdrhvek 69 
                                               ++++y+e+ye++++dp+ fw++++k +++w+kpf+kv++ s +   ++kWfedg+lnvs+nc+drh++k
  lcl|NCBI__GCF_000009985.1:WP_011386526.1  18 DNDKYNEWYERSVKDPDGFWGEHGK-RIDWIKPFTKVKNVSYSGdvSIKWFEDGTLNVSANCLDRHLAK 85 
                                               6799*********************.5************99887679********************** PP

                                 TIGR02188  70 rkdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiG 138
                                               r+d++aiiwegd+++e s ++tY +l+++vcrlan++++lGvkkgdrv+iYlpmipea++amlacaR+G
  lcl|NCBI__GCF_000009985.1:WP_011386526.1  86 RRDQTAIIWEGDDPNE-SAHITYGDLHERVCRLANAMTDLGVKKGDRVTIYLPMIPEAAVAMLACARVG 153
                                               **************96.**************************************************** PP

                                 TIGR02188 139 avhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgee 207
                                               avhs+vf+Gfs++ala Ri+d+++ l+itadeglRgg++++lk++vd+ale++  s ++v+vvkrtg +
  lcl|NCBI__GCF_000009985.1:WP_011386526.1 154 AVHSIVFGGFSPDALAGRIQDCDSSLLITADEGLRGGRKVPLKANVDKALETCW-SCKSVIVVKRTGGD 221
                                               *****************************************************8.8************* PP

                                 TIGR02188 208 vaewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvf 276
                                               ++ ++ grD+w+++lv+k a  +++p ++++edplf+LYtsGstGkPkGv+httgGyl++a++t++yvf
  lcl|NCBI__GCF_000009985.1:WP_011386526.1 222 IH-MVTGRDHWYHDLVAK-AAPTHTPVEMSAEDPLFLLYTSGSTGKPKGVVHTTGGYLVYASMTHQYVF 288
                                               77.**************7.99999********************************************* PP

                                 TIGR02188 277 dikdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiR 345
                                               d++++di+wCtaDvGWvtGhsYivygPLanGa tl+feg+p+yp+ srfw+v++k+kv+ifYtaPtaiR
  lcl|NCBI__GCF_000009985.1:WP_011386526.1 289 DYHEGDIYWCTADVGWVTGHSYIVYGPLANGAITLMFEGIPNYPTVSRFWDVVDKHKVNIFYTAPTAIR 357
                                               ********************************************************************* PP

                                 TIGR02188 346 almklgeelvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvat 414
                                               +lm++gee vkk+++ slr+lgsvGepinpeaw+Wy++vvG+++cpivdtwWqtetGgilitplpg at
  lcl|NCBI__GCF_000009985.1:WP_011386526.1 358 SLMREGEEPVKKTSRASLRLLGSVGEPINPEAWTWYHRVVGDGRCPIVDTWWQTETGGILITPLPG-AT 425
                                               ******************************************************************.6* PP

                                 TIGR02188 415 elkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkp.wPsmlrtiygdeerfvetYfkklkglyf 482
                                               +lkpgsat+P+fG+++++vd egk++e   e g L++ +p wP+++rt++gd+erf ++Yf +++g+yf
  lcl|NCBI__GCF_000009985.1:WP_011386526.1 426 ALKPGSATRPFFGVKPVMVDAEGKTLEGAVE-GNLCLAEPgWPGQMRTLWGDHERFKQSYFATYQGMYF 493
                                               ***************************8888.79***9988**************************** PP

                                 TIGR02188 483 tGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlk 551
                                               tGDgarrd+dGy+wi+GRvDdvinvsGhr+gtae+esalv+h++vaeaavvg+p++ikg+ i+a+v+l 
  lcl|NCBI__GCF_000009985.1:WP_011386526.1 494 TGDGARRDEDGYYWITGRVDDVINVSGHRMGTAEVESALVAHPKVAEAAVVGYPHDIKGQGIYAYVTLV 562
                                               ********************************************************************* PP

                                 TIGR02188 552 egveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaege.ellgdvstled 619
                                               +g+e++e+ l+kel ++vrkeigpia+pd i++ + lPktRsGkimRR+lrkiae++  +lgd+stl+d
  lcl|NCBI__GCF_000009985.1:WP_011386526.1 563 AGEEPSED-LRKELVNWVRKEIGPIASPDLIQWSPGLPKTRSGKIMRRILRKIAENDfGSLGDTSTLAD 630
                                               ******95.************************************************************ PP

                                 TIGR02188 620 psvveelke 628
                                               p vv++l++
  lcl|NCBI__GCF_000009985.1:WP_011386526.1 631 PGVVDDLID 639
                                               *****9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (645 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 12.81
//
[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