Alignments for a candidate for acs in Desulfallas geothermicus DSM 3669

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Desulfallas geothermicus DSM 3669

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_092484191.1 BM299_RS11405 acetate--CoA ligase

Query= SwissProt::Q8ZKF6
         (652 letters)



>NCBI__GCF_900115975.1:WP_092484191.1
          Length = 660

 Score =  775 bits (2001), Expect = 0.0
 Identities = 369/652 (56%), Positives = 482/652 (73%), Gaps = 8/652 (1%)

Query: 1   MSQTHKHAIPANIADRCLINP-EQYETKYKQSINDPDTFWGEQGKI-LDWITPYQKVKNT 58
           M++      P + +++  +   EQ +  Y++S+ +P+ FW E  +  ++W   +  V+  
Sbjct: 13  MAENRVFEPPKDFSEKARVKSREQRDELYRKSVEEPEAFWAEMAEENIEWFKKWDSVEEY 72

Query: 59  SFAPGNVSIKWYEDGTLNLAANCLDRHLQE-NGDRTAIIWEGDDTSQSKHISYRELHRDV 117
           SF   ++ I+++    LN++ NCLDRHL+    ++ A+IW+G+   +SK  +Y +LHR+V
Sbjct: 73  SFTD-DIYIRYFNGAQLNVSYNCLDRHLKTWRKNKAALIWQGEPLEESKTYTYAQLHREV 131

Query: 118 CRFANTLLDLGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIID 177
            +FAN L  LG+K+GD V IY+PM+PE A+AMLAC RIGA+HS++FGGFSP+A+  RI+D
Sbjct: 132 SKFANVLKGLGVKRGDRVTIYLPMIPELAIAMLACTRIGAIHSIVFGGFSPDALRDRILD 191

Query: 178 SSSRLVITADEGVRAGRSIPLKKNVDDALKN-PNVTSVEHVIVLKRTGSDIDWQEGRDLW 236
           + +  +IT + G RAG+ +  K N D AL+  PN+   ++ +V+KR   D +   GRDLW
Sbjct: 192 AKAETLITCNYGYRAGKVLKSKDNADKALEGCPNI---KNCVVVKRIDQDCNMVAGRDLW 248

Query: 237 WRDLIEKASPEHQPEAMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAATTFKYVFDYH 296
           W DL+  AS E +PE M +EDPLFILYTSGSTGKPKGV+HTTGGYL Y  TTFKY+FDY 
Sbjct: 249 WHDLMAGASQECEPERMESEDPLFILYTSGSTGKPKGVMHTTGGYLTYVTTTFKYIFDYR 308

Query: 297 PGDIYWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMCQVVDKHQVNILYT 356
             DIYWCTAD+GWVTGHSY++YGPL+ GAT+LMFEGVPN+P P R  +VV+K+ VNI YT
Sbjct: 309 DEDIYWCTADIGWVTGHSYIVYGPLSAGATSLMFEGVPNYPQPDRFWEVVEKYGVNIFYT 368

Query: 357 APTAIRALMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGKEKCPVVDTWWQT 416
           APTAIRA+M +G+K   G +  SLR+LG+VGEPINPEAW WY + IGKE CP+VDTWWQT
Sbjct: 369 APTAIRAMMRDGEKWPNGRNLESLRLLGTVGEPINPEAWMWYHRVIGKESCPIVDTWWQT 428

Query: 417 ETGGFMITPLPGAIELKAGSATRPFFGVQPALVDNEGHPQEGATEGNLVITDSWPGQART 476
           ETGG +ITPLPGAI  K GSAT PFFGV P ++  +G   +    G LV+T  WPG  R 
Sbjct: 429 ETGGILITPLPGAIPTKPGSATLPFFGVNPKVIRQDGSESDPNEGGYLVMTKPWPGIMRG 488

Query: 477 LFGDHERFEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESAL 536
           +FGD ERF+ TYF  +   YF+GDGARRDEDGY+W+ GRVDDV+NVSGHRLGTAE+ES L
Sbjct: 489 VFGDPERFKNTYFVQYPGYYFTGDGARRDEDGYFWLMGRVDDVINVSGHRLGTAEVESVL 548

Query: 537 VAHPKIAEAAVVGIPHAIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVL 596
           VAHPK+AEAAVVG PH IKG+ IYAYVTL  G E + +L  E+   VRKEIGP+ATPD +
Sbjct: 549 VAHPKVAEAAVVGYPHDIKGEGIYAYVTLKEGFEDTDDLKKELVMHVRKEIGPIATPDKI 608

Query: 597 HWTDSLPKTRSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEKQAI 648
           H++  LPKTRSGKIMRRILRK+AAG+  +LGDTSTLADP VV+ L++ +  +
Sbjct: 609 HFSVGLPKTRSGKIMRRILRKVAAGEIESLGDTSTLADPTVVDNLIKGRPQV 660


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: 1410
Number of extensions: 68
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: 660
Length adjustment: 38
Effective length of query: 614
Effective length of database: 622
Effective search space:   381908
Effective search space used:   381908
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_092484191.1 BM299_RS11405 (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.9222.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 1022.7   0.0          0 1022.5   0.0    1.0  1  lcl|NCBI__GCF_900115975.1:WP_092484191.1  BM299_RS11405 acetate--CoA ligas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900115975.1:WP_092484191.1  BM299_RS11405 acetate--CoA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1022.5   0.0         0         0       2     628 ..      32     655 ..      31     656 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1022.5 bits;  conditional E-value: 0
                                 TIGR02188   2 aeleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep..kvkWfedgelnvsyncvdrhve 68 
                                               ++ e+  ely++++e+pe+fwa++a+e++ew+k++++v + s+++   +++f++++lnvsync+drh++
  lcl|NCBI__GCF_900115975.1:WP_092484191.1  32 KSREQRDELYRKSVEEPEAFWAEMAEENIEWFKKWDSVEEYSFTDdiYIRYFNGAQLNVSYNCLDRHLK 100
                                               5778999***********************************9997789******************** PP

                                 TIGR02188  69 k.rkdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaR 136
                                               + rk+k+a+iw g+ + e+s+++tYa+l+rev+++anvlk lGvk+gdrv+iYlpmipe++iamlac+R
  lcl|NCBI__GCF_900115975.1:WP_092484191.1 101 TwRKNKAALIWQGE-PLEESKTYTYAQLHREVSKFANVLKGLGVKRGDRVTIYLPMIPELAIAMLACTR 168
                                               **************.5567************************************************** PP

                                 TIGR02188 137 iGavhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtg 205
                                               iGa+hs+vf+Gfs++al++Ri da+a+++it + g+R gkv++ k+++d+ale ++ ++++++vvkr++
  lcl|NCBI__GCF_900115975.1:WP_092484191.1 169 IGAIHSIVFGGFSPDALRDRILDAKAETLITCNYGYRAGKVLKSKDNADKALEGCP-NIKNCVVVKRID 236
                                               *******************************************************9.6*********** PP

                                 TIGR02188 206 eevaewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvky 274
                                               ++  +++ grD+ww++l++ +as+ecepe+++sedplfiLYtsGstGkPkGv+httgGyl+++++t+ky
  lcl|NCBI__GCF_900115975.1:WP_092484191.1 237 QD-CNMVAGRDLWWHDLMA-GASQECEPERMESEDPLFILYTSGSTGKPKGVMHTTGGYLTYVTTTFKY 303
                                               **.55**************.6************************************************ PP

                                 TIGR02188 275 vfdikdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPta 343
                                               +fd++dedi+wCtaD+GWvtGhsYivygPL++Gat+l+fegvp+yp+++rfwev+eky+v+ifYtaPta
  lcl|NCBI__GCF_900115975.1:WP_092484191.1 304 IFDYRDEDIYWCTADIGWVTGHSYIVYGPLSAGATSLMFEGVPNYPQPDRFWEVVEKYGVNIFYTAPTA 372
                                               ********************************************************************* PP

                                 TIGR02188 344 iRalmklgeelvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgv 412
                                               iRa+m+ ge++++ ++l+slr+lg+vGepinpeaw+Wy++v+Gke+cpivdtwWqtetGgilitplpg 
  lcl|NCBI__GCF_900115975.1:WP_092484191.1 373 IRAMMRDGEKWPNGRNLESLRLLGTVGEPINPEAWMWYHRVIGKESCPIVDTWWQTETGGILITPLPG- 440
                                               ********************************************************************. PP

                                 TIGR02188 413 atelkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkgly 481
                                               a+++kpgsatlP+fG++++v+ ++g+e +++e+ g+Lv++kpwP+++r+++gd+erf +tYf +++g+y
  lcl|NCBI__GCF_900115975.1:WP_092484191.1 441 AIPTKPGSATLPFFGVNPKVIRQDGSESDPNEG-GYLVMTKPWPGIMRGVFGDPERFKNTYFVQYPGYY 508
                                               6*****************************999.8********************************** PP

                                 TIGR02188 482 ftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvl 550
                                               ftGDgarrd+dGy+w++GRvDdvinvsGhrlgtae+es lv+h++vaeaavvg+p++ikge i+a+v+l
  lcl|NCBI__GCF_900115975.1:WP_092484191.1 509 FTGDGARRDEDGYFWLMGRVDDVINVSGHRLGTAEVESVLVAHPKVAEAAVVGYPHDIKGEGIYAYVTL 577
                                               ********************************************************************* PP

                                 TIGR02188 551 kegveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaege.ellgdvstle 618
                                               keg e ++ +l+kel ++vrkeigpia+pdki++   lPktRsGkimRR+lrk+a+ge e+lgd+stl+
  lcl|NCBI__GCF_900115975.1:WP_092484191.1 578 KEGFEDTD-DLKKELVMHVRKEIGPIATPDKIHFSVGLPKTRSGKIMRRILRKVAAGEiESLGDTSTLA 645
                                               *****999.5*********************************************************** PP

                                 TIGR02188 619 dpsvveelke 628
                                               dp+vv++l++
  lcl|NCBI__GCF_900115975.1:WP_092484191.1 646 DPTVVDNLIK 655
                                               ******9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (660 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: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 8.35
//
[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