Alignments for a candidate for acs in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Pseudomonas fluorescens FW300-N1B4

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate Pf1N1B4_2849 Acetyl-coenzyme A synthetase (EC 6.2.1.1)

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



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2849
          Length = 645

 Score =  815 bits (2104), Expect = 0.0
 Identities = 394/640 (61%), Positives = 476/640 (74%), Gaps = 5/640 (0%)

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

Query: 64  HVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKFANA 123
             +  WFA G +NVSYNC+DRHL +RGDQIAIIWEGDDP+ES  ITY++LH  VC+ AN 
Sbjct: 63  TGEASWFAGGQINVSYNCIDRHLEKRGDQIAIIWEGDDPAESAQITYKKLHHNVCRLANV 122

Query: 124 LRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVV 183
           L+ + V +GD V IYMPMIPEA  AMLAC RIGAIHSVVFGGFSP++L  RI+D   + V
Sbjct: 123 LKSRGVKKGDRVCIYMPMIPEAAYAMLACARIGAIHSVVFGGFSPDSLRDRILDADCRTV 182

Query: 184 ITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMKV 243
           ITADEGVR GK +PLK NVD AL +    ++  VIV +RT G + W + RDIWY   ++ 
Sbjct: 183 ITADEGVRGGKFVPLKQNVDTALQS--CPNVNTVIVVERTQGQVNWVEDRDIWYHQALRD 240

Query: 244 AGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYWC 303
               C P+ M AE+ LFILYTSGSTGKPKGV HTT GYLL AA+T + VFDY+ GE++WC
Sbjct: 241 VSDDCPPEPMDAEDPLFILYTSGSTGKPKGVMHTTGGYLLQAAMTFKYVFDYRDGEIFWC 300

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

Query: 364 MMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLI 423
           +M  G   ++     SLRLLG+VGEPINPEAW+WY+  VG++RC IVDTWWQTETGG++I
Sbjct: 361 LMREGPEPLKETSRESLRLLGTVGEPINPEAWEWYFNTVGEQRCTIVDTWWQTETGGIMI 420

Query: 424 SPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHDR 483
           SPL     +KPG AT+P FGV P L+D  G  I+GA  G L I  SWP Q R++YGD  R
Sbjct: 421 SPLVSTQRVKPGCATQPMFGVQPVLLDEHGKEIKGAGSGILAIKSSWPAQIRSVYGDPKR 480

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

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

Query: 604 KTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIE 643
           KTRSGKIMRRILRKIA  E D LGD STLADP VV  LI+
Sbjct: 601 KTRSGKIMRRILRKIACNELDSLGDTSTLADPSVVQGLID 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: 1349
Number of extensions: 68
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 Pf1N1B4_2849 (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.31453.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__pseudo1_N1B4:Pf1N1B4_2849  Acetyl-coenzyme A synthetase (EC


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2849  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 ! 1033.7   0.0         0         0       3     628 ..      20     640 ..      18     641 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1033.7 bits;  conditional E-value: 0
                                      TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep.kvkWfedgelnvsyncvdr 65 
                                                    ++++y++ly+++ie+p++fwa++a++ l+w  p+++v++ +l++ ++ Wf++g++nvsync+dr
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2849  20 SQDDYQRLYRQSIEHPSTFWAEQATRFLDWSAPWQTVQRYDLKTgEASWFAGGQINVSYNCIDR 83 
                                                    5789*************************************9999******************* PP

                                      TIGR02188  66 hvekrkdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeavi 129
                                                    h+ekr d++aiiwegd++ e s ++tY++l+++vcrlanvlk+ Gvkkgdrv+iY+pmipea++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2849  84 HLEKRGDQIAIIWEGDDPAE-SAQITYKKLHHNVCRLANVLKSRGVKKGDRVCIYMPMIPEAAY 146
                                                    ******************96.******************************************* PP

                                      TIGR02188 130 amlacaRiGavhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee 193
                                                    amlacaRiGa+hsvvf+Gfs+++l++Ri da++++vitadeg+Rggk ++lk++vd al++++ 
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2849 147 AMLACARIGAIHSVVFGGFSPDSLRDRILDADCRTVITADEGVRGGKFVPLKQNVDTALQSCP- 209
                                                    **************************************************************9. PP

                                      TIGR02188 194 svekvlvvkrtgeevaewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGv 257
                                                    +v++v+vv+rt+ +v+ w+e+rD+w+++++++ +s++c+pe++d+edplfiLYtsGstGkPkGv
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2849 210 NVNTVIVVERTQGQVN-WVEDRDIWYHQALRD-VSDDCPPEPMDAEDPLFILYTSGSTGKPKGV 271
                                                    6*************66.**************7.******************************* PP

                                      TIGR02188 258 lhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypd 321
                                                    +httgGyll+aa+t+kyvfd++d++ifwCtaDvGWvtGhsYivygPLanGattl+fegvp+yp+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2849 272 MHTTGGYLLQAAMTFKYVFDYRDGEIFWCTADVGWVTGHSYIVYGPLANGATTLIFEGVPSYPS 335
                                                    **************************************************************** PP

                                      TIGR02188 322 asrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpeaweWyyevv 385
                                                    +srfw+vi+k++v+ifYtaPta+Ralm++g e +k+++++slr+lg+vGepinpeaweWy+++v
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2849 336 TSRFWQVIDKHHVNIFYTAPTALRALMREGPEPLKETSRESLRLLGTVGEPINPEAWEWYFNTV 399
                                                    **************************************************************** PP

                                      TIGR02188 386 GkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggvL 449
                                                    G+++c+ivdtwWqtetGgi+i+pl + +  +kpg+at+P+fG++++++de+gke++   + g+L
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2849 400 GEQRCTIVDTWWQTETGGIMISPLVS-TQRVKPGCATQPMFGVQPVLLDEHGKEIKGAGS-GIL 461
                                                    **************************.6***************************98777.8** PP

                                      TIGR02188 450 vikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlg 513
                                                    +ik++wP+++r++ygd++r++etYfk ++g+yftGDgarrd+dG++wi+GR+DdvinvsGhr+g
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2849 462 AIKSSWPAQIRSVYGDPKRMIETYFKPYPGYYFTGDGARRDEDGDYWITGRIDDVINVSGHRIG 525
                                                    **************************************************************** PP

                                      TIGR02188 514 taeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpia 577
                                                    tae+esalv h+++aeaavvg+p+++kg+ i+afv+ ++g+e+++e l+k+l ++v+keig++a
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2849 526 TAEVESALVLHDSIAEAAVVGYPHDVKGQGIYAFVTPMNGTEPNDE-LKKQLLAHVSKEIGNFA 588
                                                    *********************************************5.***************** PP

                                      TIGR02188 578 kpdkilvveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
                                                    kpd i+++++lPktRsGkimRR+lrkia +e ++lgd+stl+dpsvv+ l++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2849 589 KPDLIQWAPALPKTRSGKIMRRILRKIACNElDSLGDTSTLADPSVVQGLID 640
                                                    ***********************************************99875 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 9.67
//
[ok]

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

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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