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

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.3631.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: 0.03u 0.02s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 9.17
//
[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:

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