Alignments for a candidate for fahA in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for fahA in Pseudomonas putida KT2440

Align fumarylacetoacetase (EC 3.7.1.2) (characterized)
to candidate PP_4620 PP_4620 Fumarylacetoacetase

Query= BRENDA::Q8RW90
         (421 letters)



>FitnessBrowser__Putida:PP_4620
          Length = 430

 Score =  374 bits (960), Expect = e-108
 Identities = 199/416 (47%), Positives = 265/416 (63%), Gaps = 18/416 (4%)

Query: 14  SHFPIQNLPYGVFKPESNSTPRPAVAIGDLVLDLSAISEAGLFDGLILKDADCFLQPNLN 73
           S FP+QNLP G+F     +  R  VAIGD +LDL A+  AGLFDG      +      LN
Sbjct: 18  SDFPLQNLPLGIFSRPGEAR-RCGVAIGDAILDLEAVLAAGLFDGAAKAAVEATRGGALN 76

Query: 74  KFLAMGRPAWKEARSTLQRILSSNEPILRDNDVLRRKSFHQMSKVEMIVPMVIGDYTDFF 133
            F AMGR A    R  LQ +L  +     ++    + +    S  ++ VP  IGDYTDF+
Sbjct: 77  AFFAMGRNARVALRERLQVLLGEHS----EHQAALKPALLPASDCQLHVPAQIGDYTDFY 132

Query: 134 ASMHHAKNCGLMFRGPENAINPNWFRLPIAYHGRASSIVISGTDIIRPRGQGHPQGNSEP 193
             + HAKN G +FR P+N + PN+  +PI YHGRAS+I  SGTD+ RP+GQ  P G++EP
Sbjct: 133 VGIEHAKNVGKLFR-PDNPLLPNYKYVPIGYHGRASTIRPSGTDVRRPKGQTLPAGHTEP 191

Query: 194 YFGPSKKLDFELEMAAVVGPGNELGKPIDVNNAADHIFGLLLMNDWSARDIQAWEYVPLG 253
            FGP  +LD+ELE+   +G GN++G+ I V +AA+H+ GL L+NDWSARDIQAWEY PLG
Sbjct: 192 SFGPCARLDYELELGIWIGQGNDMGQAIPVGDAAEHVAGLCLLNDWSARDIQAWEYQPLG 251

Query: 254 PFLGKSFGTTISPWIVTLDALEPFGCQAPKQ---DPPPLPYLAEKE---SVNYDISLEVQ 307
           PFL KSF TTISPW+VT +ALEPF C  P +   DP PL YL +K    S  +DI LEV 
Sbjct: 252 PFLSKSFITTISPWVVTAEALEPFRCAQPARPEGDPQPLSYLLDKRDQASGAFDIELEVL 311

Query: 308 LKPSGRDDSCV----ITKSNFQNLYWTITQQLAHHTVNGCNLRPGDLLGTGTISGPEPDS 363
           L      +  +    +T SN +++YWT+ Q +AHH+VNGC L+PGDL G+GT+SG  P S
Sbjct: 312 LLTERMREQGIAPHRLTLSNTRSMYWTVAQLVAHHSVNGCQLQPGDLFGSGTLSGATPGS 371

Query: 364 YGCLLELTWNGQKPLSL-NGTTQTFLEDGDQVTFSGVCKGDGY-NVGFGTCTGKIV 417
           +G LLE+T  G+ P+ L +G  + FLEDGD++     C  DG  ++GFG C G ++
Sbjct: 372 FGSLLEITEGGKLPVELASGEVRKFLEDGDEIILRARCTRDGVASIGFGECRGTVI 427


Lambda     K      H
   0.319    0.139    0.434 

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: 584
Number of extensions: 34
Number of successful extensions: 6
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: 421
Length of database: 430
Length adjustment: 32
Effective length of query: 389
Effective length of database: 398
Effective search space:   154822
Effective search space used:   154822
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate PP_4620 PP_4620 (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.24069.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.1e-196  639.6   0.0   1.3e-196  639.4   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_4620  PP_4620 Fumarylacetoacetase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_4620  PP_4620 Fumarylacetoacetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  639.4   0.0  1.3e-196  1.3e-196       1     419 [.       9     429 ..       9     430 .] 0.98

  Alignments for each domain:
  == domain 1  score: 639.4 bits;  conditional E-value: 1.3e-196
                           TIGR01266   1 sfvavak.nsdfplqnlPyGvfstkadssrrigvaiGdqildlskiaaaglfeglalkehqevfkestlnaflal 74 
                                         s+v+ a+ +sdfplqnlP+G+fs + +  rr+gvaiGd ildl++++aaglf+g a+k++ e++++++lnaf+a+
  lcl|FitnessBrowser__Putida:PP_4620   9 SWVEHANgHSDFPLQNLPLGIFS-RPGEARRCGVAIGDAILDLEAVLAAGLFDG-AAKAAVEATRGGALNAFFAM 81 
                                         8*****99***************.999***************************.99****************** PP

                           TIGR01266  75 grparkevrerlqkllsesaevlrdnaalrkeallaqaeatmhlPaqiGdytdfyssirhatnvGilfrgkdnal 149
                                         gr ar+++rerlq ll+e++e    +aal+  all++++++ h+PaqiGdytdfy++i+ha+nvG+lfr +dn+l
  lcl|FitnessBrowser__Putida:PP_4620  82 GRNARVALRERLQVLLGEHSEH---QAALK-PALLPASDCQLHVPAQIGDYTDFYVGIEHAKNVGKLFR-PDNPL 151
                                         *****************88877...66665.6899**********************************.***** PP

                           TIGR01266 150 lPnykhlPvgyhGrassvvvsGtelrrPvGqikadnakePvfgpckkldlelelaffvgtenelGeavpiekaee 224
                                         lPnyk++P+gyhGras+++ sGt++rrP+Gq+++++  eP+fgpc++ld+elel++++g++n++G+a+p+  a+e
  lcl|FitnessBrowser__Putida:PP_4620 152 LPNYKYVPIGYHGRASTIRPSGTDVRRPKGQTLPAGHTEPSFGPCARLDYELELGIWIGQGNDMGQAIPVGDAAE 226
                                         *************************************************************************** PP

                           TIGR01266 225 hifGvvllndwsardiqaweyvPlGPflaksfattvsPwvvsiealePfrvaq.lePeqdpkplpylredr..ad 296
                                         h++G++llndwsardiqawey+PlGPfl+ksf+tt+sPwvv++ealePfr aq ++Pe+dp+pl+yl ++r  a+
  lcl|FitnessBrowser__Putida:PP_4620 227 HVAGLCLLNDWSARDIQAWEYQPLGPFLSKSFITTISPWVVTAEALEPFRCAQpARPEGDPQPLSYLLDKRdqAS 301
                                         ****************************************************99**************9986577 PP

                           TIGR01266 297 tafdielevslkteGlae....aavisrsnakslywtlkqqlahhsvnGcnlraGdllgsGtisGkeeeafGsll 367
                                          afdielev l te ++e    +++++ sn++s+ywt++q +ahhsvnGc+l++Gdl+gsGt+sG+ +++fGsll
  lcl|FitnessBrowser__Putida:PP_4620 302 GAFDIELEVLLLTERMREqgiaPHRLTLSNTRSMYWTVAQLVAHHSVNGCQLQPGDLFGSGTLSGATPGSFGSLL 376
                                         89**************9999999**************************************************** PP

                           TIGR01266 368 elsakGkkevkladgetrkfledGdevilrgvckkeGvr.vGfGecaGkvlpa 419
                                         e++ +Gk +v+la+ge+rkfledGde+ilr++c ++Gv  +GfGec+G+v++a
  lcl|FitnessBrowser__Putida:PP_4620 377 EITEGGKLPVELASGEVRKFLEDGDEIILRARCTRDGVAsIGFGECRGTVIAA 429
                                         *************************************998**********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (430 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 11.28
//
[ok]

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

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Protein sequences (fasta format)
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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