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.3928253.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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 24.91
//
[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