Alignments for a candidate for acs in Saccharomonospora marina XMU15

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Saccharomonospora marina XMU15

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_009156574.1 SACMADRAFT_RS24615 acetate--CoA ligase

Query= SwissProt::P9WQD1
         (651 letters)



>NCBI__GCF_000244955.1:WP_009156574.1
          Length = 659

 Score =  895 bits (2312), Expect = 0.0
 Identities = 438/657 (66%), Positives = 513/657 (78%), Gaps = 19/657 (2%)

Query: 1   MSESTPEV------SSSYPPPAHFAEHANARAELYREAEEDRLAFWAKQANRLSWTTPFT 54
           M+E +P +      S ++PP   FA  ANA  E Y EAE+DR AFWA+QA RL W T ++
Sbjct: 1   MTEQSPALDNLLTESRTFPPSEEFAARANATPEWYAEAEQDREAFWARQAERLHWDTRWS 60

Query: 55  EVLDWSGAPFAKWFVGGELNVAYNCVDRHVEAGHGDRVAIHWEGEPVGDRRTLTYSDLLA 114
           +VLDWS APFAKWFVGG+LNVAYNCVDRHVEAGHGD+VAIHW GEP GD R +TY+ L  
Sbjct: 61  QVLDWSQAPFAKWFVGGKLNVAYNCVDRHVEAGHGDQVAIHWVGEP-GDTRDITYAQLKD 119

Query: 115 EVSKAANALTDLGLVAGDRVAIYLPLIPEAVIAMLACARLGIMHSVVFGGFTAAALQARI 174
           EV KAANALT LG+ A DRVAI L +IPEA++AMLACAR+G MHSVVFGGF+  AL++R+
Sbjct: 120 EVCKAANALTSLGVTANDRVAIQLQMIPEAIVAMLACARIGAMHSVVFGGFSPTALRSRV 179

Query: 175 VDAQAKLLITADGQFRRGKPSPLKAAADEALAAIPDCSVEHVLVVRRTGIEMAWSEGRDL 234
            DAQAK++IT+DGQ+RRGK +P+KA  DEALA     SVE V+VVRRTG ++ W++ RDL
Sbjct: 180 DDAQAKVVITSDGQYRRGKAAPMKANVDEALAGAE--SVEKVVVVRRTGDDVPWTQERDL 237

Query: 235 WWHHVVGSASPAHTPEPFDSEHPLFLLYTSGTTGKPKGIMHTSGGYLTQCCYTMRTIFDV 294
           WWH +V      HTP+ FDSEHPL++LYTSGTTGKPKGI+HTSGGYL    YT   +FD 
Sbjct: 238 WWHELVDPQPAEHTPQAFDSEHPLYILYTSGTTGKPKGILHTSGGYLAHVAYTHHAVFDH 297

Query: 295 KPDSDVFWCTADIGWVTGHTYGVYGPLCNGVTEVLYEGTPDTPDRHRHFQIIEKYGVTIY 354
           KP  DV+WCTADIGWVTGH+Y VYGPL N VT+V+YEGTP+TP   RH++II+KY V+IY
Sbjct: 298 KPGEDVYWCTADIGWVTGHSYIVYGPLANRVTQVVYEGTPNTPHEGRHWEIIQKYKVSIY 357

Query: 355 YTAPTLIRMFMKWGREIPDSHDLSSLRLLGSVGEPINPEAWRWYRDVIGGGRTPLVDTWW 414
           YTAPTLIR FMKWG EIP  +DLSSLR+LGSVGEPINPEAW WYR+ IGG R P+VDTWW
Sbjct: 358 YTAPTLIRTFMKWGNEIPAKYDLSSLRVLGSVGEPINPEAWMWYREHIGGNRCPVVDTWW 417

Query: 415 QTETGSAMISPLPGIAAAKPGSAMTPLPGISAKIVDDHGDPLPPHTEGAQHVTGYLVLDQ 474
           QTETG  MISPLPG+  AKPGSA  PLPGISAK+VDD G      TE  +   GYLVLD+
Sbjct: 418 QTETGGIMISPLPGVTHAKPGSAQRPLPGISAKVVDDTG------TEVGKGGGGYLVLDK 471

Query: 475 PWPSMLRGIWGDPARYWHSYWSKFSDKGYYFAGDGARIDPDGAIWVLGRIDDVMNVSGHR 534
           PWP MLRGIWGD  RY  +YWS+F+++G+YFAGDGA+ D DG IW+LGR+DDVMNVSGHR
Sbjct: 472 PWPGMLRGIWGDDERYKETYWSRFAEQGFYFAGDGAKYDADGDIWLLGRVDDVMNVSGHR 531

Query: 535 ISTAEVESALVAHSGVAEAAVVGVTDETTTQAICAFVVLRANYAPHDRTAEE----LRTE 590
           IST EVESALV+H  VAEAAVVG TD TT Q I AFV+LR   A  +    E    LR  
Sbjct: 532 ISTTEVESALVSHPTVAEAAVVGATDPTTGQGIVAFVILRGGVAEDEAGGTEAIQALRNH 591

Query: 591 VARVISPIARPRDVHVVPELPKTRSGKIMRRLLRDVAENRELGDTSTLLDPTVFDAI 647
           VA+ I PIA+PR + VVPELPKTRSGKIMRRLLRDVAENRE+GD +TL D +V D I
Sbjct: 592 VAKEIGPIAKPRQIMVVPELPKTRSGKIMRRLLRDVAENREIGDVTTLADSSVMDLI 648


Lambda     K      H
   0.319    0.136    0.433 

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: 1529
Number of extensions: 77
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: 651
Length of database: 659
Length adjustment: 38
Effective length of query: 613
Effective length of database: 621
Effective search space:   380673
Effective search space used:   380673
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (25.4 bits)

Align candidate WP_009156574.1 SACMADRAFT_RS24615 (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.3916673.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.1e-296  971.1   1.0   1.3e-296  970.9   1.0    1.0  1  NCBI__GCF_000244955.1:WP_009156574.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000244955.1:WP_009156574.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  970.9   1.0  1.3e-296  1.3e-296       4     627 ..      28     649 ..      25     651 .. 0.97

  Alignments for each domain:
  == domain 1  score: 970.9 bits;  conditional E-value: 1.3e-296
                             TIGR02188   4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.rkdkva 75 
                                           +++  e+y+ea++d+e+fwa++a+ +l+w++ +++vld+s++p++kWf++g+lnv+yncvdrhve+ + d+va
  NCBI__GCF_000244955.1:WP_009156574.1  28 ANATPEWYAEAEQDREAFWARQAE-RLHWDTRWSQVLDWSQAPFAKWFVGGKLNVAYNCVDRHVEAgHGDQVA 99 
                                           5677899****************9.5*********************************************** PP

                             TIGR02188  76 iiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGf 148
                                           i+w g+ +g d+r +tYa+l++evc++an+l++lGv   drvai l mipea++amlacaRiGa+hsvvf+Gf
  NCBI__GCF_000244955.1:WP_009156574.1 100 IHWVGE-PG-DTRDITYAQLKDEVCKAANALTSLGVTANDRVAIQLQMIPEAIVAMLACARIGAMHSVVFGGF 170
                                           *****9.77.59************************************************************* PP

                             TIGR02188 149 saealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwwee 221
                                           s+ al++R+ da+ak+vit+d+++R+gk+ ++k++vdeal+ ae svekv+vv+rtg++v  w+++rD+ww+e
  NCBI__GCF_000244955.1:WP_009156574.1 171 SPTALRSRVDDAQAKVVITSDGQYRRGKAAPMKANVDEALAGAE-SVEKVVVVRRTGDDVP-WTQERDLWWHE 241
                                           *****************************************998.8*************66.*********** PP

                             TIGR02188 222 lvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikd.edifwCtaDvGWv 293
                                           lv+  ++ae++p+++dse+pl+iLYtsG+tGkPkG+lht+gGyl ++a+t++ vfd+k+ ed++wCtaD+GWv
  NCBI__GCF_000244955.1:WP_009156574.1 242 LVD-PQPAEHTPQAFDSEHPLYILYTSGTTGKPKGILHTSGGYLAHVAYTHHAVFDHKPgEDVYWCTADIGWV 313
                                           ***.6*****************************************************6379*********** PP

                             TIGR02188 294 tGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvl 366
                                           tGhsYivygPLan +t++++eg+p++p+++r+we+i+kykv+i+YtaPt+iR++mk+g+e+++k+dlsslrvl
  NCBI__GCF_000244955.1:WP_009156574.1 314 TGHSYIVYGPLANRVTQVVYEGTPNTPHEGRHWEIIQKYKVSIYYTAPTLIRTFMKWGNEIPAKYDLSSLRVL 386
                                           ************************************************************************* PP

                             TIGR02188 367 gsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegke 439
                                           gsvGepinpeaw+Wy+e++G ++cp+vdtwWqtetGgi+i+plpg +t++kpgsa++Pl+Gi+a+vvd++g+e
  NCBI__GCF_000244955.1:WP_009156574.1 387 GSVGEPINPEAWMWYREHIGGNRCPVVDTWWQTETGGIMISPLPG-VTHAKPGSAQRPLPGISAKVVDDTGTE 458
                                           *********************************************.5************************** PP

                             TIGR02188 440 veeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkg..lyftGDgarrdkdGyiwilGRvDdvinvsGh 510
                                           v ++ + g+Lv++kpwP+mlr+i+gd+er+ etY++++ +  +yf+GDga+ d+dG+iw+lGRvDdv+nvsGh
  NCBI__GCF_000244955.1:WP_009156574.1 459 VGKGGG-GYLVLDKPWPGMLRGIWGDDERYKETYWSRFAEqgFYFAGDGAKYDADGDIWLLGRVDDVMNVSGH 530
                                           **9988.8*****************************98777******************************* PP

                             TIGR02188 511 rlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedee...elekelkklvrkeigpiakpd 580
                                           r++t+e+esalvsh++vaeaavvg++d ++g+ ivafv+l+ gv+ede    e  + l+++v+keigpiakp+
  NCBI__GCF_000244955.1:WP_009156574.1 531 RISTTEVESALVSHPTVAEAAVVGATDPTTGQGIVAFVILRGGVAEDEAggtEAIQALRNHVAKEIGPIAKPR 603
                                           ********************************************999988888999***************** PP

                             TIGR02188 581 kilvveelPktRsGkimRRllrkiaegeellgdvstledpsvveelk 627
                                           +i+vv+elPktRsGkimRRllr++ae++e+ gdv+tl+d+sv++ ++
  NCBI__GCF_000244955.1:WP_009156574.1 604 QIMVVPELPKTRSGKIMRRLLRDVAENREI-GDVTTLADSSVMDLIS 649
                                           **************************8876.5**********99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (659 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: 28.28
//
[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