Alignments for a candidate for acs in Epibacterium ulvae U95

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Epibacterium ulvae U95

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate WP_090216759.1 CV091_RS04885 acetate--CoA ligase

Query= reanno::pseudo3_N2E3:AO353_03060
         (651 letters)



>NCBI__GCF_002796795.1:WP_090216759.1
          Length = 651

 Score =  863 bits (2229), Expect = 0.0
 Identities = 424/645 (65%), Positives = 488/645 (75%), Gaps = 13/645 (2%)

Query: 5   SLYPVRPEVAANTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDHH 64
           S Y    +   N   D A Y  +Y  S+ +P+GFWREQ KR+DWIKPFT VK  S+D  +
Sbjct: 7   STYTPTEDFVQNAHVDAAKYDVLYAASIEDPEGFWREQGKRVDWIKPFTQVKDVSYDFGN 66

Query: 65  VDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPAE-SRNITYRELHEQVCKFANA 123
           V IKW+ADGTLNV+ NC+DRHLA+RGDQ AIIWE DDP + +++ITY++LH  VCK AN 
Sbjct: 67  VGIKWYADGTLNVAANCVDRHLAKRGDQTAIIWEPDDPKDPAQHITYKDLHTSVCKMANV 126

Query: 124 LRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVV 183
           L    V +GD V IYMPMIPEA  AMLAC R+GAIHS+VF GFSP+ALA RI  C +K+V
Sbjct: 127 LETLGVSKGDRVVIYMPMIPEAAYAMLACARVGAIHSIVFAGFSPDALAARINGCDAKLV 186

Query: 184 ITADEGLRAGKKISLKANVDDALTNPETSSIQKVIVCKRTGGNIKWNQHRDIWYEDLMKV 243
           ITADE  R GKK  LK N D AL+  + +   + +V +RTGG++ WN  RD  Y  L + 
Sbjct: 187 ITADEAPRGGKKTPLKTNADAALS--QCADAVQCLVVRRTGGDVPWNDARDRDYSKLSEG 244

Query: 244 AGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTGGYLLYAALTHERVFDYRPGEIYWC 303
           A     P EM AE+ LFILYTSGSTG+PKGV HTTGGYL+YA+LT E  FDY  G++YWC
Sbjct: 245 ANLTHTPAEMNAEDPLFILYTSGSTGQPKGVVHTTGGYLVYASLTQEVTFDYHDGDVYWC 304

Query: 304 TADVGWVTGHTYIVYGPLANGATTLLFEGVPNYPDITRVAKIIDKHKVNILYTAPTAIRA 363
           TADVGWVTGH+YIVYGPLANGATT++FEGVP YPD +R  ++ +KHKVN  YTAPTAIRA
Sbjct: 305 TADVGWVTGHSYIVYGPLANGATTVMFEGVPTYPDASRFWQVCEKHKVNQFYTAPTAIRA 364

Query: 364 MMAQGTAAVEGADGSSLRLLGSVGEPINPEAWEWYYKNVGQSRCPIVDTWWQTETGATLM 423
           +M QG   VE  D SSLRLLG+VGEPINPEAW WY   VG  RCPIVDTWWQTETG  LM
Sbjct: 365 LMGQGNEFVEKCDLSSLRLLGTVGEPINPEAWTWYNDIVGGGRCPIVDTWWQTETGGHLM 424

Query: 424 SPLPGAHGLKPGSAARPFFGVVPALVDN------LGNIIEGVAEGNLVILDSWPGQARTL 477
           +PLPGAH  KPGSA +PFFG+ P ++D        GN +EGV    L I DSWPGQ RT+
Sbjct: 425 TPLPGAHATKPGSAMKPFFGIEPVVLDPASGDEITGNDVEGV----LCIKDSWPGQMRTV 480

Query: 478 YGDHDRFVDTYFKTFRGMYFTGDGARRDADGYWWITGRVDDVLNVSGHRMGTAEIESAMV 537
           +GDHDRF  TYF  ++G YFTGDG RRDADG +WITGRVDDV+NVSGHRMGTAE+ESA+V
Sbjct: 481 WGDHDRFEKTYFSDYKGYYFTGDGCRRDADGDYWITGRVDDVINVSGHRMGTAEVESALV 540

Query: 538 AHPKVAEAAVVGVPHDIKGQGIYVYVTLNGGEEPSEALRLELKNWVRKEIGPIASPDVIQ 597
           AH  VAEAAVVG PHDIKGQGIY YVTL  GE PSE LR EL+ WVR EIGPIASPDVIQ
Sbjct: 541 AHATVAEAAVVGYPHDIKGQGIYCYVTLMNGETPSEELRKELRTWVRSEIGPIASPDVIQ 600

Query: 598 WAPGLPKTRSGKIMRRILRKIATGEYDGLGDISTLADPGVVQHLI 642
           WAPGLPKTRSGKIMRRILRKIA  +Y  LGD STLADP VV  LI
Sbjct: 601 WAPGLPKTRSGKIMRRILRKIAENDYGALGDTSTLADPSVVDDLI 645


Lambda     K      H
   0.319    0.136    0.425 

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: 1498
Number of extensions: 83
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: 651
Length of database: 651
Length adjustment: 38
Effective length of query: 613
Effective length of database: 613
Effective search space:   375769
Effective search space used:   375769
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_090216759.1 CV091_RS04885 (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.520103.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
          0 1012.5   0.0          0 1012.2   0.0    1.0  1  NCBI__GCF_002796795.1:WP_090216759.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002796795.1:WP_090216759.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1012.2   0.0         0         0       4     628 ..      23     646 ..      20     647 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1012.2 bits;  conditional E-value: 0
                             TIGR02188   4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdk 73 
                                           + +y  ly+ +iedpe fw++++k+ ++w+kpf++v+d s +     +kW++dg+lnv++ncvdrh++kr d+
  NCBI__GCF_002796795.1:WP_090216759.1  23 AAKYDVLYAASIEDPEGFWREQGKR-VDWIKPFTQVKDVSYDFgnvGIKWYADGTLNVAANCVDRHLAKRGDQ 94 
                                           6799********************5.************9987665789************************* PP

                             TIGR02188  74 vaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfa 146
                                           +aiiwe d++++ ++++tY++l+++vc++anvl++lGv kgdrv+iY+pmipea++amlacaR+Ga+hs+vfa
  NCBI__GCF_002796795.1:WP_090216759.1  95 TAIIWEPDDPKDPAQHITYKDLHTSVCKMANVLETLGVSKGDRVVIYMPMIPEAAYAMLACARVGAIHSIVFA 167
                                           ************************************************************************* PP

                             TIGR02188 147 GfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvww 219
                                           Gfs++ala Ri+ ++aklvitade+ Rggk+++lk+++d+al+++ ++v+ +lvv+rtg +v  w++ rD  +
  NCBI__GCF_002796795.1:WP_090216759.1 168 GFSPDALAARINGCDAKLVITADEAPRGGKKTPLKTNADAALSQCADAVQ-CLVVRRTGGDVP-WNDARDRDY 238
                                           *********************************************98775.**********66.********* PP

                             TIGR02188 220 eelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGW 292
                                           ++l e +a+ +++p+++++edplfiLYtsGstG+PkGv+httgGyl++a+lt++++fd++d+d++wCtaDvGW
  NCBI__GCF_002796795.1:WP_090216759.1 239 SKLSE-GANLTHTPAEMNAEDPLFILYTSGSTGQPKGVVHTTGGYLVYASLTQEVTFDYHDGDVYWCTADVGW 310
                                           *****.6****************************************************************** PP

                             TIGR02188 293 vtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrv 365
                                           vtGhsYivygPLanGatt++fegvptypdasrfw+v+ek+kv++fYtaPtaiRalm +g+e+v+k dlsslr+
  NCBI__GCF_002796795.1:WP_090216759.1 311 VTGHSYIVYGPLANGATTVMFEGVPTYPDASRFWQVCEKHKVNQFYTAPTAIRALMGQGNEFVEKCDLSSLRL 383
                                           ************************************************************************* PP

                             TIGR02188 366 lgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvd.eeg 437
                                           lg+vGepinpeaw+Wy++ vG ++cpivdtwWqtetGg+l+tplpg a ++kpgsa++P+fGie++v+d  +g
  NCBI__GCF_002796795.1:WP_090216759.1 384 LGTVGEPINPEAWTWYNDIVGGGRCPIVDTWWQTETGGHLMTPLPG-AHATKPGSAMKPFFGIEPVVLDpASG 455
                                           **********************************************.6*********************999* PP

                             TIGR02188 438 keveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGh 510
                                           +e++ ++ +gvL+ik++wP+++rt++gd++rf +tYf+++kg+yftGDg+rrd+dG++wi+GRvDdvinvsGh
  NCBI__GCF_002796795.1:WP_090216759.1 456 DEITGNDVEGVLCIKDSWPGQMRTVWGDHDRFEKTYFSDYKGYYFTGDGCRRDADGDYWITGRVDDVINVSGH 528
                                           ****666669*************************************************************** PP

                             TIGR02188 511 rlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkil 583
                                           r+gtae+esalv+h +vaeaavvg+p++ikg+ i+++v+l++g++++ee l+kel+++vr+eigpia+pd i+
  NCBI__GCF_002796795.1:WP_090216759.1 529 RMGTAEVESALVAHATVAEAAVVGYPHDIKGQGIYCYVTLMNGETPSEE-LRKELRTWVRSEIGPIASPDVIQ 600
                                           ***********************************************95.*********************** PP

                             TIGR02188 584 vveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
                                           +++ lPktRsGkimRR+lrkiae++  +lgd+stl+dpsvv++l++
  NCBI__GCF_002796795.1:WP_090216759.1 601 WAPGLPKTRSGKIMRRILRKIAENDyGALGDTSTLADPSVVDDLIA 646
                                           *************************99***************9975 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: 00:00:00.00
# Mc/sec: 42.29
//
[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:

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