GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Microvirga lotononidis WSM3557

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_009764094.1 MICLODRAFT_RS22300 acetate--CoA ligase

Query= SwissProt::Q8ZKF6
         (652 letters)



>NCBI__GCF_000262405.1:WP_009764094.1
          Length = 651

 Score =  822 bits (2122), Expect = 0.0
 Identities = 381/642 (59%), Positives = 495/642 (77%), Gaps = 2/642 (0%)

Query: 5   HKHAIPANIADRCLINPEQYETKYKQSINDPDTFWGEQGKILDWITPYQKVKNTSFAPGN 64
           H   +P+ +A    ++ + Y+  Y++SI+DP+ FW EQ +ILDW+ P+ +VKNT ++P +
Sbjct: 4   HVFPVPSALASTAHVDRQAYQDLYQRSIDDPEAFWREQARILDWVKPFTRVKNTRYSPED 63

Query: 65  VSIKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDTSQSKHISYRELHRDVCRFANTL 124
           V+I+W+ DGTLN + NCLDRH ++ GD  AI+WEGD   +++ +++ +L R V R AN L
Sbjct: 64  VTIEWFADGTLNASFNCLDRHARDRGDEAAILWEGDTPGETRKVTWTDLQRQVSRLANAL 123

Query: 125 LDLGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSSSRLVI 184
             LG+KKGD V++Y+P+VPEA  AMLACARIGAVHSV+F GFS EA+AGRI D  SR++I
Sbjct: 124 ARLGVKKGDFVSVYLPVVPEAIAAMLACARIGAVHSVVFSGFSAEALAGRIEDCRSRVLI 183

Query: 185 TADEGVRAGRSIPLKKNVDDALKNPNVTSVEHVIVLKRTGSDIDWQEGRDLWWRDLIEKA 244
           TADEG+RAG+ +PLKKN D AL+N  +  VEHV+V++RTG D+    GRD W+ + + + 
Sbjct: 184 TADEGLRAGKHVPLKKNADAALQN--LPFVEHVLVVRRTGRDVPMVAGRDRWYDEALAEV 241

Query: 245 SPEHQPEAMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAATTFKYVFDYHPGDIYWCT 304
             E  P A+ AEDPLF+LYTSGSTGKPKG+LHTTGGYLV+AAT+F+ +FDYHPGDI++CT
Sbjct: 242 PEECAPVAVGAEDPLFVLYTSGSTGKPKGMLHTTGGYLVHAATSFRAMFDYHPGDIHFCT 301

Query: 305 ADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMCQVVDKHQVNILYTAPTAIRAL 364
           ADVGWVT H+YL+YGPLA GAT ++FEGVP WP  +R  Q+V+ ++VNI YTAPTAIR+L
Sbjct: 302 ADVGWVTAHTYLIYGPLANGATIVLFEGVPTWPDSSRWWQIVETYKVNIFYTAPTAIRSL 361

Query: 365 MAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGKEKCPVVDTWWQTETGGFMIT 424
           M +G+  +   D SSLR+LGSVGEPINPEAW WY + +G  +CP+VDT+WQTETG  ++ 
Sbjct: 362 MRDGEGPVRRHDLSSLRVLGSVGEPINPEAWLWYHEVVGGGRCPIVDTYWQTETGAALLC 421

Query: 425 PLPGAIELKAGSATRPFFGVQPALVDNEGHPQEGATEGNLVITDSWPGQARTLFGDHERF 484
           PLPGA++LK GSAT+PFFGV+PAL+ ++    EG   GNL   DSWPGQART+ GD ERF
Sbjct: 422 PLPGAMDLKPGSATKPFFGVRPALLGSDATVVEGEGAGNLCFADSWPGQARTILGDRERF 481

Query: 485 EQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAE 544
            +TYFSTF   YF+GDGARRD DGYYWITGR+DDV+NVSGHRLGT E+ESAL +HP +AE
Sbjct: 482 LKTYFSTFPGYYFTGDGARRDADGYYWITGRLDDVINVSGHRLGTVEVESALASHPSVAE 541

Query: 545 AAVVGIPHAIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPK 604
           AAVVG+PH IKGQ I+A+VTL  G   + +L  ++   VR  IGP+ATPD + W   LPK
Sbjct: 542 AAVVGMPHEIKGQGIFAFVTLKEGIAENDDLRRDLIQVVRTRIGPIATPDRIEWASQLPK 601

Query: 605 TRSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEKQ 646
            RSGKI+RRIL +IAAGD  N GDTST+ADP VV +++   Q
Sbjct: 602 NRSGKILRRILARIAAGDYENHGDTSTVADPTVVAEIVRRVQ 643


Lambda     K      H
   0.317    0.135    0.423 

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: 1409
Number of extensions: 49
Number of successful extensions: 2
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: 652
Length of database: 651
Length adjustment: 38
Effective length of query: 614
Effective length of database: 613
Effective search space:   376382
Effective search space used:   376382
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_009764094.1 MICLODRAFT_RS22300 (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.961863.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.2e-291  954.5   0.0   1.4e-291  954.2   0.0    1.0  1  NCBI__GCF_000262405.1:WP_009764094.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000262405.1:WP_009764094.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  954.2   0.0  1.4e-291  1.4e-291       4     627 ..      20     639 ..      17     641 .. 0.98

  Alignments for each domain:
  == domain 1  score: 954.2 bits;  conditional E-value: 1.4e-291
                             TIGR02188   4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdk 73 
                                            ++y++ly+++i+dpe+fw+++a+  l+w+kpf++v+++  +p   +++Wf+dg+ln+s+nc+drh+++r d+
  NCBI__GCF_000262405.1:WP_009764094.1  20 RQAYQDLYQRSIDDPEAFWREQAR-ILDWVKPFTRVKNTRYSPedvTIEWFADGTLNASFNCLDRHARDRGDE 91 
                                           689*********************.6************9988877899************************* PP

                             TIGR02188  74 vaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfa 146
                                           +ai wegd +ge +rk+t+++l+r+v+rlan+l +lGvkkgd v++Ylp++pea++amlacaRiGavhsvvf+
  NCBI__GCF_000262405.1:WP_009764094.1  92 AAILWEGDTPGE-TRKVTWTDLQRQVSRLANALARLGVKKGDFVSVYLPVVPEAIAAMLACARIGAVHSVVFS 163
                                           **********96.************************************************************ PP

                             TIGR02188 147 GfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvww 219
                                           Gfsaeala Ri+d++++++itadeglR gk+++lkk++d+al++ +  ve+vlvv+rtg++v  ++ grD w+
  NCBI__GCF_000262405.1:WP_009764094.1 164 GFSAEALAGRIEDCRSRVLITADEGLRAGKHVPLKKNADAALQNLP-FVEHVLVVRRTGRDVP-MVAGRDRWY 234
                                           *********************************************9.7*************66.********* PP

                             TIGR02188 220 eelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGW 292
                                           +e++++ +++ec+p ++++edplf+LYtsGstGkPkG+lhttgGyl++aa++++ +fd++++di++CtaDvGW
  NCBI__GCF_000262405.1:WP_009764094.1 235 DEALAE-VPEECAPVAVGAEDPLFVLYTSGSTGKPKGMLHTTGGYLVHAATSFRAMFDYHPGDIHFCTADVGW 306
                                           *****6.****************************************************************** PP

                             TIGR02188 293 vtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrv 365
                                           vt h+Y++ygPLanGat +lfegvpt+pd+sr+w+++e ykv+ifYtaPtaiR+lm+ ge  v++hdlsslrv
  NCBI__GCF_000262405.1:WP_009764094.1 307 VTAHTYLIYGPLANGATIVLFEGVPTWPDSSRWWQIVETYKVNIFYTAPTAIRSLMRDGEGPVRRHDLSSLRV 379
                                           ************************************************************************* PP

                             TIGR02188 366 lgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegk 438
                                           lgsvGepinpeaw Wy+evvG ++cpivdt+WqtetG++l+ plpg a++lkpgsat+P+fG++++++ ++++
  NCBI__GCF_000262405.1:WP_009764094.1 380 LGSVGEPINPEAWLWYHEVVGGGRCPIVDTYWQTETGAALLCPLPG-AMDLKPGSATKPFFGVRPALLGSDAT 451
                                           **********************************************.6************************9 PP

                             TIGR02188 439 eveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhr 511
                                            ve e   g L++ ++wP+++rti gd erf +tYf++++g+yftGDgarrd+dGy+wi+GR+DdvinvsGhr
  NCBI__GCF_000262405.1:WP_009764094.1 452 VVEGEGA-GNLCFADSWPGQARTILGDRERFLKTYFSTFPGYYFTGDGARRDADGYYWITGRLDDVINVSGHR 523
                                           9996655.79*************************************************************** PP

                             TIGR02188 512 lgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilv 584
                                           lgt+e+esal sh++vaeaavvg+p+eikg+ i+afv+lkeg++e+++ l+++l+++vr++igpia+pd+i++
  NCBI__GCF_000262405.1:WP_009764094.1 524 LGTVEVESALASHPSVAEAAVVGMPHEIKGQGIFAFVTLKEGIAENDD-LRRDLIQVVRTRIGPIATPDRIEW 595
                                           ********************************************9995.************************ PP

                             TIGR02188 585 veelPktRsGkimRRllrkiaege.ellgdvstledpsvveelk 627
                                           +++lPk RsGki+RR+l +ia+g+ e+ gd+st++dp+vv+e+ 
  NCBI__GCF_000262405.1:WP_009764094.1 596 ASQLPKNRSGKILRRILARIAAGDyENHGDTSTVADPTVVAEIV 639
                                           ****************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (651 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: 25.45
//
[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:

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:

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:

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:

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