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

GapMind for catabolism of small carbon sources

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

Align fumarylacetoacetase (EC 3.7.1.2) (characterized)
to candidate Pf1N1B4_1024 Fumarylacetoacetase (EC 3.7.1.2)

Query= BRENDA::Q8RW90
         (421 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1024
          Length = 434

 Score =  372 bits (955), Expect = e-107
 Identities = 196/416 (47%), Positives = 261/416 (62%), Gaps = 14/416 (3%)

Query: 16  FPIQNLPYGVFKPESNSTPRPAVAIGDLVLDLSAISEAGLFDGLILKDADCFLQPNLNKF 75
           FP+QNLP GVF  +  S PR  VAIGD + DL A  +AGLFDG+  K  +      LN F
Sbjct: 20  FPLQNLPLGVFSVKG-SAPRSGVAIGDHIFDLEAALDAGLFDGVAKKAVEATRGGQLNAF 78

Query: 76  LAMGRPAWKEARSTLQRILSSNEPILRDNDVLRRKSFHQMSKVEMIVPMVIGDYTDFFAS 135
             +GR A    R  L  +      +    +    K     +  EM +P  I DYTDF+  
Sbjct: 79  FELGREARVALRERLIELFKEGSTLHGKIEAQGAKLLPLAADCEMHLPAKINDYTDFYVG 138

Query: 136 MHHAKNCGLMFRGPENAINPNWFRLPIAYHGRASSIVISGTDIIRPRGQGHPQGNSEPYF 195
           + HA+N G +FR P+N + PN+  +PI YHGRAS+I  SGTD+ RP+GQ  P G +EP F
Sbjct: 139 IEHAQNVGKLFR-PDNPLLPNYKYVPIGYHGRASTIRPSGTDVRRPKGQTLPAGQTEPTF 197

Query: 196 GPSKKLDFELEMAAVVGPGNELGKPIDVNNAADHIFGLLLMNDWSARDIQAWEYVPLGPF 255
           GP  +LD+ELE+   +G GN +G  I + +AADHI G  L+NDWSARDIQAWEY PLGPF
Sbjct: 198 GPCARLDYELELGIWIGQGNAMGDSIAIGDAADHIAGFCLLNDWSARDIQAWEYQPLGPF 257

Query: 256 LGKSFGTTISPWIVTLDALEPFGCQAPKQ---DPPPLPYLAEKE---SVNYDISLEVQLK 309
           L KSF T+ISPW+VT +ALEPF    P +   DP PLPYL +K    +  +DI LEV L 
Sbjct: 258 LSKSFITSISPWVVTAEALEPFRRAQPARPEGDPQPLPYLFDKRDQAAGAFDIELEVLLL 317

Query: 310 PSGRDDSCV----ITKSNFQNLYWTITQQLAHHTVNGCNLRPGDLLGTGTISGPEPDSYG 365
                +  +    +T SN Q++YWT+ Q +AHH+VNGC L+ GDL G+GT+SGPE   +G
Sbjct: 318 TESMREQNLPAHRLTLSNTQHMYWTVAQMVAHHSVNGCQLQAGDLFGSGTLSGPENGQFG 377

Query: 366 CLLELTWNGQKPLSL-NGTTQTFLEDGDQVTFSGVCKGDGY-NVGFGTCTGKIVPS 419
            LLE+T  G+KP+ L +G  + FLEDGD++     C  +G+ ++GFG C GK++P+
Sbjct: 378 SLLEITEGGKKPIELASGEVRKFLEDGDEIILRARCSREGFASIGFGECRGKVLPA 433


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: 588
Number of extensions: 35
Number of successful extensions: 7
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: 434
Length adjustment: 32
Effective length of query: 389
Effective length of database: 402
Effective search space:   156378
Effective search space used:   156378
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 Pf1N1B4_1024 (Fumarylacetoacetase (EC 3.7.1.2))
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.13579.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   5.2e-197  640.7   0.0   5.9e-197  640.5   0.0    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1024  Fumarylacetoacetase (EC 3.7.1.2)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1024  Fumarylacetoacetase (EC 3.7.1.2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  640.5   0.0  5.9e-197  5.9e-197       1     419 [.       9     433 ..       9     434 .] 0.96

  Alignments for each domain:
  == domain 1  score: 640.5 bits;  conditional E-value: 5.9e-197
                                      TIGR01266   1 sfvavak.nsdfplqnlPyGvfstkadssrrigvaiGdqildlskiaaaglfeglalkehqevf 63 
                                                    s+va+a+ ++dfplqnlP+Gvfs  ++s +r gvaiGd+i+dl+++++aglf+g ++k++ e++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1024   9 SWVASANgHADFPLQNLPLGVFS-VKGSAPRSGVAIGDHIFDLEAALDAGLFDG-VAKKAVEAT 70 
                                                    8******9***************.7899**************************.999****** PP

                                      TIGR01266  64 kestlnaflalgrparkevrerlqkllsesaevlrdnaalrk.eallaqaeatmhlPaqiGdyt 126
                                                    +++ lnaf+ lgr ar+++rerl +l+ e   +l  + + +  ++l  +a+++mhlPa+i dyt
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1024  71 RGGQLNAFFELGREARVALRERLIELFKEG-STLHGKIEAQGaKLLPLAADCEMHLPAKINDYT 133
                                                    ***************************965.5566666666505555578************** PP

                                      TIGR01266 127 dfyssirhatnvGilfrgkdnallPnykhlPvgyhGrassvvvsGtelrrPvGqikadnakePv 190
                                                    dfy++i+ha+nvG+lfr +dn+llPnyk++P+gyhGras+++ sGt++rrP+Gq+++++  eP+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1024 134 DFYVGIEHAQNVGKLFR-PDNPLLPNYKYVPIGYHGRASTIRPSGTDVRRPKGQTLPAGQTEPT 196
                                                    *****************.********************************************** PP

                                      TIGR01266 191 fgpckkldlelelaffvgtenelGeavpiekaeehifGvvllndwsardiqaweyvPlGPflak 254
                                                    fgpc++ld+elel++++g++n++G+++ i  a++hi+G++llndwsardiqawey+PlGPfl+k
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1024 197 FGPCARLDYELELGIWIGQGNAMGDSIAIGDAADHIAGFCLLNDWSARDIQAWEYQPLGPFLSK 260
                                                    **************************************************************** PP

                                      TIGR01266 255 sfattvsPwvvsiealePfrvaq.lePeqdpkplpylredr..adtafdielevslkteGlae. 314
                                                    sf+t++sPwvv++ealePfr+aq ++Pe+dp+plpyl ++r  a  afdielev l te ++e 
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1024 261 SFITSISPWVVTAEALEPFRRAQpARPEGDPQPLPYLFDKRdqAAGAFDIELEVLLLTESMREq 324
                                                    ***********************9***************99556789***************98 PP

                                      TIGR01266 315 ...aavisrsnakslywtlkqqlahhsvnGcnlraGdllgsGtisGkeeeafGsllelsakGkk 375
                                                       a++++ sn++++ywt++q++ahhsvnGc+l+aGdl+gsGt+sG+e+++fGslle++ +Gkk
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1024 325 nlpAHRLTLSNTQHMYWTVAQMVAHHSVNGCQLQAGDLFGSGTLSGPENGQFGSLLEITEGGKK 388
                                                    99889*********************************************************** PP

                                      TIGR01266 376 evkladgetrkfledGdevilrgvckkeGvr.vGfGecaGkvlpa 419
                                                    +++la+ge+rkfledGde+ilr++c +eG   +GfGec+Gkvlpa
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1024 389 PIELASGEVRKFLEDGDEIILRARCSREGFAsIGFGECRGKVLPA 433
                                                    *****************************988************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (434 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: 6.65
//
[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