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.4489.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 8.35
//
[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