GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Duganella sacchari Sac-22

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_072784733.1 BUA36_RS11840 acetate--CoA ligase

Query= SwissProt::P31638
         (660 letters)



>NCBI__GCF_900143065.1:WP_072784733.1
          Length = 661

 Score = 1111 bits (2874), Expect = 0.0
 Identities = 520/651 (79%), Positives = 586/651 (90%)

Query: 9   QEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPFTKVLDQS 68
           QE RVF P   FA+QA +  M+AY ALC EA  DYEGFW+R A+E + W +PFT+ L++ 
Sbjct: 10  QESRVFAPSPAFAAQATVSGMDAYNALCAEAAADYEGFWSRLAKEHIEWQQPFTRTLNED 69

Query: 69  NAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHGKVCRFAN 128
           NAPFYKWFEDG+LN SYNCLDRNLQNGNADK AI+FEADDG  TRV+Y+ELH KVC+FAN
Sbjct: 70  NAPFYKWFEDGKLNVSYNCLDRNLQNGNADKTAIIFEADDGKTTRVSYKELHEKVCKFAN 129

Query: 129 GLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERLVDVGAVA 188
           GLKA GI+KGDRV+IYM MSVEGV AMQACAR+GATHSVVFGGFSAKSLQER++D GAVA
Sbjct: 130 GLKARGIKKGDRVIIYMSMSVEGVAAMQACARIGATHSVVFGGFSAKSLQERIIDAGAVA 189

Query: 189 LITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRDRWMEDVSA 248
           +ITADEQ+RGGK LPLKAI D+ALALGGC+ +++VIVY+RTGG +A+ EGRD W+ D+  
Sbjct: 190 VITADEQLRGGKNLPLKAIVDEALALGGCDTIKDVIVYQRTGGNIAFKEGRDLWLHDLVE 249

Query: 249 GQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFDIKPDDLFW 308
           GQ   CE E V AEHPLF+LYTSGSTG PKGVQHS+GGYLLWA +TMKW+FDIKP D++W
Sbjct: 250 GQSAECEPEWVEAEHPLFILYTSGSTGTPKGVQHSSGGYLLWAALTMKWSFDIKPSDVYW 309

Query: 309 CTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIFYTAPTAIR 368
           CTADIGWVTGH+YIAYGP A GATQVVFEGVPTYPNAGRFW+ IA+HKV+IFYTAPTAIR
Sbjct: 310 CTADIGWVTGHSYIAYGPTAVGATQVVFEGVPTYPNAGRFWETIAKHKVNIFYTAPTAIR 369

Query: 369 SLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIVDTFWQTET 428
           SLIKA++ D K+HPK YDLSSLRLLGTVGEPINPEAWMWYY  +G E+CPIVDTFWQTET
Sbjct: 370 SLIKASDVDAKVHPKNYDLSSLRLLGTVGEPINPEAWMWYYTQVGGEKCPIVDTFWQTET 429

Query: 429 GGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPWPAMIRTIW 488
           GGHMITPLPGATP+VPGSCTLPLPGIMAAIVDE+GHDVPNG GGILVVKRPWP+MIRTIW
Sbjct: 430 GGHMITPLPGATPMVPGSCTLPLPGIMAAIVDESGHDVPNGQGGILVVKRPWPSMIRTIW 489

Query: 489 GDPERFRKSYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRMGTMEIESA 548
            +P+RF+ SYFPEELGGK+YLAGDG+IR+KDTGYFTI GRIDDVLNVSGHRMGTMEIESA
Sbjct: 490 NNPDRFKTSYFPEELGGKMYLAGDGAIRNKDTGYFTITGRIDDVLNVSGHRMGTMEIESA 549

Query: 549 LVSNPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVGKEIGPIAK 608
           LV+NPLVAEAAVVG+PDD TGE+ICAFVVLK++RPTG++A K+A ELRNWV KEIGPIAK
Sbjct: 550 LVANPLVAEAAVVGKPDDTTGESICAFVVLKQARPTGDDAKKLALELRNWVAKEIGPIAK 609

Query: 609 PKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQLKQA 659
           PK+IRFGDNLPKTRSGKIMRRLLR LAKGE ITQD STLENPAILEQLK+A
Sbjct: 610 PKEIRFGDNLPKTRSGKIMRRLLRVLAKGEVITQDVSTLENPAILEQLKEA 660


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: 1565
Number of extensions: 67
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: 660
Length of database: 661
Length adjustment: 38
Effective length of query: 622
Effective length of database: 623
Effective search space:   387506
Effective search space used:   387506
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_072784733.1 BUA36_RS11840 (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.2679797.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.8e-299  978.2   0.0     9e-299  978.0   0.0    1.0  1  NCBI__GCF_900143065.1:WP_072784733.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900143065.1:WP_072784733.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  978.0   0.0    9e-299    9e-299       2     628 ..      28     659 ..      27     660 .. 0.97

  Alignments for each domain:
  == domain 1  score: 978.0 bits;  conditional E-value: 9e-299
                             TIGR02188   2 aeleeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.rkdk 73 
                                           + +++y++l++ea++d+e fw++lake++ew++pf+++l+e+++p++kWfedg+lnvsync+dr++++ ++dk
  NCBI__GCF_900143065.1:WP_072784733.1  28 SGMDAYNALCAEAAADYEGFWSRLAKEHIEWQQPFTRTLNEDNAPFYKWFEDGKLNVSYNCLDRNLQNgNADK 100
                                           56899******************************************************************** PP

                             TIGR02188  74 vaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfa 146
                                           +aii+e+d+ +  + +++Y+el+++vc++an lk+ G+kkgdrv+iY+ m +e v+am+acaRiGa+hsvvf+
  NCBI__GCF_900143065.1:WP_072784733.1 101 TAIIFEADDGK--TTRVSYKELHEKVCKFANGLKARGIKKGDRVIIYMSMSVEGVAAMQACARIGATHSVVFG 171
                                           ********775..699********************************************************* PP

                             TIGR02188 147 GfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDvw 218
                                           Gfsa++l+eRi+da a  vitade+lRggk+++lk+ivdeal+   + ++++v+v++rtg ++a +kegrD+w
  NCBI__GCF_900143065.1:WP_072784733.1 172 GFSAKSLQERIIDAGAVAVITADEQLRGGKNLPLKAIVDEALALGGCdTIKDVIVYQRTGGNIA-FKEGRDLW 243
                                           ******************************************9988889*************77.******** PP

                             TIGR02188 219 weelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvG 291
                                           +++lve ++saecepe++++e+plfiLYtsGstG+PkGv+h++gGyll+aalt+k+ fdik++d++wCtaD+G
  NCBI__GCF_900143065.1:WP_072784733.1 244 LHDLVE-GQSAECEPEWVEAEHPLFILYTSGSTGTPKGVQHSSGGYLLWAALTMKWSFDIKPSDVYWCTADIG 315
                                           ******.6***************************************************************** PP

                             TIGR02188 292 WvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklg....eelvkkhdl 360
                                           WvtGhsYi ygP a+Gat+++fegvptyp+a+rfwe+i k+kv+ifYtaPtaiR+l+k++    + ++k++dl
  NCBI__GCF_900143065.1:WP_072784733.1 316 WVTGHSYIAYGPTAVGATQVVFEGVPTYPNAGRFWETIAKHKVNIFYTAPTAIRSLIKASdvdaKVHPKNYDL 388
                                           **********************************************************97443356899**** PP

                             TIGR02188 361 sslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevv 433
                                           sslr+lg+vGepinpeaw+Wyy++vG ekcpivdt+WqtetGg++itplpg at++ pgs+tlPl+Gi+a++v
  NCBI__GCF_900143065.1:WP_072784733.1 389 SSLRLLGTVGEPINPEAWMWYYTQVGGEKCPIVDTFWQTETGGHMITPLPG-ATPMVPGSCTLPLPGIMAAIV 460
                                           ***************************************************.6******************** PP

                             TIGR02188 434 deegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkg..lyftGDgarrdkd.GyiwilGRvDd 503
                                           de+g++v ++++ g+Lv+k+pwPsm+rti+++++rf ++Yf +  g  +y++GDga r+kd Gy++i+GR+Dd
  NCBI__GCF_900143065.1:WP_072784733.1 461 DESGHDVPNGQG-GILVVKRPWPSMIRTIWNNPDRFKTSYFPEELGgkMYLAGDGAIRNKDtGYFTITGRIDD 532
                                           *********999.8***************************9876567***********999*********** PP

                             TIGR02188 504 vinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedee..elekelkklvrkeig 574
                                           v+nvsGhr+gt+eiesalv+++ vaeaavvg+pd+++ge+i+afvvlk+++ + ++  +l+ el+++v+keig
  NCBI__GCF_900143065.1:WP_072784733.1 533 VLNVSGHRMGTMEIESALVANPLVAEAAVVGKPDDTTGESICAFVVLKQARPTGDDakKLALELRNWVAKEIG 605
                                           *************************************************9987665569************** PP

                             TIGR02188 575 piakpdkilvveelPktRsGkimRRllrkiaegeellgdvstledpsvveelke 628
                                           piakp++i++ ++lPktRsGkimRRllr +a+ge +++dvstle+p+++e+lke
  NCBI__GCF_900143065.1:WP_072784733.1 606 PIAKPKEIRFGDNLPKTRSGKIMRRLLRVLAKGEVITQDVSTLENPAILEQLKE 659
                                           ***************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (661 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 0.02s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 16.33
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

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:

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