Alignments for a candidate for acs in Streptacidiphilus oryzae TH49

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Streptacidiphilus oryzae TH49

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_037574635.1 BS73_RS20690 acetate--CoA ligase

Query= SwissProt::P9WQD1
         (651 letters)



>NCBI__GCF_000744815.1:WP_037574635.1
          Length = 652

 Score =  858 bits (2217), Expect = 0.0
 Identities = 426/640 (66%), Positives = 495/640 (77%), Gaps = 14/640 (2%)

Query: 12  YPPPAHFAEHANARAELYREAEEDRLAFWAKQANRLSWTTPFTEVLDWSGAPFAKWFVGG 71
           + PP   A  AN  A+ Y  A+EDRLAFWA+QA RLSW    TE LDWS  PFAKWF  G
Sbjct: 16  FAPPRELAAAANVTADAYAHAKEDRLAFWAEQARRLSWEVEPTETLDWSNPPFAKWFQDG 75

Query: 72  ELNVAYNCVDRHVEAGHGDRVAIHWEGEPVGDRRTLTYSDLLAEVSKAANALTDLGLVAG 131
            LNVAYNCVDRHVEAGHGDRVAIH+EGEP GD RTLTY+ L  EV KAANALT+LG+  G
Sbjct: 76  RLNVAYNCVDRHVEAGHGDRVAIHFEGEP-GDGRTLTYAQLKDEVGKAANALTELGIRKG 134

Query: 132 DRVAIYLPLIPEAVIAMLACARLGIMHSVVFGGFTAAALQARIVDAQAKLLITADGQFRR 191
           DRVA+Y+P+IPE  IAMLACAR+G  HSVVFGGF+A AL ARI DA AKL+ITADG +RR
Sbjct: 135 DRVAVYMPMIPETAIAMLACARIGAAHSVVFGGFSAEALSARIQDADAKLVITADGGYRR 194

Query: 192 GKPSPLKAAADEALAAIPDCSVEHVLVVRRTGIEMAWSEGRDLWWHHVVGSASPAHTPEP 251
           GKP+ LKA  DEA+   P  ++E+VLVVRRTG +++W E +D WWH +V   SP HTPE 
Sbjct: 195 GKPNALKAIVDEAVPRCP--TIENVLVVRRTGQDVSWGE-KDKWWHELVEGQSPEHTPEA 251

Query: 252 FDSEHPLFLLYTSGTTGKPKGIMHTSGGYLTQCCYTMRTIFDVKPDSDVFWCTADIGWVT 311
           F++EHPLF+LYTSGTTGKPKGI+HTSGGYLTQ  YT   +FD+KP++DV+WCTADIGWVT
Sbjct: 252 FEAEHPLFILYTSGTTGKPKGILHTSGGYLTQVSYTHHAVFDLKPETDVYWCTADIGWVT 311

Query: 312 GHTYGVYGPLCNGVTEVLYEGTPDTPDRHRHFQIIEKYGVTIYYTAPTLIRMFMKWGREI 371
           GH+Y VYGPL NG T+V+YEGTPDTP + R ++II+KY V+I Y APT IR FMKWG +I
Sbjct: 312 GHSYFVYGPLSNGATQVMYEGTPDTPHQGRFWEIIQKYKVSILYAAPTAIRTFMKWGDDI 371

Query: 372 PDSHDLSSLRLLGSVGEPINPEAWRWYRDVIGGGRTPLVDTWWQTETGSAMISPLPGIAA 431
           P   DLSSLR+LGSVGEPINPEAW WYR  IGG R P+VDTWWQTETG+ MISPLPG+  
Sbjct: 372 PAKFDLSSLRVLGSVGEPINPEAWIWYRKNIGGERCPIVDTWWQTETGAIMISPLPGVTE 431

Query: 432 AKPGSAMTPLPGISAKIVDDHGDPLPPHTEGAQHVTGYLVLDQPWPSMLRGIWGDPARYW 491
            KPG+A  PLPGISA +VDD G  +P   +GA    GYLVL +PWPSMLR IWGD  RY 
Sbjct: 432 TKPGAAQVPLPGISATVVDDEGREVP---DGA---GGYLVLTEPWPSMLRTIWGDDQRYI 485

Query: 492 HSYWSKFSDKGYYFAGDGARIDPDGAIWVLGRIDDVMNVSGHRISTAEVESALVAHSGVA 551
            +YWS+F   G YFAGDGA+ D DG IW+LGR+DDVM VSGH IST EVESALV+H  VA
Sbjct: 486 DTYWSRF--PGRYFAGDGAKKDDDGDIWLLGRVDDVMLVSGHNISTTEVESALVSHPKVA 543

Query: 552 EAAVVGVTDETTTQAICAFVVLRANYAPHDRTA--EELRTEVARVISPIARPRDVHVVPE 609
           E+AVVG TD TT QAI AFV+LR   A  D  A   ELR  V + + PIA+P+ +  V E
Sbjct: 544 ESAVVGATDATTGQAIVAFVILRGTAASDDGDALLAELRDHVGKTLGPIAKPKRILTVTE 603

Query: 610 LPKTRSGKIMRRLLRDVAENRELGDTSTLLDPTVFDAIRA 649
           LPKTRSGKIMRRLLRDVAENR++GD +TL D TV D I+A
Sbjct: 604 LPKTRSGKIMRRLLRDVAENRQIGDVTTLADSTVMDLIQA 643


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: 1472
Number of extensions: 83
Number of successful extensions: 7
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: 652
Length adjustment: 38
Effective length of query: 613
Effective length of database: 614
Effective search space:   376382
Effective search space used:   376382
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_037574635.1 BS73_RS20690 (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.2864455.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.3e-299  978.1   0.0   9.5e-299  977.9   0.0    1.0  1  NCBI__GCF_000744815.1:WP_037574635.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000744815.1:WP_037574635.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  977.9   0.0  9.5e-299  9.5e-299       7     628 ..      29     643 ..      23     644 .. 0.97

  Alignments for each domain:
  == domain 1  score: 977.9 bits;  conditional E-value: 9.5e-299
                             TIGR02188   7 ykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.rkdkvaiiw 78 
                                            ++ y++a+ed+ +fwa++a++ l+w  + +++ld+s++p++kWf+dg+lnv+yncvdrhve+ + d+vai++
  NCBI__GCF_000744815.1:WP_037574635.1  29 TADAYAHAKEDRLAFWAEQARR-LSWEVEPTETLDWSNPPFAKWFQDGRLNVAYNCVDRHVEAgHGDRVAIHF 100
                                           678899***************5.************************************************** PP

                             TIGR02188  79 egdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsae 151
                                           eg+ +g d r+ltYa+l++ev ++an+l+elG++kgdrva+Y+pmipe++iamlacaRiGa hsvvf+Gfsae
  NCBI__GCF_000744815.1:WP_037574635.1 101 EGE-PG-DGRTLTYAQLKDEVGKAANALTELGIRKGDRVAVYMPMIPETAIAMLACARIGAAHSVVFGGFSAE 171
                                           ***.77.59**************************************************************** PP

                             TIGR02188 152 alaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwweelve 224
                                           al  Ri+da+aklvitad+g+R+gk  +lk+ivdea+ +++ ++e+vlvv+rtg++v+ w  ++D+ww+elve
  NCBI__GCF_000744815.1:WP_037574635.1 172 ALSARIQDADAKLVITADGGYRRGKPNALKAIVDEAVPRCP-TIENVLVVRRTGQDVS-WG-EKDKWWHELVE 241
                                           ****************************************9.7*************76.87.79********* PP

                             TIGR02188 225 keasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdik.dedifwCtaDvGWvtGh 296
                                            ++s e++pe++++e+plfiLYtsG+tGkPkG+lht+gGyl+++++t++ vfd+k ++d++wCtaD+GWvtGh
  NCBI__GCF_000744815.1:WP_037574635.1 242 -GQSPEHTPEAFEAEHPLFILYTSGTTGKPKGILHTSGGYLTQVSYTHHAVFDLKpETDVYWCTADIGWVTGH 313
                                           .6*****************************************************668*************** PP

                             TIGR02188 297 sYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsv 369
                                           sY vygPL+nGat++++eg+p++p+++rfwe+i+kykv+i+Y+aPtaiR++mk+g+++++k dlsslrvlgsv
  NCBI__GCF_000744815.1:WP_037574635.1 314 SYFVYGPLSNGATQVMYEGTPDTPHQGRFWEIIQKYKVSILYAAPTAIRTFMKWGDDIPAKFDLSSLRVLGSV 386
                                           ************************************************************************* PP

                             TIGR02188 370 GepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkevee 442
                                           Gepinpeaw Wy++++G e+cpivdtwWqtetG+i+i+plpg +te+kpg+a++Pl+Gi+a+vvd+eg+ev +
  NCBI__GCF_000744815.1:WP_037574635.1 387 GEPINPEAWIWYRKNIGGERCPIVDTWWQTETGAIMISPLPG-VTETKPGAAQVPLPGISATVVDDEGREVPD 458
                                           ******************************************.5***************************** PP

                             TIGR02188 443 eeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgta 515
                                           +++ g+Lv+++pwPsmlrti+gd++r+++tY+++++g yf+GDga++d+dG+iw+lGRvDdv+ vsGh+++t+
  NCBI__GCF_000744815.1:WP_037574635.1 459 GAG-GYLVLTEPWPSMLRTIWGDDQRYIDTYWSRFPGRYFAGDGAKKDDDGDIWLLGRVDDVMLVSGHNISTT 530
                                           999.8******************************************************************** PP

                             TIGR02188 516 eiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedee.elekelkklvrkeigpiakpdkilvvee 587
                                           e+esalvsh++vae+avvg++d ++g+aivafv+l+ ++++d+  +l +el+++v k++gpiakp++il+v+e
  NCBI__GCF_000744815.1:WP_037574635.1 531 EVESALVSHPKVAESAVVGATDATTGQAIVAFVILRGTAASDDGdALLAELRDHVGKTLGPIAKPKRILTVTE 603
                                           ************************************9998877659*************************** PP

                             TIGR02188 588 lPktRsGkimRRllrkiaegeellgdvstledpsvveelke 628
                                           lPktRsGkimRRllr++ae++++ gdv+tl+d++v++ +++
  NCBI__GCF_000744815.1:WP_037574635.1 604 LPKTRSGKIMRRLLRDVAENRQI-GDVTTLADSTVMDLIQA 643
                                           ******************98765.6***********98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (652 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: 35.92
//
[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