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.15723.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: 0.02u 0.02s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 11.54
//
[ok]

This GapMind analysis is from Sep 17 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:

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:

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:

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:

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