Alignments for a candidate for acs in Methylovulum miyakonense HT12

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Methylovulum miyakonense HT12

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate WP_019865511.1 METMI_RS0106740 acetate--CoA ligase

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



>NCBI__GCF_000384075.1:WP_019865511.1
          Length = 646

 Score =  863 bits (2231), Expect = 0.0
 Identities = 417/638 (65%), Positives = 491/638 (76%), Gaps = 5/638 (0%)

Query: 6   LYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKR-LDWIKPFTTVKQTSFDDHH 64
           LY V+PE+AA       TY+ +YQQS+  P+ FW  QA+R L W K +  V    +   +
Sbjct: 6   LYHVKPEIAARAHITAETYQTLYQQSIDQPEAFWDGQAERFLTWDKRWDKVMDYDYPTAY 65

Query: 65  VDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKFANAL 124
             I+WF  G LNVS NCLDRHLA RGDQ AIIWEGD+PS+ + I+Y+ELH  VCKFAN L
Sbjct: 66  --IRWFEGGRLNVSANCLDRHLAARGDQTAIIWEGDNPSQDKKISYKELHRLVCKFANVL 123

Query: 125 RGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVVI 184
           + Q V +GD V IY+PMI EA V MLACTRIGA+HSVVFGGFS EAL  RI+D +   ++
Sbjct: 124 KAQGVQKGDHVCIYLPMIVEAAVVMLACTRIGAVHSVVFGGFSAEALKDRILDGQCHYLV 183

Query: 185 TADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMKVA 244
            ADEG R GK IP+KA VD A  +    S++K+IV + T   + W   RD+WY + M  A
Sbjct: 184 CADEGYRGGKVIPIKATVDKAAAH--CPSLEKIIVIQNTGQTVAWQAGRDVWYHEAMAQA 241

Query: 245 GTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYWCT 304
              C P+ M AE+ LFILYTSGSTGKPKGVQH+T GYLLYAA+TH+ +FDY  G+VYWCT
Sbjct: 242 SENCEPESMDAEDPLFILYTSGSTGKPKGVQHSTGGYLLYAAMTHKYIFDYHDGDVYWCT 301

Query: 305 ADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIRAM 364
           ADVGW+TGHSY++YGPL NGATTL+FEGVP YP+  R  +VIDKH+V+I YTAPTAIRA+
Sbjct: 302 ADVGWITGHSYVLYGPLCNGATTLMFEGVPTYPEADRFWQVIDKHRVNIFYTAPTAIRAL 361

Query: 365 MASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLIS 424
           MA G A VE  D SSLR+LGSVGEPIN EAW+WYY  VG+ RCPIVDTWWQTETGG+LI+
Sbjct: 362 MAQGNAYVERTDRSSLRILGSVGEPINSEAWEWYYHTVGERRCPIVDTWWQTETGGILIT 421

Query: 425 PLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHDRF 484
           PLPG TALKPGSAT PFFGV PA++D+ G L+EG AEG LV+  SWPGQART+YGDH RF
Sbjct: 422 PLPGVTALKPGSATLPFFGVQPAIIDSRGKLLEGVAEGVLVLSRSWPGQARTIYGDHQRF 481

Query: 485 VDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVAE 544
           +DTYFK + G YFTGDGARRD DGYYWITGRVDDVLNVSGHR+GTAEIESA+  H  VAE
Sbjct: 482 IDTYFKAYPGYYFTGDGARRDADGYYWITGRVDDVLNVSGHRLGTAEIESALDLHEFVAE 541

Query: 545 AAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLPK 604
           +AVVG PHDIKGQGIY +VTL+ G   +E ++ EL N VR EIG IA+PD +QWAP LPK
Sbjct: 542 SAVVGFPHDIKGQGIYAFVTLDVGVNPTEQIKKELVNLVRNEIGAIATPDAVQWAPSLPK 601

Query: 605 TRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLI 642
           TRSGKIMRRILRKIA+ E D LGDISTLAD  VV  +I
Sbjct: 602 TRSGKIMRRILRKIASNELDNLGDISTLADSSVVEEII 639


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: 1399
Number of extensions: 57
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: 651
Length of database: 646
Length adjustment: 38
Effective length of query: 613
Effective length of database: 608
Effective search space:   372704
Effective search space used:   372704
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_019865511.1 METMI_RS0106740 (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.6882.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 1036.3   0.1          0 1036.0   0.1    1.0  1  lcl|NCBI__GCF_000384075.1:WP_019865511.1  METMI_RS0106740 acetate--CoA lig


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000384075.1:WP_019865511.1  METMI_RS0106740 acetate--CoA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1036.0   0.1         0         0       3     628 ..      20     640 ..      18     641 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1036.0 bits;  conditional E-value: 0
                                 TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep.kvkWfedgelnvsyncvdrhvekr 70 
                                               ++e+y++ly+++i++pe+fw+ +a++ l+w+k ++kv+d + ++  ++Wfe+g+lnvs+nc+drh+++r
  lcl|NCBI__GCF_000384075.1:WP_019865511.1  20 TAETYQTLYQQSIDQPEAFWDGQAERFLTWDKRWDKVMDYDYPTaYIRWFEGGRLNVSANCLDRHLAAR 88 
                                               5799*************************************999899********************** PP

                                 TIGR02188  71 kdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGa 139
                                                d++aiiwegd++++  +k++Y+el+r vc++anvlk++Gv+kgd+v+iYlpmi+ea+++mlac+RiGa
  lcl|NCBI__GCF_000384075.1:WP_019865511.1  89 GDQTAIIWEGDNPSQ-DKKISYKELHRLVCKFANVLKAQGVQKGDHVCIYLPMIVEAAVVMLACTRIGA 156
                                               *************97.9**************************************************** PP

                                 TIGR02188 140 vhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeev 208
                                               vhsvvf+Gfsaeal++Ri d +++++++adeg+Rggkvi++k++vd+a ++++ s+ek++v++ tg+ v
  lcl|NCBI__GCF_000384075.1:WP_019865511.1 157 VHSVVFGGFSAEALKDRILDGQCHYLVCADEGYRGGKVIPIKATVDKAAAHCP-SLEKIIVIQNTGQTV 224
                                               ****************************************************9.7*************7 PP

                                 TIGR02188 209 aewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfd 277
                                               a w+ grDvw++e++++ as++cepe++d+edplfiLYtsGstGkPkGv+h+tgGyll+aa+t+ky+fd
  lcl|NCBI__GCF_000384075.1:WP_019865511.1 225 A-WQAGRDVWYHEAMAQ-ASENCEPESMDAEDPLFILYTSGSTGKPKGVQHSTGGYLLYAAMTHKYIFD 291
                                               6.**************6.*************************************************** PP

                                 TIGR02188 278 ikdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRa 346
                                               ++d+d++wCtaDvGW+tGhsY++ygPL+nGattl+fegvptyp+a+rfw+vi+k++v+ifYtaPtaiRa
  lcl|NCBI__GCF_000384075.1:WP_019865511.1 292 YHDGDVYWCTADVGWITGHSYVLYGPLCNGATTLMFEGVPTYPEADRFWQVIDKHRVNIFYTAPTAIRA 360
                                               ********************************************************************* PP

                                 TIGR02188 347 lmklgeelvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvate 415
                                               lm++g++ v+++d+sslr+lgsvGepin+eaweWyy++vG+ +cpivdtwWqtetGgilitplpg +t+
  lcl|NCBI__GCF_000384075.1:WP_019865511.1 361 LMAQGNAYVERTDRSSLRILGSVGEPINSEAWEWYYHTVGERRCPIVDTWWQTETGGILITPLPG-VTA 428
                                               *****************************************************************.5** PP

                                 TIGR02188 416 lkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftG 484
                                               lkpgsatlP+fG++++++d++gk +e  +e gvLv++++wP+++rtiygd++rf++tYfk+++g+yftG
  lcl|NCBI__GCF_000384075.1:WP_019865511.1 429 LKPGSATLPFFGVQPAIIDSRGKLLEGVAE-GVLVLSRSWPGQARTIYGDHQRFIDTYFKAYPGYYFTG 496
                                               *************************98888.8************************************* PP

                                 TIGR02188 485 DgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkeg 553
                                               Dgarrd+dGy+wi+GRvDdv+nvsGhrlgtaeiesal  he vae+avvg+p++ikg+ i+afv+l  g
  lcl|NCBI__GCF_000384075.1:WP_019865511.1 497 DGARRDADGYYWITGRVDDVLNVSGHRLGTAEIESALDLHEFVAESAVVGFPHDIKGQGIYAFVTLDVG 565
                                               ********************************************************************* PP

                                 TIGR02188 554 veedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaege.ellgdvstledps 621
                                               v+++e +++kel +lvr+eig+ia+pd ++++++lPktRsGkimRR+lrkia++e ++lgd+stl+d+s
  lcl|NCBI__GCF_000384075.1:WP_019865511.1 566 VNPTE-QIKKELVNLVRNEIGAIATPDAVQWAPSLPKTRSGKIMRRILRKIASNElDNLGDISTLADSS 633
                                               ****9.6************************************************************** PP

                                 TIGR02188 622 vveelke 628
                                               vvee+++
  lcl|NCBI__GCF_000384075.1:WP_019865511.1 634 VVEEIIA 640
                                               ****986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (646 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 13.02
//
[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