Alignments for a candidate for acs in Novosphingobium barchaimii LL02

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Novosphingobium barchaimii LL02

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate WP_059150183.1 V474_RS03815 acetate--CoA ligase

Query= reanno::pseudo5_N2C3_1:AO356_18695
         (651 letters)



>NCBI__GCF_001046635.1:WP_059150183.1
          Length = 649

 Score =  894 bits (2309), Expect = 0.0
 Identities = 427/641 (66%), Positives = 508/641 (79%), Gaps = 3/641 (0%)

Query: 3   AASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDD 62
           A ++YPV  E A ++L D+A Y+ MY++SV +PD FWR++A+RLDWIKPFT VKQTSF +
Sbjct: 2   ADAVYPVPTEWAENSLIDDARYQEMYEKSVADPDAFWRQEAQRLDWIKPFTVVKQTSFHE 61

Query: 63  HHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSE-SRNITYRELHEEVCKFA 121
               I WF DGTLN+S NCLDRHL   GD IAI+WE D P +  R ITYR+LHE+VC+FA
Sbjct: 62  EDFGISWFTDGTLNLSANCLDRHLDAHGDDIAILWEPDSPDQPERRITYRQLHEQVCRFA 121

Query: 122 NALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSK 181
           N L+ + V +G+ VTIY+PM+PEA VAMLAC RIGAIHS+VF GFSP+ALAGRI DC S+
Sbjct: 122 NLLKAKGVKKGERVTIYLPMVPEAAVAMLACARIGAIHSIVFAGFSPDALAGRITDCDSR 181

Query: 182 VVITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLM 241
           +V+TADEG+R GKK+PLKANVD+A+    +S +  VIV   T G     + RDI +   +
Sbjct: 182 IVLTADEGLRGGKKVPLKANVDEAVQR--SSCVDTVIVLAHTGGGTPLVEGRDIDWASAV 239

Query: 242 KVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVY 301
                 CAP+EM AE+ LFILYTSGSTGKPKGV HTT GY ++A++THE VFDY+PG+++
Sbjct: 240 ADQSADCAPEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYSVWASMTHEYVFDYRPGQIF 299

Query: 302 WCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAI 361
           WC ADVGWVTGHSY VYGPL NGATT++FEGVPN+PD +R  +++DK  V I Y APTA+
Sbjct: 300 WCAADVGWVTGHSYAVYGPLMNGATTVMFEGVPNFPDPSRFWQIVDKFGVEIFYGAPTAL 359

Query: 362 RAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGV 421
           RA+M  G   V+     SLRLLGSVGEPINPEAW WY++ VG+ RCPIVDTWWQTETGG+
Sbjct: 360 RALMREGDDWVKKTSRKSLRLLGSVGEPINPEAWSWYHEVVGEGRCPIVDTWWQTETGGI 419

Query: 422 LISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDH 481
           +I+PLPGATALKPGSATRP FGV P LVD  G  IEGA +G LV+ DSWPGQ RT++GDH
Sbjct: 420 MITPLPGATALKPGSATRPMFGVQPRLVDTEGKEIEGAGDGCLVLTDSWPGQMRTVWGDH 479

Query: 482 DRFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPK 541
           DRF  TYF TF G YFTGDG RRDEDGYYWITGR+DDV+NVSGHRMGTAE+ESA+VAHPK
Sbjct: 480 DRFFQTYFSTFKGTYFTGDGCRRDEDGYYWITGRIDDVINVSGHRMGTAEVESALVAHPK 539

Query: 542 VAEAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPG 601
           VAEAAVVG+PH+IKGQGIY +VT NA  E  EALR +L  WVR EIGPIA+PDVIQ+APG
Sbjct: 540 VAEAAVVGMPHEIKGQGIYAFVTTNAEVEPDEALRKDLIAWVRHEIGPIATPDVIQFAPG 599

Query: 602 LPKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLI 642
           LPKTRSGKIMRRILRKI   ++  LGD STLADP VV  LI
Sbjct: 600 LPKTRSGKIMRRILRKIGENDFSNLGDTSTLADPSVVDSLI 640


Lambda     K      H
   0.318    0.135    0.418 

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: 1473
Number of extensions: 59
Number of successful extensions: 3
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: 649
Length adjustment: 38
Effective length of query: 613
Effective length of database: 611
Effective search space:   374543
Effective search space used:   374543
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_059150183.1 V474_RS03815 (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.3805398.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 1020.7   0.0          0 1020.5   0.0    1.0  1  NCBI__GCF_001046635.1:WP_059150183.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001046635.1:WP_059150183.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1020.5   0.0         0         0       5     628 ..      21     641 ..      17     642 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1020.5 bits;  conditional E-value: 0
                             TIGR02188   5 eeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdkv 74 
                                            +y+e+ye++++dp++fw+++a+ +l+w+kpf+ v+++s+++    + Wf+dg+ln+s+nc+drh+ ++ d +
  NCBI__GCF_001046635.1:WP_059150183.1  21 ARYQEMYEKSVADPDAFWRQEAQ-RLDWIKPFTVVKQTSFHEedfGISWFTDGTLNLSANCLDRHLDAHGDDI 92 
                                           68*********************.5**************99877779************************** PP

                             TIGR02188  75 aiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaG 147
                                           ai we d++++ +r++tY++l+++vcr+an+lk+ Gvkkg+rv+iYlpm+pea++amlacaRiGa+hs+vfaG
  NCBI__GCF_001046635.1:WP_059150183.1  93 AILWEPDSPDQPERRITYRQLHEQVCRFANLLKAKGVKKGERVTIYLPMVPEAAVAMLACARIGAIHSIVFAG 165
                                           ************************************************************************* PP

                             TIGR02188 148 fsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwwe 220
                                           fs++ala Ri+d+++++v+tadeglRggk+++lk++vdea+++++  v++v+v+ +tg   ++++egrD+ w 
  NCBI__GCF_001046635.1:WP_059150183.1 166 FSPDALAGRITDCDSRIVLTADEGLRGGKKVPLKANVDEAVQRSS-CVDTVIVLAHTGGG-TPLVEGRDIDWA 236
                                           ******************************************998.5*************.66********** PP

                             TIGR02188 221 elvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWv 293
                                           ++v++ +sa+c+pe++++edplfiLYtsGstGkPkGvlhttgGy ++a++t++yvfd+++++ifwC+aDvGWv
  NCBI__GCF_001046635.1:WP_059150183.1 237 SAVAD-QSADCAPEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYSVWASMTHEYVFDYRPGQIFWCAADVGWV 308
                                           ****7.******************************************************************* PP

                             TIGR02188 294 tGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvl 366
                                           tGhsY vygPL+nGatt++fegvp++pd+srfw++++k++v+ifY aPta+Ralm++g+++vkk++++slr+l
  NCBI__GCF_001046635.1:WP_059150183.1 309 TGHSYAVYGPLMNGATTVMFEGVPNFPDPSRFWQIVDKFGVEIFYGAPTALRALMREGDDWVKKTSRKSLRLL 381
                                           ************************************************************************* PP

                             TIGR02188 367 gsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegke 439
                                           gsvGepinpeaw+Wy+evvG+++cpivdtwWqtetGgi+itplpg at+lkpgsat+P+fG+++++vd+egke
  NCBI__GCF_001046635.1:WP_059150183.1 382 GSVGEPINPEAWSWYHEVVGEGRCPIVDTWWQTETGGIMITPLPG-ATALKPGSATRPMFGVQPRLVDTEGKE 453
                                           *********************************************.6************************** PP

                             TIGR02188 440 veeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrl 512
                                           +e   + g+Lv++++wP+++rt++gd++rf++tYf+++kg+yftGDg+rrd+dGy+wi+GR+DdvinvsGhr+
  NCBI__GCF_001046635.1:WP_059150183.1 454 IEGAGD-GCLVLTDSWPGQMRTVWGDHDRFFQTYFSTFKGTYFTGDGCRRDEDGYYWITGRIDDVINVSGHRM 525
                                           *97766.8***************************************************************** PP

                             TIGR02188 513 gtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvv 585
                                           gtae+esalv+h++vaeaavvg+p+eikg+ i+afv+ +++ve+de +l+k+l+++vr+eigpia+pd i+++
  NCBI__GCF_001046635.1:WP_059150183.1 526 GTAEVESALVAHPKVAEAAVVGMPHEIKGQGIYAFVTTNAEVEPDE-ALRKDLIAWVRHEIGPIATPDVIQFA 597
                                           *********************************************9.5************************* PP

                             TIGR02188 586 eelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
                                           + lPktRsGkimRR+lrki e++ ++lgd+stl+dpsvv++l++
  NCBI__GCF_001046635.1:WP_059150183.1 598 PGLPKTRSGKIMRRILRKIGENDfSNLGDTSTLADPSVVDSLIA 641
                                           ****************************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (649 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 20.10
//
[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