Alignments for a candidate for acs in Chryseobacterium angstadtii KM

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Chryseobacterium angstadtii KM

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_048507311.1 ACM46_RS14065 acetate--CoA ligase

Query= SwissProt::Q8ZKF6
         (652 letters)



>NCBI__GCF_001045465.1:WP_048507311.1
          Length = 636

 Score =  672 bits (1733), Expect = 0.0
 Identities = 337/630 (53%), Positives = 438/630 (69%), Gaps = 15/630 (2%)

Query: 24  YETKYKQSINDPDTFWGEQGKILD----WITPYQKVKNTSFAPGNVSIKWYEDGTLNLAA 79
           Y  +YK+SI +P  FW    KI D    W   + KV    +      I W+++  LN+  
Sbjct: 12  YFEEYKKSIKNPKKFWD---KIADQNFVWYQRWSKV--VKYDMNEAKITWFKNAKLNITK 66

Query: 80  NCLDRHLQENGDRTAIIWEGDDTSQ-SKHISYRELHRDVCRFANTLLDLGIKKGDVVAIY 138
           NC+DRHL   G++TAIIWE +D  + ++HISY +L+  V + AN L ++GI+KGD V IY
Sbjct: 67  NCIDRHLAVRGEKTAIIWEPNDPKEEAQHISYNDLYTRVNKTANVLREMGIEKGDRVCIY 126

Query: 139 MPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSSSRLVITADEGVRAGRSIPL 198
           +PM+PE A+ MLACA++GAVHSVIF GFS  AVA R+ D  ++++IT+D   R  + + L
Sbjct: 127 LPMIPELAITMLACAKLGAVHSVIFAGFSASAVASRVNDCHAKMIITSDGSYRGNKVLDL 186

Query: 199 KKNVDDALKNPNVTSVEHVIVLKRTGSDIDWQEGRDLWWRDLIEKASPEHQPEAMNAEDP 258
           K  VD+AL+     SVE V+V+KRT ++I  +EGRD W  DL EKAS +     M+AEDP
Sbjct: 187 KSIVDEALEK--TPSVESVLVVKRTHNEIKMKEGRDYWMADLYEKASADFVTVIMDAEDP 244

Query: 259 LFILYTSGSTGKPKGVLHTTGGYLVYAATTFKYVFDYHPGDIYWCTADVGWVTGHSYLLY 318
           LFILYTSGSTGKPKG+LHT  GY+VY A TFK VF+Y   DIYWCTAD+GW+TGHSY+LY
Sbjct: 245 LFILYTSGSTGKPKGMLHTCAGYMVYTAYTFKNVFNYKENDIYWCTADIGWITGHSYILY 304

Query: 319 GPLACGATTLMFEGVPNWPTPARMCQVVDKHQVNILYTAPTAIRALMAEGDKAIEGTDRS 378
           GPL  GATT++FEGVP +P P R  +V++KH++   YTAPTAIR+L  E  + ++  D S
Sbjct: 305 GPLLNGATTVIFEGVPTYPEPDRFWEVIEKHKITQFYTAPTAIRSLAKESTEWVDKHDLS 364

Query: 379 SLRILGSVGEPINPEAWEWYWKKIGKEKCPVVDTWWQTETGGFMITPLPGAIELKAGSAT 438
           +L+++GSVGEPIN EAW W+   +GK+KCPVVDTWWQTETGG MI+PLP     K   AT
Sbjct: 365 TLKVIGSVGEPINEEAWHWFNDHVGKKKCPVVDTWWQTETGGIMISPLPFVTPTKPTYAT 424

Query: 439 RPFFGVQPALVDNEGHPQEG-ATEGNLVITDSWPGQARTLFGDHERFEQTYFSTFKNMYF 497
            P  G+QP L+D++ +   G    GNL I   WPG ART++GDH+R+++TYFS F   YF
Sbjct: 425 LPLPGIQPVLMDDKRNEITGNQVTGNLCIRFPWPGIARTIWGDHQRYKETYFSAFPGKYF 484

Query: 498 SGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAVVGIPHAIKGQ 557
           +GDGA RDE GYY ITGRVDDV+ VSGH LGTA IE ++  HP +AE+A+VG PH IKG 
Sbjct: 485 TGDGALRDEVGYYRITGRVDDVIIVSGHNLGTAPIEDSINEHPAVAESAIVGYPHDIKGN 544

Query: 558 AIYAYVTLNH-GEEPSPE-LYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRSGKIMRRIL 615
           A+Y +V L   GE    E L  E+   +  +IGP+A  D + +   LPKTRSGKIMRRIL
Sbjct: 545 ALYGFVILKETGEGRDKENLKKEINQLISDQIGPIAKLDKIQFVSGLPKTRSGKIMRRIL 604

Query: 616 RKIAAGDTSNLGDTSTLADPGVVEKLLEEK 645
           RKIA GD SN GD STL +P +VE++  E+
Sbjct: 605 RKIAEGDFSNFGDISTLLNPEIVEEIKNER 634


Lambda     K      H
   0.317    0.135    0.423 

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: 1270
Number of extensions: 64
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: 652
Length of database: 636
Length adjustment: 38
Effective length of query: 614
Effective length of database: 598
Effective search space:   367172
Effective search space used:   367172
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_048507311.1 ACM46_RS14065 (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.980689.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.3e-293  959.2   0.7   4.9e-293  959.0   0.7    1.0  1  NCBI__GCF_001045465.1:WP_048507311.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001045465.1:WP_048507311.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  959.0   0.7  4.9e-293  4.9e-293       4     628 ..       9     632 ..       6     633 .. 0.98

  Alignments for each domain:
  == domain 1  score: 959.0 bits;  conditional E-value: 4.9e-293
                             TIGR02188   4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslep.kvkWfedgelnvsyncvdrhvekrkdkva 75 
                                           l +y e y+++i++p+kfw+k a +++ w + ++kv++ ++++ k++Wf++++ln++ nc+drh++ r +k+a
  NCBI__GCF_001045465.1:WP_048507311.1   9 LPHYFEEYKKSIKNPKKFWDKIADQNFVWYQRWSKVVKYDMNEaKITWFKNAKLNITKNCIDRHLAVRGEKTA 81 
                                           6689999*******************************999888***************************** PP

                             TIGR02188  76 iiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGf 148
                                           iiwe ++++e++++++Y++l+++v+++anvl+e+G++kgdrv+iYlpmipe++i+mlaca++Gavhsv+faGf
  NCBI__GCF_001045465.1:WP_048507311.1  82 IIWEPNDPKEEAQHISYNDLYTRVNKTANVLREMGIEKGDRVCIYLPMIPELAITMLACAKLGAVHSVIFAGF 154
                                           ************************************************************************* PP

                             TIGR02188 149 saealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwwee 221
                                           sa+a+a+R++d++ak++it+d+++Rg+kv++lk+ivdealek++ sve+vlvvkrt +e++ +kegrD+w+ +
  NCBI__GCF_001045465.1:WP_048507311.1 155 SASAVASRVNDCHAKMIITSDGSYRGNKVLDLKSIVDEALEKTP-SVESVLVVKRTHNEIK-MKEGRDYWMAD 225
                                           *******************************************9.7*************76.*********** PP

                             TIGR02188 222 lvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvt 294
                                           l ek asa+  +  +d+edplfiLYtsGstGkPkG+lht +Gy++++a+t+k vf++k++di+wCtaD+GW+t
  NCBI__GCF_001045465.1:WP_048507311.1 226 LYEK-ASADFVTVIMDAEDPLFILYTSGSTGKPKGMLHTCAGYMVYTAYTFKNVFNYKENDIYWCTADIGWIT 297
                                           ***7.99999999************************************************************ PP

                             TIGR02188 295 GhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlg 367
                                           GhsYi+ygPL+nGatt++fegvptyp+++rfweviek+k+t+fYtaPtaiR+l k+++e+v+khdls+l+v+g
  NCBI__GCF_001045465.1:WP_048507311.1 298 GHSYILYGPLLNGATTVIFEGVPTYPEPDRFWEVIEKHKITQFYTAPTAIRSLAKESTEWVDKHDLSTLKVIG 370
                                           ************************************************************************* PP

                             TIGR02188 368 svGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkev 440
                                           svGepin eaw+W++++vGk+kcp+vdtwWqtetGgi+i+plp  +t++kp  atlPl+Gi+++++d++ +e+
  NCBI__GCF_001045465.1:WP_048507311.1 371 SVGEPINEEAWHWFNDHVGKKKCPVVDTWWQTETGGIMISPLPF-VTPTKPTYATLPLPGIQPVLMDDKRNEI 442
                                           ********************************************.6*************************** PP

                             TIGR02188 441 eeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlg 513
                                           + ++ +g L+i+ pwP+++rti+gd++r+ etYf++++g yftGDga rd+ Gy+ i+GRvDdvi vsGh+lg
  NCBI__GCF_001045465.1:WP_048507311.1 443 TGNQVTGNLCIRFPWPGIARTIWGDHQRYKETYFSAFPGKYFTGDGALRDEVGYYRITGRVDDVIIVSGHNLG 515
                                           *777779****************************************************************** PP

                             TIGR02188 514 taeiesalvsheavaeaavvgvpdeikgeaivafvvlkegve.edeeelekelkklvrkeigpiakpdkilvv 585
                                           ta ie+++ +h+avae+a+vg+p++ikg+a++ fv+lke+ e  d+e+l+ke+++l++++igpiak dki++v
  NCBI__GCF_001045465.1:WP_048507311.1 516 TAPIEDSINEHPAVAESAIVGYPHDIKGNALYGFVILKETGEgRDKENLKKEINQLISDQIGPIAKLDKIQFV 588
                                           **************************************9877356669************************* PP

                             TIGR02188 586 eelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
                                           + lPktRsGkimRR+lrkiaeg+ ++ gd+stl +p++vee+k+
  NCBI__GCF_001045465.1:WP_048507311.1 589 SGLPKTRSGKIMRRILRKIAEGDfSNFGDISTLLNPEIVEEIKN 632
                                           ******************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (636 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: 39.29
//
[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