Alignments for a candidate for acs in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Klebsiella michiganensis M5al

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate BWI76_RS02095 BWI76_RS02095 acetyl-coenzyme A synthetase

Query= SwissProt::P27550
         (652 letters)



>FitnessBrowser__Koxy:BWI76_RS02095
          Length = 652

 Score = 1271 bits (3289), Expect = 0.0
 Identities = 605/652 (92%), Positives = 631/652 (96%)

Query: 1   MSQIHKHTIPANIADRCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSF 60
           MSQIHKH IPA IA+RCLINP+QY+A YQQS+  PD FWGEQGKILDW+KPY +VKNTSF
Sbjct: 1   MSQIHKHPIPATIAERCLINPEQYQAQYQQSVTDPDAFWGEQGKILDWMKPYTRVKNTSF 60

Query: 61  APGNVSIKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRF 120
           APGN+SIKWYEDGTLNLAANCLDRHL E GD+TAI+WEGDDASQSK+I+Y+ELHRDVCRF
Sbjct: 61  APGNISIKWYEDGTLNLAANCLDRHLAERGDQTAIVWEGDDASQSKNITYRELHRDVCRF 120

Query: 121 ANTLLELGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNS 180
           AN LL+LGIKKGDVVAIYMPMVPEAAVAMLACARIGA+HSVIFGGFSPEAVAGRIIDSNS
Sbjct: 121 ANVLLDLGIKKGDVVAIYMPMVPEAAVAMLACARIGAIHSVIFGGFSPEAVAGRIIDSNS 180

Query: 181 RLVITSDEGVRAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDL 240
           RLVIT+DEG+RAGR+IPLKKNVDDALKNPNV S+E+VVVLKRTGGKIDWQEGRDLWW DL
Sbjct: 181 RLVITADEGLRAGRAIPLKKNVDDALKNPNVKSIENVVVLKRTGGKIDWQEGRDLWWSDL 240

Query: 241 VEQASDQHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDI 300
           +E+AS +HQ EEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAA TFKYVFDYHPGDI
Sbjct: 241 IEKASAEHQPEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAASTFKYVFDYHPGDI 300

Query: 301 YWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTA 360
           YWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARM QVVDKHQVNILYTAPTA
Sbjct: 301 YWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMCQVVDKHQVNILYTAPTA 360

Query: 361 IRALMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGG 420
           IRALMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPV+DTWWQTETGG
Sbjct: 361 IRALMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVMDTWWQTETGG 420

Query: 421 FMITPLPGATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGD 480
           FMITPLPGA ELKAGSATRPFFGVQP LVDNEG PLEGATEG+L I DSWPGQARTLFGD
Sbjct: 421 FMITPLPGAIELKAGSATRPFFGVQPVLVDNEGTPLEGATEGNLAIADSWPGQARTLFGD 480

Query: 481 HERFEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHP 540
           HERFEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALV+HP
Sbjct: 481 HERFEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVSHP 540

Query: 541 KIAEAAVVGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTD 600
           KIAEAAVVGIPHNIKGQAIYAYVTLNHGEEP+PELYAEVRNWVRKEIGPLATPDVLHWTD
Sbjct: 541 KIAEAAVVGIPHNIKGQAIYAYVTLNHGEEPTPELYAEVRNWVRKEIGPLATPDVLHWTD 600

Query: 601 SLPKTRSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEKQAIAMPS 652
           SLPKTRSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEKQAIAMPS
Sbjct: 601 SLPKTRSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEKQAIAMPS 652


Lambda     K      H
   0.317    0.135    0.421 

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: 1692
Number of extensions: 52
Number of successful extensions: 1
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: 652
Length adjustment: 38
Effective length of query: 614
Effective length of database: 614
Effective search space:   376996
Effective search space used:   376996
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 BWI76_RS02095 BWI76_RS02095 (acetyl-coenzyme A synthetase)
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.6137.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 1033.9   0.0          0 1033.7   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS02095  BWI76_RS02095 acetyl-coenzyme A 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS02095  BWI76_RS02095 acetyl-coenzyme A synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1033.7   0.0         0         0       3     628 ..      20     643 ..      18     644 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1033.7 bits;  conditional E-value: 0
                               TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekr 70 
                                             + e+y++ y+++++dp++fw++++k  l+w+kp+++v+++s++p   ++kW+edg+ln+++nc+drh+++r
  lcl|FitnessBrowser__Koxy:BWI76_RS02095  20 NPEQYQAQYQQSVTDPDAFWGEQGK-ILDWMKPYTRVKNTSFAPgniSIKWYEDGTLNLAANCLDRHLAER 89 
                                             679**********************.6****************99899*********************** PP

                               TIGR02188  71 kdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavh 141
                                              d++ai+wegd++++ s+++tY+el+r+vcr+anvl +lG+kkgd vaiY+pm+pea++amlacaRiGa+h
  lcl|FitnessBrowser__Koxy:BWI76_RS02095  90 GDQTAIVWEGDDASQ-SKNITYRELHRDVCRFANVLLDLGIKKGDVVAIYMPMVPEAAVAMLACARIGAIH 159
                                             ***********9996.******************************************************* PP

                               TIGR02188 142 svvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaew 211
                                             sv+f+Gfs+ea+a Ri+d++++lvitadeglR g++i+lkk+vd+al++ +  s+e+v+v+krtg ++  w
  lcl|FitnessBrowser__Koxy:BWI76_RS02095 160 SVIFGGFSPEAVAGRIIDSNSRLVITADEGLRAGRAIPLKKNVDDALKNPNVkSIENVVVLKRTGGKID-W 229
                                             *************************************************99889*************66.* PP

                               TIGR02188 212 kegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikded 282
                                             +egrD+ww++l+ek asae++pe++++edplfiLYtsGstGkPkGvlhttgGyl++aa t+kyvfd++++d
  lcl|FitnessBrowser__Koxy:BWI76_RS02095 230 QEGRDLWWSDLIEK-ASAEHQPEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAASTFKYVFDYHPGD 299
                                             *************7.******************************************************** PP

                               TIGR02188 283 ifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgee 353
                                             i+wCtaDvGWvtGhsY++ygPLa+Gattl+fegvp++p+++r+++v++k++v+i+YtaPtaiRalm++g++
  lcl|FitnessBrowser__Koxy:BWI76_RS02095 300 IYWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMCQVVDKHQVNILYTAPTAIRALMAEGDK 370
                                             *********************************************************************** PP

                               TIGR02188 354 lvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlP 424
                                             +++ +d+sslr+lgsvGepinpeaweWy++++G+ekcp++dtwWqtetGg++itplpg a+elk+gsat+P
  lcl|FitnessBrowser__Koxy:BWI76_RS02095 371 AIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVMDTWWQTETGGFMITPLPG-AIELKAGSATRP 440
                                             **********************************************************.6*********** PP

                               TIGR02188 425 lfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyi 495
                                             +fG+++++vd+eg+++e  +e g L+i ++wP+++rt++gd+erf +tYf+++k++yf+GDgarrd+dGy+
  lcl|FitnessBrowser__Koxy:BWI76_RS02095 441 FFGVQPVLVDNEGTPLEGATE-GNLAIADSWPGQARTLFGDHERFEQTYFSTFKNMYFSGDGARRDEDGYY 510
                                             *****************8777.79*********************************************** PP

                               TIGR02188 496 wilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelk 566
                                             wi+GRvDdv+nvsGhrlgtaeiesalvsh+++aeaavvg+p++ikg+ai+a+v+l++g+e++ e l +e++
  lcl|FitnessBrowser__Koxy:BWI76_RS02095 511 WITGRVDDVLNVSGHRLGTAEIESALVSHPKIAEAAVVGIPHNIKGQAIYAYVTLNHGEEPTPE-LYAEVR 580
                                             ***************************************************************5.****** PP

                               TIGR02188 567 klvrkeigpiakpdkilvveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
                                             ++vrkeigp+a+pd ++++++lPktRsGkimRR+lrkia+g+ ++lgd+stl+dp vve+l e
  lcl|FitnessBrowser__Koxy:BWI76_RS02095 581 NWVRKEIGPLATPDVLHWTDSLPKTRSGKIMRRILRKIAAGDtSNLGDTSTLADPGVVEKLLE 643
                                             ******************************************99***************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (652 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 11.52
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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