Alignments for a candidate for acs in Erythrobacter gangjinensis K7-2

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Erythrobacter gangjinensis K7-2

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_047005978.1 AAW01_RS03860 acetate--CoA ligase

Query= SwissProt::Q8ZKF6
         (652 letters)



>NCBI__GCF_001010925.1:WP_047005978.1
          Length = 642

 Score =  834 bits (2154), Expect = 0.0
 Identities = 402/629 (63%), Positives = 491/629 (78%), Gaps = 9/629 (1%)

Query: 21  PEQYETKYKQSINDPDTFWGEQGKI-LDWITPYQKVKNTSFAPGNVSIKWYEDGTLNLAA 79
           PEQY+  Y++S+ DPD FW EQ K  LDW T   K    S+ P  V IKW+ DGTLN+  
Sbjct: 18  PEQYDALYERSVQDPDGFWLEQAKERLDWYTAPTKGAEWSYDP--VDIKWFSDGTLNICY 75

Query: 80  NCLDRHLQENGDRTAIIWEGDDT-SQSKHISYRELHRDVCRFANTLLDLGIKKGDVVAIY 138
           N +DRHL  +GD+ A+I+E D   +  + ++YR+LH++V R AN L  +G++KGD V +Y
Sbjct: 76  NAVDRHLDTHGDQIALIFEPDSPDAPGRSLTYRQLHKEVTRVANALKAMGVRKGDRVTLY 135

Query: 139 MPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSSSRLVITADEGVRAGRSIPL 198
           MPM+ E A+ MLACARIGA+HSV+FGGFSPEA+AGRI+   SR V+ AD+G+R  +++PL
Sbjct: 136 MPMIVEGALTMLACARIGAIHSVVFGGFSPEALAGRIMACESRFVVCADQGLRGSKTVPL 195

Query: 199 KKNVDDALKNPNVTSVEHVIVLKRTGSDIDWQEGRDLWWRDLIEKASPEHQP-EAMNAED 257
           K NVD AL    V SV+ V+V   TG +I+  +GRD W+ D    AS +  P E MNAED
Sbjct: 196 KANVDAALAMQGV-SVDGVLVFDHTGGEIEMVDGRDHWFADF---ASDDECPCEEMNAED 251

Query: 258 PLFILYTSGSTGKPKGVLHTTGGYLVYAATTFKYVFDYHPGDIYWCTADVGWVTGHSYLL 317
           PLFILYTSGSTG PKGVLHTTGGY ++AATTF Y FDY PGDI+WC+AD+GWVTGH+Y+ 
Sbjct: 252 PLFILYTSGSTGTPKGVLHTTGGYALWAATTFHYTFDYQPGDIFWCSADIGWVTGHTYVT 311

Query: 318 YGPLACGATTLMFEGVPNWPTPARMCQVVDKHQVNILYTAPTAIRALMAEGDKAIEGTDR 377
           YGPL    T+L+FEGVPN+P   R   V+DKH+VN+ YTAPTAIRALM EGD  +   + 
Sbjct: 312 YGPLINAGTSLIFEGVPNYPDHGRFWDVIDKHKVNLFYTAPTAIRALMREGDSFVTSRNL 371

Query: 378 SSLRILGSVGEPINPEAWEWYWKKIGKEKCPVVDTWWQTETGGFMITPLPGAIELKAGSA 437
           SSLR+LG+VGEPINPEAW WY++ +GK+ CP+VDTWWQTETGG MIT LP A ++K GSA
Sbjct: 372 SSLRVLGTVGEPINPEAWRWYYEVVGKKNCPIVDTWWQTETGGHMITTLPYAHDMKPGSA 431

Query: 438 TRPFFGVQPALVDNEGHPQEGATEGNLVITDSWPGQARTLFGDHERFEQTYFSTFKNMYF 497
            +PFFG+QP LVDN+G+  EGATEGNL IT SWPGQART++GDH+RFEQ YFST+   YF
Sbjct: 432 GKPFFGIQPLLVDNDGNTLEGATEGNLCITHSWPGQARTVYGDHDRFEQAYFSTYPGRYF 491

Query: 498 SGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAVVGIPHAIKGQ 557
           +GDG RRDEDGYYWITGRVDDV+NVSGHR+GTAE+ESALV HPK+AEAAVVG PH IKGQ
Sbjct: 492 TGDGCRRDEDGYYWITGRVDDVINVSGHRMGTAEVESALVLHPKVAEAAVVGYPHDIKGQ 551

Query: 558 AIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRSGKIMRRILRK 617
            IY YVTLN GEE S ELY+E+R  VRKEIGP+ATPD L +TD LPKTRSGKIMRRILRK
Sbjct: 552 GIYCYVTLNAGEEGSDELYSELRQHVRKEIGPIATPDHLQFTDGLPKTRSGKIMRRILRK 611

Query: 618 IAAGDTSNLGDTSTLADPGVVEKLLEEKQ 646
           IA  D  +LGDTSTLADP +V++L+E +Q
Sbjct: 612 IAENDYGSLGDTSTLADPSLVDRLIEGRQ 640


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: 1481
Number of extensions: 74
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: 642
Length adjustment: 38
Effective length of query: 614
Effective length of database: 604
Effective search space:   370856
Effective search space used:   370856
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_047005978.1 AAW01_RS03860 (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.2836529.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.9e-301  985.2   0.0   6.9e-301  985.0   0.0    1.0  1  NCBI__GCF_001010925.1:WP_047005978.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001010925.1:WP_047005978.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  985.0   0.0  6.9e-301  6.9e-301       4     628 ..      18     637 ..      15     638 .. 0.99

  Alignments for each domain:
  == domain 1  score: 985.0 bits;  conditional E-value: 6.9e-301
                             TIGR02188   4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslep.kvkWfedgelnvsyncvdrhvekrkdkva 75 
                                            e+y +lye++++dp+ fw ++ake+l+w +  +k  ++s +p ++kWf+dg+ln++yn+vdrh+ ++ d++a
  NCBI__GCF_001010925.1:WP_047005978.1  18 PEQYDALYERSVQDPDGFWLEQAKERLDWYTAPTKGAEWSYDPvDIKWFSDGTLNICYNAVDRHLDTHGDQIA 90 
                                           689***************************************99***************************** PP

                             TIGR02188  76 iiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGf 148
                                           +i+e d+++   r+ltY++l++ev+r+an+lk++Gv+kgdrv++Y+pmi+e +++mlacaRiGa+hsvvf+Gf
  NCBI__GCF_001010925.1:WP_047005978.1  91 LIFEPDSPDAPGRSLTYRQLHKEVTRVANALKAMGVRKGDRVTLYMPMIVEGALTMLACARIGAIHSVVFGGF 163
                                           *********9*************************************************************** PP

                             TIGR02188 149 saealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwwee 221
                                           s+eala Ri+ +e+++v++ad+glRg k+++lk++vd+al+++  sv+ vlv+ +tg e++ +++grD+w+ +
  NCBI__GCF_001010925.1:WP_047005978.1 164 SPEALAGRIMACESRFVVCADQGLRGSKTVPLKANVDAALAMQGVSVDGVLVFDHTGGEIE-MVDGRDHWFAD 235
                                           ***********************************************************66.*********** PP

                             TIGR02188 222 lvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvt 294
                                             ++   +ec++e++++edplfiLYtsGstG+PkGvlhttgGy+l+aa+t++y+fd++++difwC+aD+GWvt
  NCBI__GCF_001010925.1:WP_047005978.1 236 FASD---DECPCEEMNAEDPLFILYTSGSTGTPKGVLHTTGGYALWAATTFHYTFDYQPGDIFWCSADIGWVT 305
                                           9996...9***************************************************************** PP

                             TIGR02188 295 GhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlg 367
                                           Gh+Y+ ygPL+n  t+l+fegvp+ypd++rfw+vi+k+kv+ fYtaPtaiRalm++g+++v++++lsslrvlg
  NCBI__GCF_001010925.1:WP_047005978.1 306 GHTYVTYGPLINAGTSLIFEGVPNYPDHGRFWDVIDKHKVNLFYTAPTAIRALMREGDSFVTSRNLSSLRVLG 378
                                           ************************************************************************* PP

                             TIGR02188 368 svGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkev 440
                                           +vGepinpeaw+WyyevvGk++cpivdtwWqtetGg++it+lp  a ++kpgsa +P+fGi++ +vd++g+++
  NCBI__GCF_001010925.1:WP_047005978.1 379 TVGEPINPEAWRWYYEVVGKKNCPIVDTWWQTETGGHMITTLPY-AHDMKPGSAGKPFFGIQPLLVDNDGNTL 450
                                           ********************************************.6*************************** PP

                             TIGR02188 441 eeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlg 513
                                           e  +e g L+i+++wP+++rt+ygd++rf ++Yf++++g yftGDg+rrd+dGy+wi+GRvDdvinvsGhr+g
  NCBI__GCF_001010925.1:WP_047005978.1 451 EGATE-GNLCITHSWPGQARTVYGDHDRFEQAYFSTYPGRYFTGDGCRRDEDGYYWITGRVDDVINVSGHRMG 522
                                           *8777.79***************************************************************** PP

                             TIGR02188 514 taeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvve 586
                                           tae+esalv h++vaeaavvg+p++ikg+ i+++v+l++g+e ++e l +el+++vrkeigpia+pd++++++
  NCBI__GCF_001010925.1:WP_047005978.1 523 TAEVESALVLHPKVAEAAVVGYPHDIKGQGIYCYVTLNAGEEGSDE-LYSELRQHVRKEIGPIATPDHLQFTD 594
                                           ******************************************9995.************************** PP

                             TIGR02188 587 elPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
                                            lPktRsGkimRR+lrkiae++  +lgd+stl+dps v++l+e
  NCBI__GCF_001010925.1:WP_047005978.1 595 GLPKTRSGKIMRRILRKIAENDyGSLGDTSTLADPSLVDRLIE 637
                                           **********************99***************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (642 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 38.51
//
[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 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