Alignments for a candidate for hutF in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutF in Burkholderia phytofirmans PsJN

Align Formiminoglutamic iminohydrolase (EC 3.5.3.13) (characterized)
to candidate BPHYT_RS07580 BPHYT_RS07580 N-formimino-L-glutamate deiminase

Query= reanno::acidovorax_3H11:Ac3H11_2549
         (464 letters)



>FitnessBrowser__BFirm:BPHYT_RS07580
          Length = 468

 Score =  451 bits (1160), Expect = e-131
 Identities = 244/460 (53%), Positives = 307/460 (66%), Gaps = 16/460 (3%)

Query: 1   MSEPLQRQ---LFAADALLPTGWARDVLVAWDGAGRITAVTPNAQ--PNGAAVAPGPLLP 55
           M+EP ++    LFA  A L  GW R+VL+ WD  G +TAVTP+    P G   A GP+LP
Sbjct: 1   MTEPHKQSNQSLFAEYAYLRDGWRRNVLLEWDTNGTLTAVTPDTSTPPIGVQKAAGPILP 60

Query: 56  GMPNLHSHAFQRAFAGLTEYRGE---SQDSFWSWRNLMYRFAARITPESLEAIATWLYVE 112
           GMPNLHSHAFQRA AGLTEYR     + D+FWSWR+LMYRFAARITPE L ++A WLY+E
Sbjct: 61  GMPNLHSHAFQRAMAGLTEYRASGAGATDNFWSWRDLMYRFAARITPEGLASVAQWLYIE 120

Query: 113 MLEAGYTSVCEFHYVHHDQDGRPYADDATLSLALLRAAKSAGIGITLLPVLYQTSGFGAK 172
           ML+AGYTSVCEFHYVHH  DG  YA+ A L+  ++ AA ++GIG+T+LPVLYQ SGFG++
Sbjct: 121 MLKAGYTSVCEFHYVHHTPDGSRYANQAELAQRVVDAASASGIGMTMLPVLYQYSGFGSR 180

Query: 173 PPRADQARFIRSTDNMLSLLERLA---PATRALGGILGLAPHSLRAVPPDSLAAAVQGLT 229
            PR DQ RFI + +++L LL  L    P T AL    G+APHSLRAV  +SL   + G+ 
Sbjct: 181 APREDQQRFINTPESLLDLLGTLRAARPETAALR--YGVAPHSLRAVSAESLRTLLGGI- 237

Query: 230 ALNPQAPIHIHIAEQTQEVEDCIAWSGQRPVQWLLEHAPVDERWCLVHATHMTPQEYADA 289
             +  AP+HIHIAEQT EV+ C+   G RPVQWLL+   +D RWCLVHATH+   E    
Sbjct: 238 --DNTAPVHIHIAEQTAEVDACVETEGARPVQWLLDRFDIDSRWCLVHATHVDANETLAL 295

Query: 290 ARTGAVAGICPTTEANLGDGIFDMPLWLQHGGRWGVGSDSHACVNAAEELLMLEYGQRLS 349
           A++GAVAG+C TTEANLGDGIF    +L   GR GVGSDSH  V+   EL +LEYGQRL+
Sbjct: 296 AKSGAVAGLCLTTEANLGDGIFPAQEYLDAQGRIGVGSDSHIGVDWRAELRLLEYGQRLA 355

Query: 350 LRQRNVLASRSQAEVATAMTLQAVQGGAQASGRSVSGLAVGQQADLVALDARHVALAGLP 409
            RQRNVLAS     VA  +   +++GGA A+GR+V  L  G++AD + LDA H ++A   
Sbjct: 356 RRQRNVLASAQATHVADRLFAASLEGGAHATGRAVGALQTGRRADWLVLDANHSSIAEHA 415

Query: 410 APSMLSSHVFGSHRTSAIDSLWVAGVLRVAQGRHALHDAA 449
             + LS  VF  H  + I  ++  G   V   RH   + A
Sbjct: 416 PNAWLSGVVFCEHGETPIRDVYAGGDKVVDNRRHRDEEGA 455


Lambda     K      H
   0.320    0.132    0.403 

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: 687
Number of extensions: 18
Number of successful extensions: 5
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: 464
Length of database: 468
Length adjustment: 33
Effective length of query: 431
Effective length of database: 435
Effective search space:   187485
Effective search space used:   187485
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: 51 (24.3 bits)

Align candidate BPHYT_RS07580 BPHYT_RS07580 (N-formimino-L-glutamate deiminase)
to HMM TIGR02022 (hutF: formiminoglutamate deiminase (EC 3.5.3.13))

# 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/TIGR02022.hmm
# target sequence database:        /tmp/gapView.29249.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02022  [M=455]
Accession:   TIGR02022
Description: hutF: formiminoglutamate deiminase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   1.8e-181  589.7   3.6   2.1e-181  589.6   3.6    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS07580  BPHYT_RS07580 N-formimino-L-glut


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS07580  BPHYT_RS07580 N-formimino-L-glutamate deiminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  589.6   3.6  2.1e-181  2.1e-181       2     454 ..      10     467 ..       9     468 .] 0.98

  Alignments for each domain:
  == domain 1  score: 589.6 bits;  conditional E-value: 2.1e-181
                                TIGR02022   2 kvyfaerallpdgwaegvrlavaedGrilavetgvsa.aedaerlsgvvlpglanlHsHAFqralaGlae 70 
                                              + +fae a+l dgw ++v l+ + +G ++av  ++s+ + ++++ +g++lpg++nlHsHAFqra+aGl+e
  lcl|FitnessBrowser__BFirm:BPHYT_RS07580  10 QSLFAEYAYLRDGWRRNVLLEWDTNGTLTAVTPDTSTpPIGVQKAAGPILPGMPNLHSHAFQRAMAGLTE 79 
                                              5689********************************97889***************************** PP

                                TIGR02022  71 vagsg...aDsFWtWRevmYrlverldPeqleaiarqlyvemlkaGftrvgEFHYlHHaadGtpYadpae 137
                                              +++sg    D+FW+WR++mYr+++r++Pe l  +a+ ly+emlkaG+t+v EFHY+HH +dG++Ya++ae
  lcl|FitnessBrowser__BFirm:BPHYT_RS07580  80 YRASGagaTDNFWSWRDLMYRFAARITPEGLASVAQWLYIEMLKAGYTSVCEFHYVHHTPDGSRYANQAE 149
                                              **9987778************************************************************* PP

                                TIGR02022 138 laeriaaAAadaGigltlLpvlYahagFGgaaanegqrrfiddveaflrlvealrkelaaqeearlGlai 207
                                              la+r++ AA+ +Gig+t+LpvlY ++gFG+ a+ e q+rfi+++e+ l+l+ +lr +  ++++ r G+a+
  lcl|FitnessBrowser__BFirm:BPHYT_RS07580 150 LAQRVVDAASASGIGMTMLPVLYQYSGFGSRAPREDQQRFINTPESLLDLLGTLRAARPETAALRYGVAP 219
                                              ********************************************************************** PP

                                TIGR02022 208 HslRAvtaeelaavlqaserqlPvHiHvaEqqkEvddClaasgrrPvewLldhaevdarwclvHatHltd 277
                                              HslRAv+ae l+++l   ++++PvHiH+aEq++Evd+C+ + g rPv+wLld+ ++d+rwclvHatH+++
  lcl|FitnessBrowser__BFirm:BPHYT_RS07580 220 HSLRAVSAESLRTLLGGIDNTAPVHIHIAEQTAEVDACVETEGARPVQWLLDRFDIDSRWCLVHATHVDA 289
                                              ********************************************************************** PP

                                TIGR02022 278 eevkllaksgavaglCpttEanLgDGifpaadfvaaggrlgiGsDshvvvdvleElRllEygqRLrdraR 347
                                              +e+ +laksgavaglC+ttEanLgDGifpa++++ a+gr+g+GsDsh+ vd   ElRllEygqRL +r+R
  lcl|FitnessBrowser__BFirm:BPHYT_RS07580 290 NETLALAKSGAVAGLCLTTEANLGDGIFPAQEYLDAQGRIGVGSDSHIGVDWRAELRLLEYGQRLARRQR 359
                                              ********************************************************************** PP

                                TIGR02022 348 nvlaageeasvaralydaAlaggaqalGlaegeleaGarADlltldledpslagakgdalldsllfaae. 416
                                              nvla+ + + va++l+ a l gga+a G+a g+l++G rAD+l+ld+++ s+a+  ++a l  ++f  + 
  lcl|FitnessBrowser__BFirm:BPHYT_RS07580 360 NVLASAQATHVADRLFAASLEGGAHATGRAVGALQTGRRADWLVLDANHSSIAEHAPNAWLSGVVFCEHg 429
                                              ******************************************************************9761 PP

                                TIGR02022 417 kaavrdvvvaGrkvvrdgrHaleeeierafakvlrall 454
                                              ++ +rdv+ +G kvv ++rH++ee +  ++  +l +ll
  lcl|FitnessBrowser__BFirm:BPHYT_RS07580 430 ETPIRDVYAGGDKVVDNRRHRDEEGAYARYRMALADLL 467
                                              567************************99999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (468 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 9.62
//
[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:

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