GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Amantichitinum ursilacus IGB-41

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_053937296.1 WG78_RS08045 acetate--CoA ligase

Query= SwissProt::P31638
         (660 letters)



>NCBI__GCF_001294205.1:WP_053937296.1
          Length = 655

 Score =  951 bits (2457), Expect = 0.0
 Identities = 455/657 (69%), Positives = 547/657 (83%), Gaps = 6/657 (0%)

Query: 1   MSAIESVMQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKP 60
           MS I+SV++E+R+F P E F  +A +  ME Y ALC++A  DYEGFWA   REL+ W +P
Sbjct: 1   MSTIDSVLKENRLFPPSEDFRVKANVSGMEGYNALCEQANNDYEGFWADLGRELVSWKQP 60

Query: 61  FTKVLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELH 120
           FTKVL+ + APFYKWFEDG LN SYNCLDR+L  G+ DK AI+FEADDG+ T VTYRELH
Sbjct: 61  FTKVLNSTEAPFYKWFEDGTLNVSYNCLDRHLA-GSGDKPAIIFEADDGTSTPVTYRELH 119

Query: 121 GKVCRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQER 180
            +VC+FANGL++LG++KGDRVV+YMPM VE VVAMQACAR+GA HSVVFGGFSAKSLQER
Sbjct: 120 QRVCQFANGLRSLGVKKGDRVVVYMPMGVEAVVAMQACARIGAIHSVVFGGFSAKSLQER 179

Query: 181 LVDVGAVALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRD 240
           + D  A  +ITA+E +RGGK++PL+A+ DDALALGGCE++++++V++RT    A  + R+
Sbjct: 180 IGDARASLVITANEGLRGGKSVPLQAVVDDALALGGCESIQHIVVFQRTQTAPAQWDARN 239

Query: 241 RWMEDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFD 300
            W  +++A QP  CE E ++AE PLF+LYTSGSTGKPKG+QHS+GGYLL  L+TMKW FD
Sbjct: 240 VWWHELTAQQPTECEPEWMNAEDPLFILYTSGSTGKPKGIQHSSGGYLLGTLVTMKWVFD 299

Query: 301 IKPDDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIF 360
            KPDD+FWCTAD+GW+TGH+Y+ YGPLA GATQVVFEG+PTYP+A RFW MIARHKV+ F
Sbjct: 300 YKPDDVFWCTADVGWITGHSYVCYGPLAIGATQVVFEGIPTYPDANRFWSMIARHKVTTF 359

Query: 361 YTAPTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIV 420
           YTAPTAIRSLIK   AD    P Q+DLSSLRLLGTVGEPINPEAW+WY++ +G  RCPIV
Sbjct: 360 YTAPTAIRSLIKLG-AD---LPGQHDLSSLRLLGTVGEPINPEAWIWYHEVVGGGRCPIV 415

Query: 421 DTFWQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPW 480
           DT+WQTETG HMI PLPGA    PGSCTLPLPGI+A IVDE+G  V  G GG LV+K+PW
Sbjct: 416 DTWWQTETGAHMIAPLPGAVATKPGSCTLPLPGILADIVDESGAPVEPGKGGALVIKKPW 475

Query: 481 PAMIRTIWGDPERFRKSYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRM 540
           P+M+RTIWGDP+RF+K+YFPEE  G+LYLAGD +  D + GY  IMGRIDDVLNVSGHR+
Sbjct: 476 PSMVRTIWGDPDRFKKTYFPEEFNGQLYLAGDSAHTD-ENGYIWIMGRIDDVLNVSGHRL 534

Query: 541 GTMEIESALVSNPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVG 600
           GTMEIESALV+NPLVAEAAVVGRP ++ GEA+ AFVVLK++RP GE+A +IA ELR WV 
Sbjct: 535 GTMEIESALVANPLVAEAAVVGRPHEIKGEAVVAFVVLKQNRPEGEDAKRIARELREWVA 594

Query: 601 KEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQLK 657
            EIG IA+P +IRFG+NLPKTRSGKIMRRLLR +AKGEEITQD STLENPAILEQL+
Sbjct: 595 HEIGKIAQPDEIRFGENLPKTRSGKIMRRLLRVIAKGEEITQDVSTLENPAILEQLR 651


Lambda     K      H
   0.319    0.136    0.422 

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: 1477
Number of extensions: 57
Number of successful extensions: 4
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: 660
Length of database: 655
Length adjustment: 38
Effective length of query: 622
Effective length of database: 617
Effective search space:   383774
Effective search space used:   383774
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 (21.7 bits)
S2: 54 (25.4 bits)

Align candidate WP_053937296.1 WG78_RS08045 (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.978599.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.1e-303  994.2   0.0   1.3e-303  993.9   0.0    1.0  1  NCBI__GCF_001294205.1:WP_053937296.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001294205.1:WP_053937296.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  993.9   0.0  1.3e-303  1.3e-303       3     627 ..      28     651 ..      26     653 .. 0.97

  Alignments for each domain:
  == domain 1  score: 993.9 bits;  conditional E-value: 1.3e-303
                             TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvekrkdkva 75 
                                            +e y++l+e+a++d+e fwa+l++e ++w++pf+kvl+++++p++kWfedg+lnvsync+drh++ + dk a
  NCBI__GCF_001294205.1:WP_053937296.1  28 GMEGYNALCEQANNDYEGFWADLGRELVSWKQPFTKVLNSTEAPFYKWFEDGTLNVSYNCLDRHLAGSGDKPA 100
                                           6889********************************************************************* PP

                             TIGR02188  76 iiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGf 148
                                           ii+e+d+ +  s  +tY+el+++vc++an l++lGvkkgdrv++Y+pm +eav+am+acaRiGa+hsvvf+Gf
  NCBI__GCF_001294205.1:WP_053937296.1 101 IIFEADDGT--STPVTYRELHQRVCQFANGLRSLGVKKGDRVVVYMPMGVEAVVAMQACARIGAIHSVVFGGF 171
                                           ******765..79************************************************************ PP

                             TIGR02188 149 saealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDvwwe 220
                                           sa++l+eRi da+a lvita+eglRggk+++l+++vd+al+   + s+++++v++rt++  a+w + r+vww+
  NCBI__GCF_001294205.1:WP_053937296.1 172 SAKSLQERIGDARASLVITANEGLRGGKSVPLQAVVDDALALGGCeSIQHIVVFQRTQTAPAQW-DARNVWWH 243
                                           ****************************************9988779***********997766.59****** PP

                             TIGR02188 221 elvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWv 293
                                           el+++ +++ecepe++++edplfiLYtsGstGkPkG++h++gGyll + +t+k+vfd+k++d+fwCtaDvGW+
  NCBI__GCF_001294205.1:WP_053937296.1 244 ELTAQ-QPTECEPEWMNAEDPLFILYTSGSTGKPKGIQHSSGGYLLGTLVTMKWVFDYKPDDVFWCTADVGWI 315
                                           ****6.******************************************************************* PP

                             TIGR02188 294 tGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvl 366
                                           tGhsY++ygPLa+Gat+++feg+ptypda+rfw++i ++kvt+fYtaPtaiR+l+klg +l+ +hdlsslr+l
  NCBI__GCF_001294205.1:WP_053937296.1 316 TGHSYVCYGPLAIGATQVVFEGIPTYPDANRFWSMIARHKVTTFYTAPTAIRSLIKLGADLPGQHDLSSLRLL 388
                                           ************************************************************************* PP

                             TIGR02188 367 gsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegke 439
                                           g+vGepinpeaw Wy+evvG ++cpivdtwWqtetG+++i+plpg a+++kpgs+tlPl+Gi a++vde+g +
  NCBI__GCF_001294205.1:WP_053937296.1 389 GTVGEPINPEAWIWYHEVVGGGRCPIVDTWWQTETGAHMIAPLPG-AVATKPGSCTLPLPGILADIVDESGAP 460
                                           *********************************************.6************************** PP

                             TIGR02188 440 veeeeeggvLvikkpwPsmlrtiygdeerfvetYfkk.lkg.lyftGDgarrdkdGyiwilGRvDdvinvsGh 510
                                           ve++++ g+LvikkpwPsm+rti+gd++rf +tYf + ++g ly++GD+a++d++Gyiwi+GR+Ddv+nvsGh
  NCBI__GCF_001294205.1:WP_053937296.1 461 VEPGKG-GALVIKKPWPSMVRTIWGDPDRFKKTYFPEeFNGqLYLAGDSAHTDENGYIWIMGRIDDVLNVSGH 532
                                           ***999.8***************************75255579****************************** PP

                             TIGR02188 511 rlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedee..elekelkklvrkeigpiakpdk 581
                                           rlgt+eiesalv+++ vaeaavvg+p+eikgea+vafvvlk+++ e e+  ++++el+++v++eig+ia+pd+
  NCBI__GCF_001294205.1:WP_053937296.1 533 RLGTMEIESALVANPLVAEAAVVGRPHEIKGEAVVAFVVLKQNRPEGEDakRIARELREWVAHEIGKIAQPDE 605
                                           ******************************************9986655559********************* PP

                             TIGR02188 582 ilvveelPktRsGkimRRllrkiaegeellgdvstledpsvveelk 627
                                           i++ e+lPktRsGkimRRllr ia+gee+++dvstle+p+++e+l+
  NCBI__GCF_001294205.1:WP_053937296.1 606 IRFGENLPKTRSGKIMRRLLRVIAKGEEITQDVSTLENPAILEQLR 651
                                           *******************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (655 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: 32.79
//
[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