GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Azospirillum brasilense Sp245

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate AZOBR_RS00270 AZOBR_RS00270 acetyl-CoA synthetase

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



>FitnessBrowser__azobra:AZOBR_RS00270
          Length = 646

 Score =  936 bits (2420), Expect = 0.0
 Identities = 443/643 (68%), Positives = 516/643 (80%), Gaps = 3/643 (0%)

Query: 1   MSAASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60
           MS  S +PV+ E+A +   DEA Y  +Y+QS+ +P+ FW EQ KR+DWIKP++ VK  S+
Sbjct: 1   MSDNSFFPVKQEIAKTAYVDEAAYARLYEQSINDPEAFWGEQGKRIDWIKPYSKVKDVSY 60

Query: 61  DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKF 120
               V IKWF DGTLNVS NC+DRHLA RGDQ AII+EGDDP  S++ITY+ELHE+VC+ 
Sbjct: 61  TGD-VHIKWFYDGTLNVSANCVDRHLATRGDQTAIIFEGDDPGVSKHITYKELHEQVCRL 119

Query: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180
           AN L+   V +GD VTIY+PMIPEA  AMLAC R+GAIHS+VFGGFSP++L  RI+DC S
Sbjct: 120 ANVLKKNGVKKGDRVTIYLPMIPEAAYAMLACARVGAIHSIVFGGFSPDSLKDRIVDCDS 179

Query: 181 KVVITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDL 240
             VIT+DEG+R G+K+PLKAN D A+       ++ V+V K T GN+ W + RD+WY + 
Sbjct: 180 HFVITSDEGLRGGRKVPLKANADKAVA--AAPGVKHVLVVKHTGGNVAWTEGRDLWYHEE 237

Query: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEV 300
           +      C P+EM AE+ LFILYTSGSTGKPKGV HTT GYL+YA++TH+ VFDYK GEV
Sbjct: 238 IASVSADCPPEEMSAEDPLFILYTSGSTGKPKGVLHTTGGYLVYASMTHQYVFDYKDGEV 297

Query: 301 YWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTA 360
           YWCTADVGWVTGHSYIVYGPLANGATTL+FEGVP YPDI+R  +V+DKHKV+I YTAPTA
Sbjct: 298 YWCTADVGWVTGHSYIVYGPLANGATTLMFEGVPTYPDISRFWQVVDKHKVNIFYTAPTA 357

Query: 361 IRAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGG 420
           IR++M  G   V+    SSLR+LGSVGEPINPEAW WYY  VG  RCPIVDTWWQTETGG
Sbjct: 358 IRSLMREGEGPVKKTSRSSLRILGSVGEPINPEAWLWYYNVVGDGRCPIVDTWWQTETGG 417

Query: 421 VLISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGD 480
           +LI+PLPGA   KPGSAT+PFFGV P +VDN G  +EG  EGNL I DSWPGQ RT++GD
Sbjct: 418 ILITPLPGAIGQKPGSATKPFFGVKPVVVDNDGKELEGETEGNLCIADSWPGQMRTVFGD 477

Query: 481 HDRFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHP 540
           H+RFV TYF TF+G YFTGDG RRD DGYYWITGRVDDV+NVSGHRMGTAE+ESA+VAHP
Sbjct: 478 HERFVQTYFSTFAGYYFTGDGCRRDADGYYWITGRVDDVINVSGHRMGTAEVESALVAHP 537

Query: 541 KVAEAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAP 600
           KVAEAAVVG PHD+KGQGIY YVTLNAGE  +E LR EL  WVRKEIGPIASPD+IQW+P
Sbjct: 538 KVAEAAVVGYPHDLKGQGIYAYVTLNAGESPTEELRKELVAWVRKEIGPIASPDLIQWSP 597

Query: 601 GLPKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIE 643
           GLPKTRSGKIMRRILRKIA  E+D LGD STLADP VV  LIE
Sbjct: 598 GLPKTRSGKIMRRILRKIAANEHDSLGDTSTLADPTVVTDLIE 640


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: 1472
Number of extensions: 70
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 AZOBR_RS00270 AZOBR_RS00270 (acetyl-CoA 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.8422.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 1052.7   0.0          0 1052.5   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS00270  AZOBR_RS00270 acetyl-CoA synthet


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS00270  AZOBR_RS00270 acetyl-CoA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1052.5   0.0         0         0       4     628 ..      21     640 ..      18     641 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1052.5 bits;  conditional E-value: 0
                                 TIGR02188   4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslep..kvkWfedgelnvsyncvdrhvekr 70 
                                                 +y++lye++i+dpe+fw++++k +++w+kp++kv+d s +   ++kWf dg+lnvs+ncvdrh+++r
  lcl|FitnessBrowser__azobra:AZOBR_RS00270  21 EAAYARLYEQSINDPEAFWGEQGK-RIDWIKPYSKVKDVSYTGdvHIKWFYDGTLNVSANCVDRHLATR 88 
                                               578*********************.5*************9987779*********************** PP

                                 TIGR02188  71 kdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGa 139
                                                d++aii+egd++g  s+++tY+el+++vcrlanvlk+ Gvkkgdrv+iYlpmipea++amlacaR+Ga
  lcl|FitnessBrowser__azobra:AZOBR_RS00270  89 GDQTAIIFEGDDPGV-SKHITYKELHEQVCRLANVLKKNGVKKGDRVTIYLPMIPEAAYAMLACARVGA 156
                                               **************7.***************************************************** PP

                                 TIGR02188 140 vhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeev 208
                                               +hs+vf+Gfs+++l++Rivd+++++vit+deglRgg++++lk+++d+a+++a+  v++vlvvk+tg +v
  lcl|FitnessBrowser__azobra:AZOBR_RS00270 157 IHSIVFGGFSPDSLKDRIVDCDSHFVITSDEGLRGGRKVPLKANADKAVAAAP-GVKHVLVVKHTGGNV 224
                                               ****************************************************9.6*************7 PP

                                 TIGR02188 209 aewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfd 277
                                               a w+egrD+w++e++++ +sa+c+pe++++edplfiLYtsGstGkPkGvlhttgGyl++a++t++yvfd
  lcl|FitnessBrowser__azobra:AZOBR_RS00270 225 A-WTEGRDLWYHEEIAS-VSADCPPEEMSAEDPLFILYTSGSTGKPKGVLHTTGGYLVYASMTHQYVFD 291
                                               7.**************6.*************************************************** PP

                                 TIGR02188 278 ikdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRa 346
                                               +kd++++wCtaDvGWvtGhsYivygPLanGattl+fegvptypd srfw+v++k+kv+ifYtaPtaiR+
  lcl|FitnessBrowser__azobra:AZOBR_RS00270 292 YKDGEVYWCTADVGWVTGHSYIVYGPLANGATTLMFEGVPTYPDISRFWQVVDKHKVNIFYTAPTAIRS 360
                                               ********************************************************************* PP

                                 TIGR02188 347 lmklgeelvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvate 415
                                               lm++ge  vkk+++sslr+lgsvGepinpeaw Wyy+vvG+++cpivdtwWqtetGgilitplpg a+ 
  lcl|FitnessBrowser__azobra:AZOBR_RS00270 361 LMREGEGPVKKTSRSSLRILGSVGEPINPEAWLWYYNVVGDGRCPIVDTWWQTETGGILITPLPG-AIG 428
                                               *****************************************************************.6** PP

                                 TIGR02188 416 lkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftG 484
                                               +kpgsat+P+fG++++vvd++gke+e e+e g L+i ++wP+++rt++gd+erfv+tYf+++ g+yftG
  lcl|FitnessBrowser__azobra:AZOBR_RS00270 429 QKPGSATKPFFGVKPVVVDNDGKELEGETE-GNLCIADSWPGQMRTVFGDHERFVQTYFSTFAGYYFTG 496
                                               **************************8887.79************************************ PP

                                 TIGR02188 485 DgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkeg 553
                                               Dg+rrd+dGy+wi+GRvDdvinvsGhr+gtae+esalv+h++vaeaavvg+p+++kg+ i+a+v+l++g
  lcl|FitnessBrowser__azobra:AZOBR_RS00270 497 DGCRRDADGYYWITGRVDDVINVSGHRMGTAEVESALVAHPKVAEAAVVGYPHDLKGQGIYAYVTLNAG 565
                                               ********************************************************************* PP

                                 TIGR02188 554 veedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaege.ellgdvstledps 621
                                               ++++ee l+kel ++vrkeigpia+pd i++ + lPktRsGkimRR+lrkia++e ++lgd+stl+dp+
  lcl|FitnessBrowser__azobra:AZOBR_RS00270 566 ESPTEE-LRKELVAWVRKEIGPIASPDLIQWSPGLPKTRSGKIMRRILRKIAANEhDSLGDTSTLADPT 633
                                               ***995.************************************************99************ PP

                                 TIGR02188 622 vveelke 628
                                               vv +l+e
  lcl|FitnessBrowser__azobra:AZOBR_RS00270 634 VVTDLIE 640
                                               **99986 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: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.05
# Mc/sec: 7.50
//
[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