Alignments for a candidate for acs in Rhodanobacter denitrificans FW104-10B01

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Rhodanobacter denitrificans FW104-10B01

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate WP_007510054.1 LRK54_RS08420 acetate--CoA ligase

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



>NCBI__GCF_021560695.1:WP_007510054.1
          Length = 646

 Score =  908 bits (2347), Expect = 0.0
 Identities = 433/640 (67%), Positives = 512/640 (80%)

Query: 4   ASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDH 63
           + LYPV P  AA++      Y  +Y +SV +P+GFW    +RLDWIKP T +K  SFD  
Sbjct: 2   SKLYPVNPSFAAASRLRRDDYTRLYAESVSDPEGFWGRIGQRLDWIKPPTKIKDVSFDPK 61

Query: 64  HVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKFANA 123
            + I+W+ DG LNVS NCLDR L +RGD++AII+EGDDP +SR ITYRELH EVCKFAN 
Sbjct: 62  DLHIRWYEDGELNVSANCLDRQLEKRGDKVAIIFEGDDPKDSRKITYRELHAEVCKFANT 121

Query: 124 LRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVV 183
           L+   V +GD V IY+PMIPEA VAMLAC R+GAIHSVVFGGFSP++LAGRI+D ++KVV
Sbjct: 122 LKHLGVVKGDRVAIYLPMIPEAAVAMLACARLGAIHSVVFGGFSPDSLAGRIVDSQAKVV 181

Query: 184 ITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMKV 243
           ITADEG RAGK IPLK NVD AL  P T+S++ VIV + T G +     RD ++  LM+ 
Sbjct: 182 ITADEGRRAGKHIPLKVNVDAALERPGTNSVETVIVVRHTGGAVHMQSPRDRYWHTLMEG 241

Query: 244 AGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYWC 303
               CAP  + AE  LF+LYTSGSTGKPKGVQH+T GYL++ + THE+VFD +  ++YWC
Sbjct: 242 QSADCAPTPVEAEHPLFVLYTSGSTGKPKGVQHSTGGYLVFISYTHEQVFDLREDDIYWC 301

Query: 304 TADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIRA 363
           TADVGWVTGHSY+VYGPL NGATT++FEGVPNYPD +R  +VIDKH+VSI YTAPTAIRA
Sbjct: 302 TADVGWVTGHSYVVYGPLCNGATTVMFEGVPNYPDHSRFWQVIDKHQVSIFYTAPTAIRA 361

Query: 364 MMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLI 423
           +M  G A V+    +SLRLLGSVGEPINPEAW+WYY+ VG+ERCPIVDTWWQTETGG++I
Sbjct: 362 LMREGEAPVKKCSRASLRLLGSVGEPINPEAWEWYYRVVGEERCPIVDTWWQTETGGIMI 421

Query: 424 SPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHDR 483
           SPLPGA A KPGSAT PFFGV PA++D  G + EG AEGNL+I DSWPGQ RT+YGDH R
Sbjct: 422 SPLPGAIATKPGSATLPFFGVKPAIIDAEGTVQEGVAEGNLLITDSWPGQVRTIYGDHQR 481

Query: 484 FVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVA 543
           F++TYF  + G YF+GDGARRDEDGYYWITGRVDDV+NVSGHR+GTAE+ESA+VAHPKVA
Sbjct: 482 FIETYFSAYPGNYFSGDGARRDEDGYYWITGRVDDVINVSGHRLGTAEVESALVAHPKVA 541

Query: 544 EAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLP 603
           EAAVVG PH+IKGQGIY YVTL AGE  S+ LR EL  WVRKEIGPIA+PD +QWAPGLP
Sbjct: 542 EAAVVGCPHEIKGQGIYAYVTLVAGETGSDELRKELIAWVRKEIGPIATPDYLQWAPGLP 601

Query: 604 KTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIE 643
           KTRSGKIMRRILRKI     D LGDI+TLADP VV +L++
Sbjct: 602 KTRSGKIMRRILRKIGENLPDQLGDITTLADPSVVKNLVD 641


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: 1432
Number of extensions: 63
Number of successful extensions: 1
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: 646
Length adjustment: 38
Effective length of query: 613
Effective length of database: 608
Effective search space:   372704
Effective search space used:   372704
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_007510054.1 LRK54_RS08420 (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.2857384.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 1023.4   0.0          0 1023.1   0.0    1.0  1  NCBI__GCF_021560695.1:WP_007510054.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_021560695.1:WP_007510054.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1023.1   0.0         0         0       4     627 ..      19     640 ..      17     642 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1023.1 bits;  conditional E-value: 0
                             TIGR02188   4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdk 73 
                                            ++y++ly+e+++dpe fw++ ++ +l+w+kp +k++d s++p   +++W+edgelnvs+nc+dr++ekr dk
  NCBI__GCF_021560695.1:WP_007510054.1  19 RDDYTRLYAESVSDPEGFWGRIGQ-RLDWIKPPTKIKDVSFDPkdlHIRWYEDGELNVSANCLDRQLEKRGDK 90 
                                           589********************9.5***************998889************************** PP

                             TIGR02188  74 vaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfa 146
                                           vaii+egd+++ dsrk+tY+el++evc++an+lk+lGv kgdrvaiYlpmipea++amlacaR+Ga+hsvvf+
  NCBI__GCF_021560695.1:WP_007510054.1  91 VAIIFEGDDPK-DSRKITYRELHAEVCKFANTLKHLGVVKGDRVAIYLPMIPEAAVAMLACARLGAIHSVVFG 162
                                           **********9.5************************************************************ PP

                             TIGR02188 147 GfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDvw 218
                                           Gfs+++la Rivd++ak+vitadeg R gk+i+lk +vd+ale+  + sve+v+vv++tg  v+ +++ rD +
  NCBI__GCF_021560695.1:WP_007510054.1 163 GFSPDSLAGRIVDSQAKVVITADEGRRAGKHIPLKVNVDAALERPGTnSVETVIVVRHTGGAVH-MQSPRDRY 234
                                           ********************************************9988**************76.******** PP

                             TIGR02188 219 weelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvG 291
                                           w++l+e ++sa+c+p+++++e+plf+LYtsGstGkPkGv+h+tgGyl+ +++t++ vfd++++di+wCtaDvG
  NCBI__GCF_021560695.1:WP_007510054.1 235 WHTLME-GQSADCAPTPVEAEHPLFVLYTSGSTGKPKGVQHSTGGYLVFISYTHEQVFDLREDDIYWCTADVG 306
                                           ******.6***************************************************************** PP

                             TIGR02188 292 WvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslr 364
                                           WvtGhsY+vygPL+nGatt++fegvp+ypd+srfw+vi+k++v+ifYtaPtaiRalm++ge+ vkk ++ slr
  NCBI__GCF_021560695.1:WP_007510054.1 307 WVTGHSYVVYGPLCNGATTVMFEGVPNYPDHSRFWQVIDKHQVSIFYTAPTAIRALMREGEAPVKKCSRASLR 379
                                           ************************************************************************* PP

                             TIGR02188 365 vlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeeg 437
                                           +lgsvGepinpeaweWyy+vvG+e+cpivdtwWqtetGgi+i+plpg a+++kpgsatlP+fG++++++d eg
  NCBI__GCF_021560695.1:WP_007510054.1 380 LLGSVGEPINPEAWEWYYRVVGEERCPIVDTWWQTETGGIMISPLPG-AIATKPGSATLPFFGVKPAIIDAEG 451
                                           ***********************************************.6************************ PP

                             TIGR02188 438 keveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGh 510
                                           +  e  +e g L i+++wP+++rtiygd++rf+etYf++++g yf+GDgarrd+dGy+wi+GRvDdvinvsGh
  NCBI__GCF_021560695.1:WP_007510054.1 452 TVQEGVAE-GNLLITDSWPGQVRTIYGDHQRFIETYFSAYPGNYFSGDGARRDEDGYYWITGRVDDVINVSGH 523
                                           98886666.89************************************************************** PP

                             TIGR02188 511 rlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkil 583
                                           rlgtae+esalv+h++vaeaavvg p+eikg+ i+a+v+l +g++ ++ el+kel+++vrkeigpia+pd ++
  NCBI__GCF_021560695.1:WP_007510054.1 524 RLGTAEVESALVAHPKVAEAAVVGCPHEIKGQGIYAYVTLVAGETGSD-ELRKELIAWVRKEIGPIATPDYLQ 595
                                           ********************************************9999.5*********************** PP

                             TIGR02188 584 vveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelk 627
                                           +++ lPktRsGkimRR+lrki e+  ++lgd++tl+dpsvv++l 
  NCBI__GCF_021560695.1:WP_007510054.1 596 WAPGLPKTRSGKIMRRILRKIGENLpDQLGDITTLADPSVVKNLV 640
                                           ************************99****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (646 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: 21.89
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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