Alignments for a candidate for aacS in Dyadobacter tibetensis Y620-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for aacS in Dyadobacter tibetensis Y620-1

Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_044198804.1 X939_RS0107425 acetoacetate--CoA ligase

Query= BRENDA::D6EQU8
         (658 letters)



>NCBI__GCF_000566685.1:WP_044198804.1
          Length = 649

 Score =  598 bits (1541), Expect = e-175
 Identities = 294/645 (45%), Positives = 413/645 (64%), Gaps = 13/645 (2%)

Query: 9   LWQPDAQRIAQARITRFQAWAAEHHGAPAEGGYAALHRWSVDELDTFWKAVTEWFDVRFS 68
           LW+P       + + R+  W     G      Y  L  WSV +L+ FW+++ ++F+++  
Sbjct: 10  LWKPGTNLTEHSNLKRYMDWLFVKKGLYFRS-YQDLWEWSVTDLEDFWESMWQFFNIKSH 68

Query: 69  TPYARVLG--DRTMPGAQWFPGATLNYAEHALRAAGTRPDEPALLYVDETHEPAPVTWAE 126
             Y  V+      M G +WF  + LNYAEH  R       +PALL+  ET   +PVTW  
Sbjct: 69  EVYLEVISRPKSGMIGTKWFRRSKLNYAEHIFR--NKSKGKPALLFQSETRGLSPVTWER 126

Query: 127 LRRQVASLAAELRALGVRPGDRVSGYLPNIPQAVVALLATAAVGGVWTSCAPDFGARSVL 186
           L   VA++AA LR +G++PGDRV+   PN P+A++A LAT AVG VW+SC+PDFG   + 
Sbjct: 127 LEADVAAVAAWLRQIGIKPGDRVAAVFPNCPEAIIAFLATNAVGAVWSSCSPDFGVAGIA 186

Query: 187 DRFQQVEPVVLFTVDGYRYGGKEHDRRDTVAELRRELPTLRAVIHIPL--LGTEAPDGTL 244
           DRFQQ+EP VLF  DGY Y GK +        L   LP++  V+ +     G + P+ T 
Sbjct: 187 DRFQQIEPKVLFLCDGYTYNGKSYPSTTLQLALAEALPSVNDVVFVKTGDFGLQ-PERTT 245

Query: 245 DWETLTAADAEPV-YEQVPFDHPLWVLYSSGTTGLPKAIVQSQGGILVEHLKQLGLHCDL 303
            WE +       + +E VPFDHP+WVLYSSGTTG PKAI    GG L+EH K L LH ++
Sbjct: 246 AWEDILHFPHHGLEFEPVPFDHPIWVLYSSGTTGKPKAITHGVGGCLLEHYKALALHQNV 305

Query: 304 GPGDRFFWYTSTGWMMWNFLVSGLLTGTTIVLYDGSPGFPATDAQWRIAERTGATLFGTS 363
            PGDR+FWY++TGWMMWN+ +  +L G+T+V+YDG+P +P++   W +AE+   T FG+ 
Sbjct: 306 KPGDRYFWYSTTGWMMWNYALGSMLCGSTLVIYDGAPMYPSSQTLWALAEQAKITHFGSG 365

Query: 364 AAYVMACRKAGVHPARDLDLSAIQCVATTGSPLPPDGFRWLHDEFAAGGADLWIASVSGG 423
           AAY +AC KAGV  A D  L +++ + +TGSPL  D + W++ +F     D+W+ S+SGG
Sbjct: 366 AAYFIACMKAGVSIAND-QLKSLETIGSTGSPLTADAYEWIY-KFVK--KDVWLISLSGG 421

Query: 424 TDVCSCFAGAVPTLPVHIGELQAPGLGTDLQSWDPSGDPLTDEVGELVVTNPMPSMPIRF 483
           TDVCS F G  P LPV+ GE+Q   LG  ++++D +G P  +++GE+V+T P+PSMPI F
Sbjct: 422 TDVCSAFVGGSPLLPVYAGEIQCRMLGCKIEAYDENGQPQLNQLGEMVITQPLPSMPIYF 481

Query: 484 WNDPDGSRYHDSYFDTYPGVWRHGDWITLTSRGSVVIHGRSDSTLNRQGVRMGSADIYEA 543
           WNDP+  RY  SYF+TYP +WRHGDWI +  RG VVI GRSD+TLNR GVR+G+A+IY A
Sbjct: 482 WNDPNQERYLSSYFETYPNIWRHGDWIKINDRGGVVIQGRSDTTLNRGGVRIGTAEIYSA 541

Query: 544 VERLPEIRESLVIGIEQPDGGYWMPLFVHLAPGATLDDALLDRIKRTIRVNLSPRHVPDE 603
           VE LP +++SLV+ +E+ DG   + LFV L  G  L + L   IK T+R   SPRHVPD 
Sbjct: 542 VESLPPVKDSLVVYLEKSDGEGTISLFVVLKKGHQLTEELKKTIKNTLRQQYSPRHVPDT 601

Query: 604 VIEVPGIPHTLTGKRIEVPVKRLLQGTPLDKAVNPGSIDNLDLLH 648
           + EV  IP+T++GK++E PVK++L G     + N  ++ N + L+
Sbjct: 602 IEEVADIPYTISGKKMEAPVKKILMGQDPKTSANLATMRNPEALN 646


Lambda     K      H
   0.320    0.138    0.442 

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: 1340
Number of extensions: 63
Number of successful extensions: 6
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: 658
Length of database: 649
Length adjustment: 38
Effective length of query: 620
Effective length of database: 611
Effective search space:   378820
Effective search space used:   378820
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 (21.8 bits)
S2: 54 (25.4 bits)

Align candidate WP_044198804.1 X939_RS0107425 (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.2989119.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.6e-240  784.9   0.0   3.1e-240  784.6   0.0    1.0  1  NCBI__GCF_000566685.1:WP_044198804.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000566685.1:WP_044198804.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  784.6   0.0  3.1e-240  3.1e-240       5     642 ..       9     646 ..       5     649 .] 0.97

  Alignments for each domain:
  == domain 1  score: 784.6 bits;  conditional E-value: 3.1e-240
                             TIGR01217   5 vlwepdaervkdarlarfraavgerfGaalgdydalyrwsvdeldafwkavwefsdvvfssaekevvdd..sk 75 
                                           +lw+p ++  ++++l+r+ ++   + G+ +  y++l++wsv++l++fw+++w+f+++  ++ + ev+    s 
  NCBI__GCF_000566685.1:WP_044198804.1   9 ALWKPGTNLTEHSNLKRYMDWLFVKKGLYFRSYQDLWEWSVTDLEDFWESMWQFFNIKSHEVYLEVISRpkSG 81 
                                           79*****************************************************************862266 PP

                             TIGR01217  76 mlaarffpgarlnyaenllrkkgs.edallyvdeekesakvtfeelrrqvaslaaalralGvkkGdrvagylp 147
                                           m++ ++f+ ++lnyae+++r+k + ++all+++e++   +vt+e l + va +aa lr++G+k+Gdrva+++p
  NCBI__GCF_000566685.1:WP_044198804.1  82 MIGTKWFRRSKLNYAEHIFRNKSKgKPALLFQSETRGLSPVTWERLEADVAAVAAWLRQIGIKPGDRVAAVFP 154
                                           9*******************9988688********************************************** PP

                             TIGR01217 148 nipeavaallatasvGaiwsscspdfGargvldrfsqiepkllfsvdgyvynGkehdrrekvrevakelpdlr 220
                                           n pea+ a+lat +vGa+wsscspdfG+ g+ drf+qiepk+lf +dgy+ynGk    +    ++a  lp+++
  NCBI__GCF_000566685.1:WP_044198804.1 155 NCPEAIIAFLATNAVGAVWSSCSPDFGVAGIADRFQQIEPKVLFLCDGYTYNGKSYPSTTLQLALAEALPSVN 227
                                           ********************************************************9999999********** PP

                             TIGR01217 221 avvlipyvgdreklapkvegaltledllaaaqaaelvfeqlpfdhplyilfssGttGvpkaivhsaGGtlvqh 293
                                            vv++        l+p  e +  +ed+l       l+fe +pfdhp+++l+ssGttG pkai h  GG l++h
  NCBI__GCF_000566685.1:WP_044198804.1 228 DVVFVKTGD--FGLQP--ERTTAWEDILHF-PHHGLEFEPVPFDHPIWVLYSSGTTGKPKAITHGVGGCLLEH 295
                                           ***997543..55667..999*****9975.8899************************************** PP

                             TIGR01217 294 lkehvlhcdltdgdrllyyttvGwmmwnflvsglatGatlvlydGsplvpatnvlfdlaeregitvlGtsaky 366
                                            k ++lh ++++gdr+++y+t+Gwmmwn+   +++ G+tlv+ydG+p+ p+++ l+ lae+ +it +G++a+y
  NCBI__GCF_000566685.1:WP_044198804.1 296 YKALALHQNVKPGDRYFWYSTTGWMMWNYALGSMLCGSTLVIYDGAPMYPSSQTLWALAEQAKITHFGSGAAY 368
                                           ************************************************************************* PP

                             TIGR01217 367 vsavrkkglkparthdlsalrlvastGsplkpegfeyvyeeikadvllasisGGtdivscfvganpslpvykG 439
                                             a+ k+g+  a++ +l++l+++ stGspl+++++e++y+ +k dv+l s+sGGtd++s fvg+ p+lpvy G
  NCBI__GCF_000566685.1:WP_044198804.1 369 FIACMKAGVSIAND-QLKSLETIGSTGSPLTADAYEWIYKFVKKDVWLISLSGGTDVCSAFVGGSPLLPVYAG 440
                                           *********98876.7********************************************************* PP

                             TIGR01217 440 eiqapglGlaveawdeeGkpvtgekGelvvtkplpsmpvrfwndedGskyrkayfdkypgvwahGdyieltpr 512
                                           eiq++ lG ++ea+de+G+p  ++ Ge+v+t+plpsmp+ fwnd++  +y ++yf++yp++w+hGd+i+++ r
  NCBI__GCF_000566685.1:WP_044198804.1 441 EIQCRMLGCKIEAYDENGQPQLNQLGEMVITQPLPSMPIYFWNDPNQERYLSSYFETYPNIWRHGDWIKINDR 513
                                           ************************************************************************* PP

                             TIGR01217 513 GgivihGrsdatlnpnGvrlGsaeiynaverldeveeslvigqeqedgeervvlfvklasGatldealvkeik 585
                                           Gg+vi+Grsd+tln++Gvr+G+aeiy ave l+ v++slv+  e+ dge  + lfv l +G++l+e+l k ik
  NCBI__GCF_000566685.1:WP_044198804.1 514 GGVVIQGRSDTTLNRGGVRIGTAEIYSAVESLPPVKDSLVVYLEKSDGEGTISLFVVLKKGHQLTEELKKTIK 586
                                           ************************************************************************* PP

                             TIGR01217 586 dairaglsprhvpskiievagiprtlsGkkvevavkdvvaGkpve...nkgalsnpeald 642
                                           +++r + sprhvp+ i eva+ip+t+sGkk+e +vk+++ G+  +   n  ++ npeal+
  NCBI__GCF_000566685.1:WP_044198804.1 587 NTLRQQYSPRHVPDTIEEVADIPYTISGKKMEAPVKKILMGQDPKtsaNLATMRNPEALN 646
                                           *****************************************8666555888999**9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (652 nodes)
Target sequences:                          1  (649 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: 40.86
//
[ok]

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

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Candidates (tab-delimited)
Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

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 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