Alignments for a candidate for acs in Pedobacter arcticus A12

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Pedobacter arcticus A12

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate WP_017257106.1 B176_RS0102045 acetate--CoA ligase

Query= reanno::pseudo5_N2C3_1:AO356_18695
         (651 letters)



>NCBI__GCF_000302595.1:WP_017257106.1
          Length = 635

 Score =  711 bits (1835), Expect = 0.0
 Identities = 359/626 (57%), Positives = 442/626 (70%), Gaps = 10/626 (1%)

Query: 24  YKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDHHVDIKWFADGTLNVSYNCLD 83
           YK  YQ+SV  P+ FW + A    W K +  V   +F +  ++  WF    LN++ NC+D
Sbjct: 11  YKEAYQRSVEQPEAFWADIADNFQWKKKWDKVLDWNFKEPKIE--WFKGAKLNITENCID 68

Query: 84  RHLAERGDQIAIIWEGDDPSES-RNITYRELHEEVCKFANALRGQDVHRGDVVTIYMPMI 142
           RHLA++GDQ AIIWE +DP+E  R +TY++LHE+VC FAN L+  DV +GD V IYMPMI
Sbjct: 69  RHLADKGDQPAIIWEANDPNEHHRVLTYKQLHEKVCLFANVLKNNDVKKGDRVCIYMPMI 128

Query: 143 PEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVVITADEGVRAGKKIPLKANV 202
           PE  +A+LAC RIGAIHSVVFGGFS +++A RI D + ++VITAD G R  K IPLK  +
Sbjct: 129 PELAIAVLACARIGAIHSVVFGGFSAQSIADRINDAQCEMVITADGGFRGPKDIPLKNVI 188

Query: 203 DDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMKVAGTV----CAPKEMGAEEA 258
           DDAL   +  S++ VIV  RT   I   + RD W++D +    T+    C  +EM AE+ 
Sbjct: 189 DDALV--QCPSVKTVIVLTRTRTPISMIKGRDKWWQDEIHKVETLGMIDCPAEEMDAEDP 246

Query: 259 LFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYWCTADVGWVTGHSYIVY 318
           LFILYTSGSTGKPKGV HTTAGY++Y A T + VF Y+P +VY+CTAD+GW+TGHSYI+Y
Sbjct: 247 LFILYTSGSTGKPKGVVHTTAGYMIYTAYTFQNVFQYQPQDVYFCTADIGWITGHSYIIY 306

Query: 319 GPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIRAMMASGTAAVEGADGS 378
           GPLA GATTL+FEGVP YPD  R   ++DK KV+ LYTAPTAIR++M SG   V+  D S
Sbjct: 307 GPLAQGATTLMFEGVPTYPDAGRFWDIVDKFKVNTLYTAPTAIRSLMQSGLDYVKDKDLS 366

Query: 379 SLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLISPLPGATALKPGSAT 438
           SL++LGSVGEPIN EAW WY  N+GK +CPIVDTWWQTE GG+LISP+   T  KP  AT
Sbjct: 367 SLKVLGSVGEPINEEAWHWYNDNIGKGKCPIVDTWWQTENGGILISPIANVTPTKPCYAT 426

Query: 439 RPFFGVVPALVDNLGNLIEG-AAEGNLVILDSWPGQARTLYGDHDRFVDTYFKTFSGMYF 497
            P  GV P LVD  G +IEG    GNL I   WPG  RT YGDH+R   TYF T+  MYF
Sbjct: 427 LPLPGVQPVLVDENGAVIEGNGVSGNLCIKFPWPGMLRTTYGDHERCKLTYFSTYEDMYF 486

Query: 498 TGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVAEAAVVGVPHDIKGQ 557
           TGDG  RDEDGYY ITGRVDDV+NVSGHR+GTAE+E+A+     V E+AVVG PH+IKGQ
Sbjct: 487 TGDGCLRDEDGYYRITGRVDDVINVSGHRIGTAEVENAINMFTDVVESAVVGYPHEIKGQ 546

Query: 558 GIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLPKTRSGKIMRRILRK 617
           GIY YV L+   E  E  + ++   V + IG IA PD IQ+  GLPKTRSGKIMRRILRK
Sbjct: 547 GIYAYVILDKESEDVELTKKDIAMTVSRIIGAIARPDKIQFVTGLPKTRSGKIMRRILRK 606

Query: 618 IATAEYDGLGDISTLADPGVVAHLIE 643
           IA  +   +GD+STL DP VV  +I+
Sbjct: 607 IAEGDMKNVGDVSTLLDPAVVEEIIK 632


Lambda     K      H
   0.318    0.135    0.418 

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: 1279
Number of extensions: 62
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: 651
Length of database: 635
Length adjustment: 38
Effective length of query: 613
Effective length of database: 597
Effective search space:   365961
Effective search space used:   365961
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)

Align candidate WP_017257106.1 B176_RS0102045 (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.520129.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-293  961.2   0.3   1.2e-293  961.0   0.3    1.0  1  NCBI__GCF_000302595.1:WP_017257106.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000302595.1:WP_017257106.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  961.0   0.3  1.2e-293  1.2e-293       2     628 ..       6     632 ..       5     633 .. 0.97

  Alignments for each domain:
  == domain 1  score: 961.0 bits;  conditional E-value: 1.2e-293
                             TIGR02188   2 aeleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep.kvkWfedgelnvsyncvdrhvekrkdk 73 
                                           ++ +eyke y++++e+pe+fwa+ a  +++w+k+++kvld+++++ k++Wf++++ln++ nc+drh++++ d+
  NCBI__GCF_000302595.1:WP_017257106.1   6 SSFDEYKEAYQRSVEQPEAFWADIAD-NFQWKKKWDKVLDWNFKEpKIEWFKGAKLNITENCIDRHLADKGDQ 77 
                                           6789*********************9.6**************9988*************************** PP

                             TIGR02188  74 vaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfa 146
                                            aiiwe+++++e++r ltY++l+++vc +anvlk+  vkkgdrv+iY+pmipe++ia+lacaRiGa+hsvvf+
  NCBI__GCF_000302595.1:WP_017257106.1  78 PAIIWEANDPNEHHRVLTYKQLHEKVCLFANVLKNNDVKKGDRVCIYMPMIPELAIAVLACARIGAIHSVVFG 150
                                           ************************************************************************* PP

                             TIGR02188 147 GfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvww 219
                                           Gfsa+++a+Ri+da++++vitad+g+Rg k i+lk+++d+al +++ sv++v+v+ rt ++++ + +grD+ww
  NCBI__GCF_000302595.1:WP_017257106.1 151 GFSAQSIADRINDAQCEMVITADGGFRGPKDIPLKNVIDDALVQCP-SVKTVIVLTRTRTPIS-MIKGRDKWW 221
                                           *********************************************9.7*************76.********* PP

                             TIGR02188 220 eelvek...easaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaD 289
                                           +++++k       +c++e++d+edplfiLYtsGstGkPkGv+htt+Gy++++a+t++ vf+++++d+++CtaD
  NCBI__GCF_000302595.1:WP_017257106.1 222 QDEIHKvetLGMIDCPAEEMDAEDPLFILYTSGSTGKPKGVVHTTAGYMIYTAYTFQNVFQYQPQDVYFCTAD 294
                                           **999832123468*********************************************************** PP

                             TIGR02188 290 vGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlss 362
                                           +GW+tGhsYi+ygPLa+Gattl+fegvptypda+rfw++++k+kv+++YtaPtaiR+lm+ g + vk +dlss
  NCBI__GCF_000302595.1:WP_017257106.1 295 IGWITGHSYIIYGPLAQGATTLMFEGVPTYPDAGRFWDIVDKFKVNTLYTAPTAIRSLMQSGLDYVKDKDLSS 367
                                           ************************************************************************* PP

                             TIGR02188 363 lrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvde 435
                                           l+vlgsvGepin eaw+Wy++++Gk+kcpivdtwWqte Ggili+p++  +t++kp  atlPl+G+++++vde
  NCBI__GCF_000302595.1:WP_017257106.1 368 LKVLGSVGEPINEEAWHWYNDNIGKGKCPIVDTWWQTENGGILISPIAN-VTPTKPCYATLPLPGVQPVLVDE 439
                                           *************************************************.6********************** PP

                             TIGR02188 436 egkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvs 508
                                           +g  +e +  +g L+ik pwP+mlrt ygd+er   tYf++++++yftGDg+ rd+dGy+ i+GRvDdvinvs
  NCBI__GCF_000302595.1:WP_017257106.1 440 NGAVIEGNGVSGNLCIKFPWPGMLRTTYGDHERCKLTYFSTYEDMYFTGDGCLRDEDGYYRITGRVDDVINVS 512
                                           ******555559************************************************************* PP

                             TIGR02188 509 Ghrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdk 581
                                           Ghr+gtae+e+a+   ++v e+avvg+p+eikg+ i+a+v+l +++e  e  ++k++ ++v++ ig+ia+pdk
  NCBI__GCF_000302595.1:WP_017257106.1 513 GHRIGTAEVENAINMFTDVVESAVVGYPHEIKGQGIYAYVILDKESEDVE-LTKKDIAMTVSRIIGAIARPDK 584
                                           ******************************************99888666.69******************** PP

                             TIGR02188 582 ilvveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
                                           i++v+ lPktRsGkimRR+lrkiaeg+ +++gdvstl dp+vvee+++
  NCBI__GCF_000302595.1:WP_017257106.1 585 IQFVTGLPKTRSGKIMRRILRKIAEGDmKNVGDVSTLLDPAVVEEIIK 632
                                           ***************************9*****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (635 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: 37.84
//
[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