Alignments for a candidate for acs in Azospirillum brasilense Sp245

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.31315.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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 11.91
//
[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:

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