Alignments for a candidate for acs in Nitriliruptor alkaliphilus DSM 45188

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Nitriliruptor alkaliphilus DSM 45188

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_052667130.1 NITAL_RS15415 acetate--CoA ligase

Query= SwissProt::P9WQD1
         (651 letters)



>NCBI__GCF_000969705.1:WP_052667130.1
          Length = 652

 Score =  801 bits (2068), Expect = 0.0
 Identities = 398/647 (61%), Positives = 477/647 (73%), Gaps = 13/647 (2%)

Query: 3   ESTPEVSSSYPPPAHF-AEHANARAELYREAEEDRLAFWAKQANRLSWTTPFTEVLDWSG 61
           E   + + ++PPP  F AE     AE+Y EA  DR  FWA+QA  L W   +  +LDW  
Sbjct: 7   EGLLDEARTFPPPGEFKAEARTTGAEIYDEANTDREGFWARQAAELEWFEEWDTILDWQ- 65

Query: 62  APFAKWFVGGELNVAYNCVDRHVEAGHGDRVAIHWEGEPVGDRRTLTYSDLLAEVSKAAN 121
           AP+AKWFVGG+LNV++NCVDRHV AGHGD++A HWEGEP GD RT+TY+ LL +V +AAN
Sbjct: 66  APYAKWFVGGKLNVSHNCVDRHVAAGHGDQIAYHWEGEP-GDTRTITYAQLLEDVQRAAN 124

Query: 122 ALTDLGLVAGDRVAIYLPLIPEAVIAMLACARLGIMHSVVFGGFTAAALQARIVDAQAKL 181
           AL +LG+  GDRVA+YLP+IPE  + MLACAR+G +HSVVF GF+A AL+ RI D+  K+
Sbjct: 125 ALKELGVERGDRVAVYLPMIPELPVTMLACARIGAVHSVVFAGFSAQALRDRINDSDCKV 184

Query: 182 LITADGQFRRGKPSPLKAAADEALAAIPDCSVEHVLVVRRTGIEMAWSEGRDLWWHHVVG 241
           ++TADG +RRG   PLK   DEAL   P  S+   LVVRRT  ++A  +GRD+WWH +V 
Sbjct: 185 VVTADGSWRRGSVFPLKEHVDEALQDTP--SITKALVVRRTENDVAMQDGRDVWWHDLVP 242

Query: 242 SASPAHTPEPFDSEHPLFLLYTSGTTGKPKGIMHTSGGYLTQCCYTMRTIFDVKPDSDVF 301
             +    PE  DSE  L+LLYTSGTTGKPKGIMHT+GGYLTQ  +T R +FD++PDSDV+
Sbjct: 243 GQAAECEPESMDSEDLLYLLYTSGTTGKPKGIMHTTGGYLTQVAFTHREVFDLRPDSDVY 302

Query: 302 WCTADIGWVTGHTYGVYGPLCNGVTEVLYEGTPDTPDRHRHFQIIEKYGVTIYYTAPTLI 361
           WC ADIGWVTGH+Y VYGPL N  T VLYEGTP+ P   R + IIE+YGVT  YTAPT I
Sbjct: 303 WCAADIGWVTGHSYIVYGPLANRATSVLYEGTPNFPAEDRFWDIIERYGVTQLYTAPTAI 362

Query: 362 RMFMKWGREIPDSHDLSSLRLLGSVGEPINPEAWRWYRDVIGGGRTPLVDTWWQTETGSA 421
           R FMKWG   P+ HDLSSLRLLG+VGEPINPEAW WYR VIGG R P+VDTWWQTETG+ 
Sbjct: 363 RAFMKWGDHHPEGHDLSSLRLLGTVGEPINPEAWMWYRKVIGGDRCPVVDTWWQTETGAI 422

Query: 422 MISPLPGIAAAKPGSAMTPLPGISAKIVDDHGDPLPPHTEGAQHVTGYLVLDQPWPSMLR 481
           MISPLPG    KPGSA  PLPGISA +VD+ G+ +     G     GYL LDQPWPSMLR
Sbjct: 423 MISPLPGATTTKPGSATFPLPGISADVVDEKGESV--GIPGG----GYLTLDQPWPSMLR 476

Query: 482 GIWGDPARYWHSYWSKFSDKGYYFAGDGARIDPDGAIWVLGRIDDVMNVSGHRISTAEVE 541
           GIWGD  RY  +YWS+F   G YFAGDGA+ D DG  W+LGR+DDVMN+SGHRIST EVE
Sbjct: 477 GIWGDAKRYEDTYWSRF--PGRYFAGDGAKRDDDGYFWLLGRVDDVMNISGHRISTTEVE 534

Query: 542 SALVAHSGVAEAAVVGVTDETTTQAICAFVVLRANYAPHDRTAEELRTEVARVISPIARP 601
           SALV+H  VAEAAVVG  D  T QAI AFV  R      D  A+ELR  VA+VISPIA+P
Sbjct: 535 SALVSHPSVAEAAVVGRADSQTGQAIAAFVTPRGGIDGDDALAKELRDHVAKVISPIAKP 594

Query: 602 RDVHVVPELPKTRSGKIMRRLLRDVAENRELGDTSTLLDPTVFDAIR 648
             +    +LPKTRSGKIMRRLL+D+AE+++LGDT+TL D +V D+I+
Sbjct: 595 ASLLFTADLPKTRSGKIMRRLLKDIAEDKQLGDTTTLADASVVDSIK 641


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: 1446
Number of extensions: 65
Number of successful extensions: 6
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_052667130.1 NITAL_RS15415 (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.815006.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.7e-298  976.0   0.0   4.3e-298  975.7   0.0    1.0  1  NCBI__GCF_000969705.1:WP_052667130.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000969705.1:WP_052667130.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  975.7   0.0  4.3e-298  4.3e-298       7     627 ..      30     641 ..      24     643 .. 0.98

  Alignments for each domain:
  == domain 1  score: 975.7 bits;  conditional E-value: 4.3e-298
                             TIGR02188   7 ykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.rkdkvaiiw 78 
                                            +e+y+ea++d+e fwa++a e lew+++++++ld++ +p +kWf++g+lnvs ncvdrhv++ + d++a +w
  NCBI__GCF_000969705.1:WP_052667130.1  30 GAEIYDEANTDREGFWARQAAE-LEWFEEWDTILDWQ-APYAKWFVGGKLNVSHNCVDRHVAAgHGDQIAYHW 100
                                           5789*****************5.*************9.789**********************9********* PP

                             TIGR02188  79 egdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsae 151
                                           eg+ +g d+r++tYa+ll++v r+an+lkelGv++gdrva+Ylpmipe+ ++mlacaRiGavhsvvfaGfsa+
  NCBI__GCF_000969705.1:WP_052667130.1 101 EGE-PG-DTRTITYAQLLEDVQRAANALKELGVERGDRVAVYLPMIPELPVTMLACARIGAVHSVVFAGFSAQ 171
                                           ***.77.59**************************************************************** PP

                             TIGR02188 152 alaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwweelve 224
                                           al++Ri+d+++k+v+tad+++R+g v++lk+ vdeal++++ s+ k lvv+rt+++va +++grDvww++lv 
  NCBI__GCF_000969705.1:WP_052667130.1 172 ALRDRINDSDCKVVVTADGSWRRGSVFPLKEHVDEALQDTP-SITKALVVRRTENDVA-MQDGRDVWWHDLVP 242
                                           ****************************************9.7*************77.************** PP

                             TIGR02188 225 keasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdik.dedifwCtaDvGWvtGh 296
                                            ++ aecepe++dsed+l++LYtsG+tGkPkG++httgGyl+++a t++ vfd++ d+d++wC+aD+GWvtGh
  NCBI__GCF_000969705.1:WP_052667130.1 243 -GQAAECEPESMDSEDLLYLLYTSGTTGKPKGIMHTTGGYLTQVAFTHREVFDLRpDSDVYWCAADIGWVTGH 314
                                           .6*****************************************************778*************** PP

                             TIGR02188 297 sYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsv 369
                                           sYivygPLan at++l+eg+p++p ++rfw++ie+y+vt++YtaPtaiRa+mk+g+++++ hdlsslr+lg+v
  NCBI__GCF_000969705.1:WP_052667130.1 315 SYIVYGPLANRATSVLYEGTPNFPAEDRFWDIIERYGVTQLYTAPTAIRAFMKWGDHHPEGHDLSSLRLLGTV 387
                                           ************************************************************************* PP

                             TIGR02188 370 GepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkevee 442
                                           Gepinpeaw+Wy++v+G ++cp+vdtwWqtetG+i+i+plpg at +kpgsat Pl+Gi+a+vvde+g++v  
  NCBI__GCF_000969705.1:WP_052667130.1 388 GEPINPEAWMWYRKVIGGDRCPVVDTWWQTETGAIMISPLPG-ATTTKPGSATFPLPGISADVVDEKGESVGI 459
                                           ******************************************.6****************************8 PP

                             TIGR02188 443 eeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgta 515
                                             + g+L++++pwPsmlr+i+gd +r+ +tY+++++g yf+GDga+rd+dGy+w+lGRvDdv+n+sGhr++t+
  NCBI__GCF_000969705.1:WP_052667130.1 460 PGG-GYLTLDQPWPSMLRGIWGDAKRYEDTYWSRFPGRYFAGDGAKRDDDGYFWLLGRVDDVMNISGHRISTT 531
                                           777.8******************************************************************** PP

                             TIGR02188 516 eiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvveel 588
                                           e+esalvsh++vaeaavvg++d  +g+ai+afv+ + g++ d+ +l+kel+++v+k i+piakp+++l++ +l
  NCBI__GCF_000969705.1:WP_052667130.1 532 EVESALVSHPSVAEAAVVGRADSQTGQAIAAFVTPRGGIDGDD-ALAKELRDHVAKVISPIAKPASLLFTADL 603
                                           ****************************************999.6**************************** PP

                             TIGR02188 589 PktRsGkimRRllrkiaegeellgdvstledpsvveelk 627
                                           PktRsGkimRRll++iae+ ++lgd++tl+d svv+++k
  NCBI__GCF_000969705.1:WP_052667130.1 604 PKTRSGKIMRRLLKDIAED-KQLGDTTTLADASVVDSIK 641
                                           *****************95.5678************997 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 36.86
//
[ok]

This GapMind analysis is from Apr 09 2024. 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