GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Pseudomonas fluorescens FW300-N2E2

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate Pf6N2E2_5149 Acetyl-coenzyme A synthetase (EC 6.2.1.1)

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



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5149
          Length = 645

 Score =  828 bits (2138), Expect = 0.0
 Identities = 401/640 (62%), Positives = 478/640 (74%), Gaps = 5/640 (0%)

Query: 5   SLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKR-LDWIKPFTTVKQTSFDDH 63
           S YP    V  +    +  YK +Y++S+ +P  FW EQA R LDW+ P+ TV++  +D  
Sbjct: 5   SQYPQADAVRRAAQLSQDEYKRLYKESIEHPSAFWAEQATRFLDWMTPWQTVQR--YDLK 62

Query: 64  HVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKFANA 123
           + D  WFA G LNVS NCLDRHL  RGDQ AIIWEGDDP+ES  ITY++LH  VC+ AN 
Sbjct: 63  NGDATWFAGGKLNVSANCLDRHLQTRGDQTAIIWEGDDPAESAEITYKKLHNHVCRLANV 122

Query: 124 LRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVV 183
           L+ + V +GD V IYMPMIPEA  AMLACTRIGA+HSVVFGGFSP++L  RI+D   + V
Sbjct: 123 LKSRGVKKGDRVCIYMPMIPEAAYAMLACTRIGAVHSVVFGGFSPDSLRDRILDADCRTV 182

Query: 184 ITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMKV 243
           ITADEGVR G+ +PLK NVD AL +    ++  V+V +RT G + W + RD+WY   M  
Sbjct: 183 ITADEGVRGGRFVPLKRNVDKALES--CPNVSTVLVVERTQGEVNWVEGRDLWYHQAMHE 240

Query: 244 AGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYWC 303
               C P+ M AE+ LFILYTSGSTGKPKGV HTT GYLL AA+T + V DY+  EV+WC
Sbjct: 241 MSDDCPPEPMDAEDPLFILYTSGSTGKPKGVLHTTGGYLLQAAMTFKYVLDYRDNEVFWC 300

Query: 304 TADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIRA 363
           TADVGWVTGHSYIVYGPLANGATTL+FEGVP+YP  +R  +VIDKH+V+I YTAPTA+RA
Sbjct: 301 TADVGWVTGHSYIVYGPLANGATTLIFEGVPSYPSSSRFWQVIDKHQVNIFYTAPTALRA 360

Query: 364 MMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLI 423
           +M  G   ++     SLRLLGSVGEPINPEAW+WY+  VG++RCPIVDTWWQTETGG+++
Sbjct: 361 LMREGAGPLQETSRKSLRLLGSVGEPINPEAWEWYFNTVGEQRCPIVDTWWQTETGGIML 420

Query: 424 SPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHDR 483
           SPL  A  LKPG ATRP FGV P L+D +G  I GA  G L I  SWPGQ R++YGDH R
Sbjct: 421 SPLVSAPRLKPGCATRPMFGVQPVLLDEVGKEISGAGSGVLAIKSSWPGQIRSVYGDHQR 480

Query: 484 FVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVA 543
            VDTYFK + G YFTGDGARRDEDG YWITGR+DDV+NVSGHR+GTAE+ESA+V H  +A
Sbjct: 481 MVDTYFKPYPGYYFTGDGARRDEDGDYWITGRIDDVINVSGHRIGTAEVESALVLHDNIA 540

Query: 544 EAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLP 603
           EAAVVG PHD+KGQGIY +VT   G E ++ L+ EL   V KEIG  A P++IQWAP LP
Sbjct: 541 EAAVVGYPHDLKGQGIYAFVTPMNGVEANDELKKELLAHVSKEIGSFAKPELIQWAPALP 600

Query: 604 KTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIE 643
           KTRSGKIMRRILRKIA  E D LGD STLADP VV  LI+
Sbjct: 601 KTRSGKIMRRILRKIACNELDSLGDTSTLADPSVVEGLID 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: 1353
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: 645
Length adjustment: 38
Effective length of query: 613
Effective length of database: 607
Effective search space:   372091
Effective search space used:   372091
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 Pf6N2E2_5149 (Acetyl-coenzyme A synthetase (EC 6.2.1.1))
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.9779.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 1030.4   0.0          0 1030.1   0.0    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5149  Acetyl-coenzyme A synthetase (EC


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5149  Acetyl-coenzyme A synthetase (EC 6.2.1.1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1030.1   0.0         0         0       3     628 ..      20     640 ..      18     641 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1030.1 bits;  conditional E-value: 0
                                      TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep.kvkWfedgelnvsyncvdr 65 
                                                    +++eyk+ly+e+ie+p++fwa++a++ l+w++p+++v++ +l++ +++Wf++g+lnvs+nc+dr
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5149  20 SQDEYKRLYKESIEHPSAFWAEQATRFLDWMTPWQTVQRYDLKNgDATWFAGGKLNVSANCLDR 83 
                                                    5799*************************************9999******************* PP

                                      TIGR02188  66 hvekrkdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeavi 129
                                                    h+++r d++aiiwegd++ e s ++tY++l+++vcrlanvlk+ Gvkkgdrv+iY+pmipea++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5149  84 HLQTRGDQTAIIWEGDDPAE-SAEITYKKLHNHVCRLANVLKSRGVKKGDRVCIYMPMIPEAAY 146
                                                    ******************96.******************************************* PP

                                      TIGR02188 130 amlacaRiGavhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee 193
                                                    amlac+RiGavhsvvf+Gfs+++l++Ri da++++vitadeg+Rgg+ ++lk++vd+ale+++ 
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5149 147 AMLACTRIGAVHSVVFGGFSPDSLRDRILDADCRTVITADEGVRGGRFVPLKRNVDKALESCP- 209
                                                    **************************************************************9. PP

                                      TIGR02188 194 svekvlvvkrtgeevaewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGv 257
                                                    +v++vlvv+rt+ ev+ w+egrD+w+++++++  s++c+pe++d+edplfiLYtsGstGkPkGv
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5149 210 NVSTVLVVERTQGEVN-WVEGRDLWYHQAMHE-MSDDCPPEPMDAEDPLFILYTSGSTGKPKGV 271
                                                    6*************66.**************6.******************************* PP

                                      TIGR02188 258 lhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypd 321
                                                    lhttgGyll+aa+t+kyv d++d+++fwCtaDvGWvtGhsYivygPLanGattl+fegvp+yp+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5149 272 LHTTGGYLLQAAMTFKYVLDYRDNEVFWCTADVGWVTGHSYIVYGPLANGATTLIFEGVPSYPS 335
                                                    **************************************************************** PP

                                      TIGR02188 322 asrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpeaweWyyevv 385
                                                    +srfw+vi+k++v+ifYtaPta+Ralm++g   +++++++slr+lgsvGepinpeaweWy+++v
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5149 336 SSRFWQVIDKHQVNIFYTAPTALRALMREGAGPLQETSRKSLRLLGSVGEPINPEAWEWYFNTV 399
                                                    **************************************************************** PP

                                      TIGR02188 386 GkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggvL 449
                                                    G+++cpivdtwWqtetGgi+++pl + a  lkpg+at+P+fG++++++de gke++   + gvL
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5149 400 GEQRCPIVDTWWQTETGGIMLSPLVS-APRLKPGCATRPMFGVQPVLLDEVGKEISGAGS-GVL 461
                                                    **************************.69**************************98777.8** PP

                                      TIGR02188 450 vikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlg 513
                                                    +ik++wP+++r++ygd++r+v+tYfk ++g+yftGDgarrd+dG++wi+GR+DdvinvsGhr+g
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5149 462 AIKSSWPGQIRSVYGDHQRMVDTYFKPYPGYYFTGDGARRDEDGDYWITGRIDDVINVSGHRIG 525
                                                    **************************************************************** PP

                                      TIGR02188 514 taeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpia 577
                                                    tae+esalv h+++aeaavvg+p+++kg+ i+afv+ ++gve+++e l+kel ++v+keig++a
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5149 526 TAEVESALVLHDNIAEAAVVGYPHDLKGQGIYAFVTPMNGVEANDE-LKKELLAHVSKEIGSFA 588
                                                    ********************************************95.***************** PP

                                      TIGR02188 578 kpdkilvveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
                                                    kp+ i+++++lPktRsGkimRR+lrkia +e ++lgd+stl+dpsvve l++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5149 589 KPELIQWAPALPKTRSGKIMRRILRKIACNElDSLGDTSTLADPSVVEGLID 640
                                                    ************************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (645 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 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 12.73
//
[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