Alignments for a candidate for acs in Porphyrobacter dokdonensis DSW-74

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Porphyrobacter dokdonensis DSW-74

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_068865627.1 I603_RS12865 acetate--CoA ligase

Query= SwissProt::P27550
         (652 letters)



>NCBI__GCF_001677335.1:WP_068865627.1
          Length = 643

 Score =  846 bits (2185), Expect = 0.0
 Identities = 407/638 (63%), Positives = 496/638 (77%), Gaps = 8/638 (1%)

Query: 11  ANIADRCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSFAPGNVSIKWY 70
           A+    CL  P+QY  MY++SI  PD FW EQ + LDW K   +    S+ P  V I W+
Sbjct: 10  AHTETHCL--PEQYAEMYRRSIETPDAFWLEQAQRLDWFKAPAQGGEWSYDP--VGISWF 65

Query: 71  EDGTLNLAANCLDRHLQENGDRTAIIWEGDD-ASQSKHISYKELHRDVCRFANTLLELGI 129
           EDGTLNL  N +DRHL  N +RTA+I+E DD A+  + ++Y ELHR+V R AN L  +G+
Sbjct: 66  EDGTLNLCHNAVDRHLATNANRTALIFEPDDPAASGRSLTYGELHREVLRMANALKAMGV 125

Query: 130 KKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITSDEG 189
           KKGD V IYMPM+ E   AMLACAR+GAVHSV+FGGFSPEA+A RI D +SR V+T+DEG
Sbjct: 126 KKGDRVTIYMPMIVEGVTAMLACARLGAVHSVVFGGFSPEALASRIEDCDSRFVVTADEG 185

Query: 190 VRAGRSIPLKKNVDDALKNPNV-TSVEHVVVLKRTGGKIDWQEGRDLWWHDLVEQASDQH 248
           +R G+ +PLK NVD AL  P+  T ++ ++V++ TG +I   EGRD W  DL   A    
Sbjct: 186 LRGGKRVPLKANVDAALAEPDHDTPIDGMLVVRHTGAEISMTEGRDYWLDDLATDADCP- 244

Query: 249 QAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTADVG 308
             EEM AEDPLFILYTSGSTGKPKGVLHTTGGY V+ A TF Y+FDY PG+++WCTAD+G
Sbjct: 245 -CEEMAAEDPLFILYTSGSTGKPKGVLHTTGGYGVWTAATFHYIFDYQPGEVFWCTADIG 303

Query: 309 WVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMAEG 368
           WVTGHSY++YGPL  GAT ++FEGVP++P   R   VVDKH+VNILYTAPTAIRALM EG
Sbjct: 304 WVTGHSYIVYGPLINGATEVVFEGVPSFPDHGRFWDVVDKHKVNILYTAPTAIRALMREG 363

Query: 369 DKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITPLPG 428
           D  +    R+SLR+LGSVGEPINPEAW WY+  +G  +CP++DTWWQTETGG MIT LPG
Sbjct: 364 DDYVTTRSRASLRLLGSVGEPINPEAWRWYFDVVGEGRCPIIDTWWQTETGGCMITTLPG 423

Query: 429 ATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGDHERFEQTY 488
           A ++K GSA  PFFG++P LVDNEG  L+GA EG+L IT SWPGQART++GDH+RF QTY
Sbjct: 424 AHDMKPGSAGLPFFGIRPQLVDNEGGVLDGAAEGNLCITHSWPGQARTVYGDHDRFVQTY 483

Query: 489 FSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAVV 548
           FST+   YF+GDG +RD+DGYYWITGRVDDV+NVSGHR+GTAE+ESALV HPK+AE+AVV
Sbjct: 484 FSTYAGKYFTGDGCKRDKDGYYWITGRVDDVINVSGHRMGTAEVESALVLHPKVAESAVV 543

Query: 549 GIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRSG 608
           G PH++KGQ IY YVTLN GE  SPEL AE+R WVRKEIGP+ATPD++ +TD LPKTRSG
Sbjct: 544 GYPHDLKGQGIYCYVTLNAGEAGSPELLAELRAWVRKEIGPIATPDLIQFTDGLPKTRSG 603

Query: 609 KIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEKQ 646
           KIMRRILRKIA  +  +LGDTSTLADP +VE+L+E +Q
Sbjct: 604 KIMRRILRKIAENEFGSLGDTSTLADPSLVERLIEGRQ 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: 1414
Number of extensions: 54
Number of successful extensions: 5
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: 643
Length adjustment: 38
Effective length of query: 614
Effective length of database: 605
Effective search space:   371470
Effective search space used:   371470
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_068865627.1 I603_RS12865 (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.3734159.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   5.5e-300  982.0   0.0    1.0  1  NCBI__GCF_001677335.1:WP_068865627.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001677335.1:WP_068865627.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  982.0   0.0  5.5e-300  5.5e-300       5     628 ..      19     638 ..      16     639 .. 0.98

  Alignments for each domain:
  == domain 1  score: 982.0 bits;  conditional E-value: 5.5e-300
                             TIGR02188   5 eeykelyeeaiedpekfwaklakeelewlkpfekvldeslep.kvkWfedgelnvsyncvdrhvekrkdkvai 76 
                                           e+y+e+y+++ie p++fw ++a+ +l+w+k   +  ++s +p  + Wfedg+ln++ n+vdrh++++++++a+
  NCBI__GCF_001677335.1:WP_068865627.1  19 EQYAEMYRRSIETPDAFWLEQAQ-RLDWFKAPAQGGEWSYDPvGISWFEDGTLNLCHNAVDRHLATNANRTAL 90 
                                           79*********************.5****************999***************************** PP

                             TIGR02188  77 iwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfs 149
                                           i+e d++  + r+ltY el+rev r+an+lk++Gvkkgdrv+iY+pmi+e v amlacaR+Gavhsvvf+Gfs
  NCBI__GCF_001677335.1:WP_068865627.1  91 IFEPDDPAASGRSLTYGELHREVLRMANALKAMGVKKGDRVTIYMPMIVEGVTAMLACARLGAVHSVVFGGFS 163
                                           ************************************************************************* PP

                             TIGR02188 150 aealaeRivdaeaklvitadeglRggkvielkkivdealekaee..svekvlvvkrtgeevaewkegrDvwwe 220
                                           +eala+Ri+d+++++v+tadeglRggk+++lk++vd+al++ ++   ++ +lvv++tg+e++ ++egrD+w++
  NCBI__GCF_001677335.1:WP_068865627.1 164 PEALASRIEDCDSRFVVTADEGLRGGKRVPLKANVDAALAEPDHdtPIDGMLVVRHTGAEIS-MTEGRDYWLD 235
                                           ****************************************9887768*************76.********** PP

                             TIGR02188 221 elvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWv 293
                                           +l ++   a+c++e++ +edplfiLYtsGstGkPkGvlhttgGy +++a+t++y+fd++++++fwCtaD+GWv
  NCBI__GCF_001677335.1:WP_068865627.1 236 DLATD---ADCPCEEMAAEDPLFILYTSGSTGKPKGVLHTTGGYGVWTAATFHYIFDYQPGEVFWCTADIGWV 305
                                           **996...9**************************************************************** PP

                             TIGR02188 294 tGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvl 366
                                           tGhsYivygPL+nGat+++fegvp++pd++rfw+v++k+kv+i+YtaPtaiRalm++g++ v+ +++ slr+l
  NCBI__GCF_001677335.1:WP_068865627.1 306 TGHSYIVYGPLINGATEVVFEGVPSFPDHGRFWDVVDKHKVNILYTAPTAIRALMREGDDYVTTRSRASLRLL 378
                                           ************************************************************************* PP

                             TIGR02188 367 gsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegke 439
                                           gsvGepinpeaw+Wy++vvG+++cpi+dtwWqtetGg +it+lpg a ++kpgsa lP+fGi++++vd+eg  
  NCBI__GCF_001677335.1:WP_068865627.1 379 GSVGEPINPEAWRWYFDVVGEGRCPIIDTWWQTETGGCMITTLPG-AHDMKPGSAGLPFFGIRPQLVDNEGGV 450
                                           *********************************************.6************************** PP

                             TIGR02188 440 veeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrl 512
                                           ++  +e g L+i+++wP+++rt+ygd++rfv+tYf+++ g yftGDg++rdkdGy+wi+GRvDdvinvsGhr+
  NCBI__GCF_001677335.1:WP_068865627.1 451 LDGAAE-GNLCITHSWPGQARTVYGDHDRFVQTYFSTYAGKYFTGDGCKRDKDGYYWITGRVDDVINVSGHRM 522
                                           **8777.79**************************************************************** PP

                             TIGR02188 513 gtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvv 585
                                           gtae+esalv h++vae+avvg+p+++kg+ i+++v+l++g++ + e l +el+++vrkeigpia+pd i+++
  NCBI__GCF_001677335.1:WP_068865627.1 523 GTAEVESALVLHPKVAESAVVGYPHDLKGQGIYCYVTLNAGEAGSPE-LLAELRAWVRKEIGPIATPDLIQFT 594
                                           *******************************************9995.************************* PP

                             TIGR02188 586 eelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
                                           + lPktRsGkimRR+lrkiae+e  +lgd+stl+dps ve+l+e
  NCBI__GCF_001677335.1:WP_068865627.1 595 DGLPKTRSGKIMRRILRKIAENEfGSLGDTSTLADPSLVERLIE 638
                                           ****************************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (643 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 33.63
//
[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:

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 2024 update 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