Alignments for a candidate for acs in Cereibacter sphaeroides ATCC 17029

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Cereibacter sphaeroides ATCC 17029

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_011841528.1 RSPH17029_RS11250 acetate--CoA ligase

Query= SwissProt::Q8ZKF6
         (652 letters)



>NCBI__GCF_000015985.1:WP_011841528.1
          Length = 653

 Score =  839 bits (2167), Expect = 0.0
 Identities = 400/626 (63%), Positives = 488/626 (77%), Gaps = 5/626 (0%)

Query: 24  YETKYKQSINDPDTFWGEQGKILDWITPYQKVKNTSFAPGNVSIKWYEDGTLNLAANCLD 83
           YE  Y  S+ DP+ FWGEQGK LDWI PY KVKNT+F PG VSIKW+EDGTLN+A NC+D
Sbjct: 27  YERMYAASVADPEAFWGEQGKRLDWIKPYTKVKNTNFRPGEVSIKWFEDGTLNIAWNCID 86

Query: 84  RHLQENGDRTAIIWEGDD-TSQSKHISYRELHRDVCRFANTLLDLGIKKGDVVAIYMPMV 142
           RHL     +TAIIWE DD  + ++HISY+ELH +VCR AN L+  G++KGD V +Y+PM+
Sbjct: 87  RHLATRAKQTAIIWEPDDPNAPAQHISYQELHDNVCRMANVLVSQGVRKGDRVVMYLPMI 146

Query: 143 PEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSSSRLVITADEGVRAGRSIPLKKNV 202
           PEAA AMLACARIGA+HSV+F GFSP+A+A RI D  +++VITAD   R GR  PLK N 
Sbjct: 147 PEAAYAMLACARIGAIHSVVFAGFSPDALANRINDCQAKVVITADTAPRGGRRTPLKSNT 206

Query: 203 DDALKNPNVTSVEHVIVLKRTGSDIDWQEGRDLWWRDLIEKASPEHQPEAMNAEDPLFIL 262
           D AL +   +     +V+K TG  I W +GRD+  ++L+  ASP+   E +NAEDPLFIL
Sbjct: 207 DAALLH--CSDRVRCLVVKHTGDQIHWMDGRDVDVKELMRHASPDCPIEEVNAEDPLFIL 264

Query: 263 YTSGSTGKPKGVLHTTGGYLVYAATTFKYVFDYHPGDIYWCTADVGWVTGHSYLLYGPLA 322
           YTSGSTGKPKGV+HT+GGYL YAA T +  FDYH GD++WCTADVGWVTGHSY++YGPLA
Sbjct: 265 YTSGSTGKPKGVVHTSGGYLTYAAMTHQMTFDYHDGDVFWCTADVGWVTGHSYIVYGPLA 324

Query: 323 CGATTLMFEGVPNWPTPARMCQVVDKHQVNILYTAPTAIRALMAEGDKAIEGTDRSSLRI 382
            GATTLMFEGVP +P   R   V +KH+VN  YTAPTAIR+LM  G + ++  D SSL++
Sbjct: 325 NGATTLMFEGVPTYPDAGRFWAVCEKHKVNQFYTAPTAIRSLMGLGPEWVDKYDLSSLKL 384

Query: 383 LGSVGEPINPEAWEWYWKKIGKEKCPVVDTWWQTETGGFMITPLPGAIELKAGSATRPFF 442
           LGSVGEPINPEAW WY   +GK +CP+VDT+WQTETGG MITPLPGAI +K G+A++PFF
Sbjct: 385 LGSVGEPINPEAWSWYNTHVGKGRCPIVDTFWQTETGGHMITPLPGAIPVKPGAASKPFF 444

Query: 443 GVQPALVD-NEGHP-QEGATEGNLVITDSWPGQARTLFGDHERFEQTYFSTFKNMYFSGD 500
           GV+P ++D  +GH   E ATEG L I DSWPGQ RTL+GDHERFE+ YFS +K  YF+GD
Sbjct: 445 GVKPVILDPTDGHELHETATEGVLCIADSWPGQMRTLWGDHERFEEAYFSQYKGYYFTGD 504

Query: 501 GARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAVVGIPHAIKGQAIY 560
           G RRD DGYYW+TGRVDDV+NVSGHR+GTAE+ESALVAH ++AEAAVVG PH IKGQ IY
Sbjct: 505 GCRRDADGYYWVTGRVDDVINVSGHRMGTAEVESALVAHAQVAEAAVVGYPHDIKGQGIY 564

Query: 561 AYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRSGKIMRRILRKIAA 620
           AYVTL +G +P+ EL  ++  WVR EIGP+A+PDV+ W   LPKTRSGKIMRRILRKIA 
Sbjct: 565 AYVTLMNGVQPTEELRKDLVKWVRTEIGPIASPDVIQWAPGLPKTRSGKIMRRILRKIAE 624

Query: 621 GDTSNLGDTSTLADPGVVEKLLEEKQ 646
            D  +LGDT+TLADP VV+ L+  ++
Sbjct: 625 NDFGSLGDTTTLADPSVVDDLIANRK 650


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: 1501
Number of extensions: 65
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: 652
Length of database: 653
Length adjustment: 38
Effective length of query: 614
Effective length of database: 615
Effective search space:   377610
Effective search space used:   377610
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_011841528.1 RSPH17029_RS11250 (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.232595.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 1026.1   0.0          0 1025.9   0.0    1.0  1  NCBI__GCF_000015985.1:WP_011841528.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000015985.1:WP_011841528.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1025.9   0.0         0         0       4     628 ..      24     647 ..      21     648 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1025.9 bits;  conditional E-value: 0
                             TIGR02188   4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdk 73 
                                           +  y+++y+ +++dpe+fw++++k +l+w+kp++kv++++++p   ++kWfedg+ln+++nc+drh+++r+++
  NCBI__GCF_000015985.1:WP_011841528.1  24 AAGYERMYAASVADPEAFWGEQGK-RLDWIKPYTKVKNTNFRPgevSIKWFEDGTLNIAWNCIDRHLATRAKQ 95 
                                           5679********************.5***************999889************************** PP

                             TIGR02188  74 vaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfa 146
                                           +aiiwe d+++  +++++Y+el+++vcr+anvl ++Gv+kgdrv++Ylpmipea++amlacaRiGa+hsvvfa
  NCBI__GCF_000015985.1:WP_011841528.1  96 TAIIWEPDDPNAPAQHISYQELHDNVCRMANVLVSQGVRKGDRVVMYLPMIPEAAYAMLACARIGAIHSVVFA 168
                                           ************************************************************************* PP

                             TIGR02188 147 GfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvww 219
                                           Gfs++ala+Ri+d++ak+vitad++ Rgg++++lk+++d+al +++++v+ +lvvk+tg++++ w +grDv +
  NCBI__GCF_000015985.1:WP_011841528.1 169 GFSPDALANRINDCQAKVVITADTAPRGGRRTPLKSNTDAALLHCSDRVR-CLVVKHTGDQIH-WMDGRDVDV 239
                                           **********************************************9887.9*********76.********* PP

                             TIGR02188 220 eelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGW 292
                                           +el+++ as +c+ e++++edplfiLYtsGstGkPkGv+ht+gGyl++aa+t++++fd++d+d+fwCtaDvGW
  NCBI__GCF_000015985.1:WP_011841528.1 240 KELMRH-ASPDCPIEEVNAEDPLFILYTSGSTGKPKGVVHTSGGYLTYAAMTHQMTFDYHDGDVFWCTADVGW 311
                                           *****6.****************************************************************** PP

                             TIGR02188 293 vtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrv 365
                                           vtGhsYivygPLanGattl+fegvptypda+rfw+v+ek+kv++fYtaPtaiR+lm lg e+v+k+dlssl++
  NCBI__GCF_000015985.1:WP_011841528.1 312 VTGHSYIVYGPLANGATTLMFEGVPTYPDAGRFWAVCEKHKVNQFYTAPTAIRSLMGLGPEWVDKYDLSSLKL 384
                                           ************************************************************************* PP

                             TIGR02188 366 lgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvd.eeg 437
                                           lgsvGepinpeaw+Wy+++vGk++cpivdt+WqtetGg++itplpg a+++kpg+a++P+fG++++++d ++g
  NCBI__GCF_000015985.1:WP_011841528.1 385 LGSVGEPINPEAWSWYNTHVGKGRCPIVDTFWQTETGGHMITPLPG-AIPVKPGAASKPFFGVKPVILDpTDG 456
                                           **********************************************.6*********************999* PP

                             TIGR02188 438 keveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGh 510
                                           +e++e++++gvL+i ++wP+++rt++gd+erf e+Yf+++kg+yftGDg+rrd+dGy+w++GRvDdvinvsGh
  NCBI__GCF_000015985.1:WP_011841528.1 457 HELHETATEGVLCIADSWPGQMRTLWGDHERFEEAYFSQYKGYYFTGDGCRRDADGYYWVTGRVDDVINVSGH 529
                                           ****99999**************************************************************** PP

                             TIGR02188 511 rlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkil 583
                                           r+gtae+esalv+h +vaeaavvg+p++ikg+ i+a+v+l++gv+++ee l+k+l k+vr+eigpia+pd i+
  NCBI__GCF_000015985.1:WP_011841528.1 530 RMGTAEVESALVAHAQVAEAAVVGYPHDIKGQGIYAYVTLMNGVQPTEE-LRKDLVKWVRTEIGPIASPDVIQ 601
                                           ***********************************************95.*********************** PP

                             TIGR02188 584 vveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
                                           +++ lPktRsGkimRR+lrkiae++  +lgd++tl+dpsvv++l++
  NCBI__GCF_000015985.1:WP_011841528.1 602 WAPGLPKTRSGKIMRRILRKIAENDfGSLGDTTTLADPSVVDDLIA 647
                                           ******************************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (653 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 23.59
//
[ok]

This GapMind analysis is from Apr 10 2024. 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