GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aacS in Tistlia consotensis USBA 355

Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_085123734.1 B9O00_RS16180 acetoacetate--CoA ligase

Query= BRENDA::Q9Z3R3
         (650 letters)



>NCBI__GCF_900177295.1:WP_085123734.1
          Length = 652

 Score =  860 bits (2221), Expect = 0.0
 Identities = 420/653 (64%), Positives = 495/653 (75%), Gaps = 4/653 (0%)

Query: 1   MQAERPLWVPDREIVERSPMAEFIDWCGERFGRSFADYDAFHDWSVSERGAFWTAVWEHC 60
           M   +PLW P  E V  + +  F+    ER G +F  YDA +DWS+ +   FW A+W+ C
Sbjct: 1   MTETQPLWTPSPERVADANLTRFMQALSERSGLAFGGYDALYDWSIRDVEGFWRAIWDWC 60

Query: 61  KVIGESG-EKALVDGDRMLDARFFPEARLNFAENLLRKTGSGDALIFRGEDKVSYRLTWD 119
            VIGE      L+DGDRM  ARFFPE  LNFAENLLR+    +A++FR EDK   RLTW 
Sbjct: 61  GVIGEGPLTPGLLDGDRMPGARFFPEVTLNFAENLLRRNDGSEAIVFRSEDKAERRLTWA 120

Query: 120 ELRALVSRLQQALRAQGIGAGDRVAAMMPNMPETIALMLATASVGAIWSSCSPDFGEQGV 179
           EL   VSR  QAL A+G+G GDRVAA +PNMPET+  MLATA++GA++SSCSPDFGEQGV
Sbjct: 121 ELTTAVSRTAQALAAEGVGPGDRVAAYLPNMPETVIAMLATAALGAVFSSCSPDFGEQGV 180

Query: 180 LDRFGQIAPKLFIVCDGYWYNGKRQDVDSKVRAVAKSLGA--PTVIVPYAGDSAALAPTV 237
           LDRFGQI PK+   CDGY+Y GK  D+ +KVRAVA  L +    V+ P  GD +A  P V
Sbjct: 181 LDRFGQIEPKVLFACDGYFYAGKTLDIRAKVRAVAAELPSVGKVVLCPLIGDGSA-EPGV 239

Query: 238 EGGVTLADFIAGFQAGPLVFERLPFGHPLYILFSSGTTGVPKCIVHSAGGTLLQHLKEHR 297
             GV LADF+A F+AGP+ + R  F  PLYI+FSSGTTG PKCIVH  GGTLLQHLKEHR
Sbjct: 240 PKGVWLADFLAPFEAGPIAYLRQGFNAPLYIMFSSGTTGKPKCIVHGVGGTLLQHLKEHR 299

Query: 298 FHCGLRDGERLFYFTTCGWMMWNWLASGLAVGATLCLYDGSPFCPDGNVLFDYAAAERFA 357
               ++ G+R+FYFTTCGWMMWNWL SGLA  ATL LYDGSPF P  +V++DY  AE+ +
Sbjct: 300 LQSDVKPGDRIFYFTTCGWMMWNWLVSGLASEATLLLYDGSPFHPTRDVVYDYLQAEKAS 359

Query: 358 VFGTSAKYIDAVRKGGFTPARTHDLSSLRLMTSTGSPLSPEGFSFVYEGIKPDVQLASIS 417
           +FGTSAKYIDA  K G  P  THDLSS+R++ STGSPL PE F +VY  +K DV L+SIS
Sbjct: 360 LFGTSAKYIDACAKAGLKPIETHDLSSVRVICSTGSPLVPESFDYVYRDVKKDVCLSSIS 419

Query: 418 GGTDIVSCFVLGNPLKPVWRGEIQGPGLGLAVDVWNDEGKPVRGEKGELVCTRAFPSMPV 477
           GGTDIVSCFVLGNP+ PVWRGEIQ  GLG+AV+VWNDEG+PV GE+GELVC R FPSMP+
Sbjct: 420 GGTDIVSCFVLGNPIGPVWRGEIQARGLGMAVEVWNDEGQPVVGEQGELVCVRPFPSMPL 479

Query: 478 MFWNDPDGAKYRAAYFDRFDNVWCHGDFAEWTPHGGIVIHGRSDATLNPGGVRIGTAEIY 537
            FWNDPDG +YRAAYF+RF  VWCHGDF E T HGGIVI+GRSDA LNPGGVRIGTAEIY
Sbjct: 480 CFWNDPDGERYRAAYFERFPGVWCHGDFVELTTHGGIVIYGRSDAVLNPGGVRIGTAEIY 539

Query: 538 NQVEQMDEVAEALCIGQDWEDDVRVVLFVRLARGVELTEALTREIKNRIRSGASPRHVPA 597
            QVE++ EV E++ IGQ+W+ DVRVVLFV+LA G  L + L   I+  IR GASPRHVPA
Sbjct: 540 RQVEKLPEVLESIVIGQNWDGDVRVVLFVKLAEGKTLDDELVARIRKTIREGASPRHVPA 599

Query: 598 KIIAVADIPRTKSGKIVELAVRDVVHGRPVKNKEALANPEALDLFAGLEELKS 650
           KI+AV DIPRT+SGKIVELAVRDVVHGRP+KN+EALANPEALD +    ELK+
Sbjct: 600 KILAVPDIPRTRSGKIVELAVRDVVHGRPIKNQEALANPEALDHYRDRSELKA 652


Lambda     K      H
   0.322    0.139    0.441 

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: 1530
Number of extensions: 56
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: 650
Length of database: 652
Length adjustment: 38
Effective length of query: 612
Effective length of database: 614
Effective search space:   375768
Effective search space used:   375768
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 (21.9 bits)
S2: 54 (25.4 bits)

Align candidate WP_085123734.1 B9O00_RS16180 (acetoacetate--CoA ligase)
to HMM TIGR01217 (acetoacetate-CoA ligase (EC 6.2.1.16))

# 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/TIGR01217.hmm
# target sequence database:        /tmp/gapView.3119149.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01217  [M=652]
Accession:   TIGR01217
Description: ac_ac_CoA_syn: acetoacetate-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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.5e-303  993.9   0.0   1.7e-303  993.7   0.0    1.0  1  NCBI__GCF_900177295.1:WP_085123734.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900177295.1:WP_085123734.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  993.7   0.0  1.7e-303  1.7e-303       3     651 ..       4     651 ..       2     652 .] 0.99

  Alignments for each domain:
  == domain 1  score: 993.7 bits;  conditional E-value: 1.7e-303
                             TIGR01217   3 eqvlwepdaervkdarlarfraavgerfGaalgdydalyrwsvdeldafwkavwefsdvvfssaek.evvdds 74 
                                            q+lw+p  erv+da+l+rf +a +er G+a+g+ydaly+ws+++ + fw+a+w++++v+++ +    ++d++
  NCBI__GCF_900177295.1:WP_085123734.1   4 TQPLWTPSPERVADANLTRFMQALSERSGLAFGGYDALYDWSIRDVEGFWRAIWDWCGVIGEGPLTpGLLDGD 76 
                                           59************************************************************9875379**** PP

                             TIGR01217  75 kmlaarffpgarlnyaenllrkkgsedallyvdeekesakvtfeelrrqvaslaaalralGvkkGdrvagylp 147
                                           +m++arffp+ +ln+aenllr+++  +a+++++e+k   ++t++el   v++ a+al a Gv++Gdrva+ylp
  NCBI__GCF_900177295.1:WP_085123734.1  77 RMPGARFFPEVTLNFAENLLRRNDGSEAIVFRSEDKAERRLTWAELTTAVSRTAQALAAEGVGPGDRVAAYLP 149
                                           ************************************************************************* PP

                             TIGR01217 148 nipeavaallatasvGaiwsscspdfGargvldrfsqiepkllfsvdgyvynGkehdrrekvrevakelpdlr 220
                                           n+pe+v a+lata++Ga++sscspdfG++gvldrf+qiepk+lf++dgy y Gk  d r kvr+va elp++ 
  NCBI__GCF_900177295.1:WP_085123734.1 150 NMPETVIAMLATAALGAVFSSCSPDFGEQGVLDRFGQIEPKVLFACDGYFYAGKTLDIRAKVRAVAAELPSVG 222
                                           ************************************************************************* PP

                             TIGR01217 221 avvlipyvgdreklapkvegaltledllaaaqaaelvfeqlpfdhplyilfssGttGvpkaivhsaGGtlvqh 293
                                           +vvl p++gd ++ +p v+ ++ l+d+la ++a+++ + +  f+ plyi+fssGttG pk+ivh  GGtl+qh
  NCBI__GCF_900177295.1:WP_085123734.1 223 KVVLCPLIGDGSA-EPGVPKGVWLADFLAPFEAGPIAYLRQGFNAPLYIMFSSGTTGKPKCIVHGVGGTLLQH 294
                                           *********7665.577******************************************************** PP

                             TIGR01217 294 lkehvlhcdltdgdrllyyttvGwmmwnflvsglatGatlvlydGsplvpatnvlfdlaeregitvlGtsaky 366
                                           lkeh+l +d+++gdr++y+tt+Gwmmwn+lvsgla  atl lydGsp+ p+ +v +d+ ++e+++++Gtsaky
  NCBI__GCF_900177295.1:WP_085123734.1 295 LKEHRLQSDVKPGDRIFYFTTCGWMMWNWLVSGLASEATLLLYDGSPFHPTRDVVYDYLQAEKASLFGTSAKY 367
                                           ************************************************************************* PP

                             TIGR01217 367 vsavrkkglkparthdlsalrlvastGsplkpegfeyvyeeikadvllasisGGtdivscfvganpslpvykG 439
                                           ++a+ k+glkp++thdls++r++ stGspl pe+f+yvy+ +k dv l+sisGGtdivscfv++np  pv++G
  NCBI__GCF_900177295.1:WP_085123734.1 368 IDACAKAGLKPIETHDLSSVRVICSTGSPLVPESFDYVYRDVKKDVCLSSISGGTDIVSCFVLGNPIGPVWRG 440
                                           ************************************************************************* PP

                             TIGR01217 440 eiqapglGlaveawdeeGkpvtgekGelvvtkplpsmpvrfwndedGskyrkayfdkypgvwahGdyieltpr 512
                                           eiqa+glG+ave+w++eG+pv ge+Gelv+ +p+psmp+ fwnd+dG +yr+ayf+++pgvw+hGd++elt++
  NCBI__GCF_900177295.1:WP_085123734.1 441 EIQARGLGMAVEVWNDEGQPVVGEQGELVCVRPFPSMPLCFWNDPDGERYRAAYFERFPGVWCHGDFVELTTH 513
                                           ************************************************************************* PP

                             TIGR01217 513 GgivihGrsdatlnpnGvrlGsaeiynaverldeveeslvigqeqedgeervvlfvklasGatldealvkeik 585
                                           Ggivi+Grsda lnp+Gvr+G+aeiy +ve+l+ev es+vigq++ dg++rvvlfvkla+G+tld++lv +i+
  NCBI__GCF_900177295.1:WP_085123734.1 514 GGIVIYGRSDAVLNPGGVRIGTAEIYRQVEKLPEVLESIVIGQNW-DGDVRVVLFVKLAEGKTLDDELVARIR 585
                                           *******************************************98.89************************* PP

                             TIGR01217 586 dairaglsprhvpskiievagiprtlsGkkvevavkdvvaGkpvenkgalsnpealdlyeeleelk 651
                                           ++ir g+sprhvp+ki++v++iprt sGk+ve+av+dvv+G+p++n++al+npeald y++ +elk
  NCBI__GCF_900177295.1:WP_085123734.1 586 KTIREGASPRHVPAKILAVPDIPRTRSGKIVELAVRDVVHGRPIKNQEALANPEALDHYRDRSELK 651
                                           *************************************************************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (652 nodes)
Target sequences:                          1  (652 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 35.39
//
[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