GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fahA in Pseudomonas simiae WCS417

Align fumarylacetoacetase (EC 3.7.1.2) (characterized)
to candidate GFF990 PS417_05020 fumarylacetoacetase

Query= BRENDA::Q94272
         (418 letters)



>FitnessBrowser__WCS417:GFF990
          Length = 428

 Score =  364 bits (934), Expect = e-105
 Identities = 204/419 (48%), Positives = 266/419 (63%), Gaps = 20/419 (4%)

Query: 10  NSDFPIQNLPYGVFSTKADSSRHIGVAIGDQILNLAEIANLFDGPQLKAHQDVFKQSTLN 69
           ++DFP+QNLP GVFS    + R  GVAIGD IL+L    + FDG   +A +       LN
Sbjct: 17  HTDFPLQNLPLGVFSINGSAPR-AGVAIGDSILDLQAAIDEFDGEARRAIEAT-AGGQLN 74

Query: 70  AFMALPRPAWLEARARIQQLLSEDCAVLRDNAHLRSRALVAQSDATMHLPAQIGDYTDFY 129
           AF AL R   +  R R+ +LL+E   +    A +  RA    +D  MH+PAQI DYTDFY
Sbjct: 75  AFFALGRGPRVALRERLLELLAEGSTLHTREAQVLHRA----ADCQMHVPAQINDYTDFY 130

Query: 130 SSIHHATNVGIMFRGKENALMPNWKWLPVGYHGRASSIVVSGTDLKRPVGQTKAPDAEVP 189
             I HA NVG +FR  +N L+PN+K++P+GYHGRAS+I  SGTD++RP GQT       P
Sbjct: 131 VGIEHAQNVGKLFR-PDNPLLPNYKYVPIGYHGRASTIRTSGTDVRRPKGQTLPAGQSEP 189

Query: 190 SFGPSKLMDFELEMAFFVGGPENELGTRVPIEKAEDRIFGVVLMNDWSARDIQAWEYVPL 249
           +FGP   +D+ELE+  ++G   NE+G  + I  A D I G  L+NDWSARDIQAWEY PL
Sbjct: 190 TFGPCARLDYELELGIWIG-QGNEMGDSIAIGDAADHIAGFCLLNDWSARDIQAWEYQPL 248

Query: 250 GPFLAKSFATTVSPWVVSIEALRPYFVENPVQ---DPVPPAYL---HHDDPFTLDINLAV 303
           GPFL+KSF TT+SPWVV+ EAL P+    P +   DP P +YL          LDI L V
Sbjct: 249 GPFLSKSFITTISPWVVTAEALEPFRKAQPARPEGDPQPLSYLLDKRDQAAGALDIELEV 308

Query: 304 SIRP----EGDAVDHIVCKTNFKHLYWTLKQQLAHHTVNGCNLRAGDLLGSGTVSGPEEG 359
            +      E +   H +  +N  H+YWT+ Q +AHH+VNGC L+AGDL GSGT+SGP+ G
Sbjct: 309 LLTTAAMREQNLPAHRLALSNSLHMYWTVAQLVAHHSVNGCQLQAGDLFGSGTLSGPQAG 368

Query: 360 AYGSMLELSWRGAKEVPVGS-EIRKFLKDGDEVNLSGVCEKNG-VRIGFGECRGKVLPA 416
            +GS+LE++  G K V + S E+RKFL+DGDE+ L   C + G   IGFGECRG V+ A
Sbjct: 369 QFGSLLEMTEGGKKPVELPSGEVRKFLEDGDEIILRARCNREGFASIGFGECRGTVIAA 427


Lambda     K      H
   0.319    0.137    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: 548
Number of extensions: 30
Number of successful extensions: 8
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: 418
Length of database: 428
Length adjustment: 32
Effective length of query: 386
Effective length of database: 396
Effective search space:   152856
Effective search space used:   152856
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate GFF990 PS417_05020 (fumarylacetoacetase)
to HMM TIGR01266 (fahA: fumarylacetoacetase (EC 3.7.1.2))

# 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/TIGR01266.hmm
# target sequence database:        /tmp/gapView.5479.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01266  [M=420]
Accession:   TIGR01266
Description: fum_ac_acetase: fumarylacetoacetase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   2.9e-190  618.5   0.0   3.3e-190  618.3   0.0    1.0  1  lcl|FitnessBrowser__WCS417:GFF990  PS417_05020 fumarylacetoacetase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF990  PS417_05020 fumarylacetoacetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  618.3   0.0  3.3e-190  3.3e-190       1     419 [.       9     427 ..       9     428 .] 0.97

  Alignments for each domain:
  == domain 1  score: 618.3 bits;  conditional E-value: 3.3e-190
                          TIGR01266   1 sfvavak.nsdfplqnlPyGvfstkadssrrigvaiGdqildlskiaaaglfeglalkehqevfkestlnaflalg 75 
                                        s+va+a+ ++dfplqnlP+Gvfs  ++s +r gvaiGd+ildl+++ +   f+g  ++++ e++ ++ lnaf+alg
  lcl|FitnessBrowser__WCS417:GFF990   9 SWVASANgHTDFPLQNLPLGVFS-INGSAPRAGVAIGDSILDLQAAID--EFDG-EARRAIEATAGGQLNAFFALG 80 
                                        8******9***************.7899****************9999..9***.8899***************** PP

                          TIGR01266  76 rparkevrerlqkllsesaevlrdnaalrkeallaqaeatmhlPaqiGdytdfyssirhatnvGilfrgkdnallP 151
                                        r  r+++rerl++ll+e +       +   ++l+ +a+++mh+Paqi dytdfy++i+ha+nvG+lfr +dn+llP
  lcl|FitnessBrowser__WCS417:GFF990  81 RGPRVALRERLLELLAEGSTL----HTREAQVLHRAADCQMHVPAQINDYTDFYVGIEHAQNVGKLFR-PDNPLLP 151
                                        ****************77766....4556789************************************.******* PP

                          TIGR01266 152 nykhlPvgyhGrassvvvsGtelrrPvGqikadnakePvfgpckkldlelelaffvgtenelGeavpiekaeehif 227
                                        nyk++P+gyhGras++++sGt++rrP+Gq+++++ +eP+fgpc++ld+elel++++g++ne+G+++ i  a++hi+
  lcl|FitnessBrowser__WCS417:GFF990 152 NYKYVPIGYHGRASTIRTSGTDVRRPKGQTLPAGQSEPTFGPCARLDYELELGIWIGQGNEMGDSIAIGDAADHIA 227
                                        **************************************************************************** PP

                          TIGR01266 228 GvvllndwsardiqaweyvPlGPflaksfattvsPwvvsiealePfrvaq.lePeqdpkplpylredr..adtafd 300
                                        G++llndwsardiqawey+PlGPfl+ksf+tt+sPwvv++ealePfr+aq ++Pe+dp+pl+yl ++r  a  a+d
  lcl|FitnessBrowser__WCS417:GFF990 228 GFCLLNDWSARDIQAWEYQPLGPFLSKSFITTISPWVVTAEALEPFRKAQpARPEGDPQPLSYLLDKRdqAAGALD 303
                                        **************************************************9**************999556689** PP

                          TIGR01266 301 ielevslkteGlae....aavisrsnakslywtlkqqlahhsvnGcnlraGdllgsGtisGkeeeafGsllelsak 372
                                        ielev l+t+ ++e    a++++ sn++++ywt++q +ahhsvnGc+l+aGdl+gsGt+sG++ ++fGslle++ +
  lcl|FitnessBrowser__WCS417:GFF990 304 IELEVLLTTAAMREqnlpAHRLALSNSLHMYWTVAQLVAHHSVNGCQLQAGDLFGSGTLSGPQAGQFGSLLEMTEG 379
                                        *************9889889******************************************************** PP

                          TIGR01266 373 GkkevkladgetrkfledGdevilrgvckkeGvr.vGfGecaGkvlpa 419
                                        Gkk+v+l +ge+rkfledGde+ilr++c++eG   +GfGec+G+v++a
  lcl|FitnessBrowser__WCS417:GFF990 380 GKKPVELPSGEVRKFLEDGDEIILRARCNREGFAsIGFGECRGTVIAA 427
                                        ********************************988**********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (428 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: 00:00:00.02
# Mc/sec: 7.08
//
[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