Alignments for a candidate for hutF in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutF in Paraburkholderia bryophila 376MFSha3.1

Align Formiminoglutamic iminohydrolase (EC 3.5.3.13) (characterized)
to candidate H281DRAFT_04868 H281DRAFT_04868 formimidoylglutamate deiminase (EC 3.5.3.13)

Query= reanno::pseudo6_N2E2:Pf6N2E2_3808
         (454 letters)



>FitnessBrowser__Burk376:H281DRAFT_04868
          Length = 465

 Score =  465 bits (1197), Expect = e-135
 Identities = 245/456 (53%), Positives = 304/456 (66%), Gaps = 7/456 (1%)

Query: 5   FAERALLPSGWAHDVRLEVDAEGVLTHIQAGSHADGAE--RLGGPLLPGMPNLHSHAFQR 62
           FAE A LP GW  DV LE D +G LT ++  +    A   R  GP++PGMPNLHSHAFQR
Sbjct: 9   FAEHAYLPGGWRRDVLLEWDVDGNLTTVEPDTRDVPASVARAAGPVMPGMPNLHSHAFQR 68

Query: 63  AMAGLAEVAGNPN----DSFWTWRDLMYRLVGKISPDQLGIIARQLYIEMLKAGYTSVAE 118
           AMAGL E  G+      D+FW+WRDLMYR   +ISP+ L  +A+ LYIEMLKAGYTSV E
Sbjct: 69  AMAGLTEYRGSSATGAADNFWSWRDLMYRFAARISPEGLASVAQWLYIEMLKAGYTSVCE 128

Query: 119 FHYVHHDTDGAPYADPAELALRISHAASAAGIGLTLLPVLYSHSGFGGQAPNDGQRRFIN 178
           FHYVHH  DG  Y +PAELA R+  AASA+GIG+T+LPVLY +SGFG +AP D QRRFIN
Sbjct: 129 FHYVHHTPDGGRYGNPAELAQRVVDAASASGIGMTMLPVLYQYSGFGARAPRDDQRRFIN 188

Query: 179 STENYLKLQSRLQPILAGQPSQALGLCFHSLRAVTPGQIQDVLAASDRECPVHIHIAEQQ 238
           +  + L+L   L+       +   G+  HSLRAV+   ++++L   D   PVHIHIAEQ 
Sbjct: 189 TPGSLLELLGALRAARPENAALRYGVAPHSLRAVSEQSLRELLGGLDGSAPVHIHIAEQT 248

Query: 239 KEVDDCLSWSGARPLQWLYENTEVDQRWCLVHATHANAQEVSLMARSRAIAGLCLTTEAN 298
            EVD C+   GARP+QWL +  +VD RWCLVHATH +A E   +ARS A+AGLCLTTEAN
Sbjct: 249 AEVDACVETEGARPVQWLLDRFDVDSRWCLVHATHVDANETLALARSGAVAGLCLTTEAN 308

Query: 299 LGDGIFPAVDFLAQGGRLGIGSDSHVSLSVVEELRWLEYGQRLRDQRRNRLYRADQPMVG 358
           LGDG+FPA ++L   GR+G+GSDSH+ +    ELR LEYGQRL  ++RN L  A  P V 
Sbjct: 309 LGDGLFPAQEYLDAKGRIGVGSDSHIGVDWRAELRLLEYGQRLTRRQRNVLASAQTPYVA 368

Query: 359 RTLFDAALEGGAQALGQPIGALDIGKRADWLVLDGSDPYLATAQGDAILNRWLFA-GGDR 417
             LFDAALEGGAQA G+  GAL +G RADWLVLD +   +A     A L+  +F   G+ 
Sbjct: 369 DRLFDAALEGGAQATGRATGALQVGHRADWLVLDPNHASIAEHAPSAWLSGVVFCEHGET 428

Query: 418 QVRDVMVGGRWVVRDGRHAGEEESARAFTQVLRELL 453
            +RDV  GG  VV + RH  EE +   +   L +LL
Sbjct: 429 PIRDVYAGGDKVVDNRRHRDEEGAYARYRVALADLL 464


Lambda     K      H
   0.321    0.137    0.421 

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: 664
Number of extensions: 41
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: 454
Length of database: 465
Length adjustment: 33
Effective length of query: 421
Effective length of database: 432
Effective search space:   181872
Effective search space used:   181872
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 H281DRAFT_04868 H281DRAFT_04868 (formimidoylglutamate deiminase (EC 3.5.3.13))
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.7502.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   2.7e-183  595.7   1.8   3.1e-183  595.6   1.8    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_04868  H281DRAFT_04868 formimidoylgluta


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_04868  H281DRAFT_04868 formimidoylglutamate deiminase (EC 3.5.3.13)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  595.6   1.8  3.1e-183  3.1e-183       2     454 ..       6     464 ..       5     465 .] 0.98

  Alignments for each domain:
  == domain 1  score: 595.6 bits;  conditional E-value: 3.1e-183
                                    TIGR02022   2 kvyfaerallpdgwaegvrlavaedGrilavetgvsa.aedaerlsgvvlpglanlHsHAFqrala 66 
                                                  +++fae+a+lp+gw ++v l+ + dG++++ve ++   +  ++r +g+v+pg++nlHsHAFqra+a
  lcl|FitnessBrowser__Burk376:H281DRAFT_04868   6 QTLFAEHAYLPGGWRRDVLLEWDVDGNLTTVEPDTRDvPASVARAAGPVMPGMPNLHSHAFQRAMA 71 
                                                  689******************************999878999************************ PP

                                    TIGR02022  67 Glaevagsg....aDsFWtWRevmYrlverldPeqleaiarqlyvemlkaGftrvgEFHYlHHaad 128
                                                  Gl+e++gs+    aD+FW+WR++mYr+++r++Pe l  +a+ ly+emlkaG+t+v EFHY+HH +d
  lcl|FitnessBrowser__Burk376:H281DRAFT_04868  72 GLTEYRGSSatgaADNFWSWRDLMYRFAARISPEGLASVAQWLYIEMLKAGYTSVCEFHYVHHTPD 137
                                                  *******9877888**************************************************** PP

                                    TIGR02022 129 GtpYadpaelaeriaaAAadaGigltlLpvlYahagFGgaaanegqrrfiddveaflrlvealrke 194
                                                  G +Y +paela+r++ AA+ +Gig+t+LpvlY ++gFG+ a+ + qrrfi+++ + l+l+ alr +
  lcl|FitnessBrowser__Burk376:H281DRAFT_04868 138 GGRYGNPAELAQRVVDAASASGIGMTMLPVLYQYSGFGARAPRDDQRRFINTPGSLLELLGALRAA 203
                                                  ****************************************************************** PP

                                    TIGR02022 195 laaqeearlGlaiHslRAvtaeelaavlqaserqlPvHiHvaEqqkEvddClaasgrrPvewLldh 260
                                                    ++++ r G+a+HslRAv+++ l+++l   + ++PvHiH+aEq++Evd+C+ + g rPv+wLld+
  lcl|FitnessBrowser__Burk376:H281DRAFT_04868 204 RPENAALRYGVAPHSLRAVSEQSLRELLGGLDGSAPVHIHIAEQTAEVDACVETEGARPVQWLLDR 269
                                                  ****************************************************************** PP

                                    TIGR02022 261 aevdarwclvHatHltdeevkllaksgavaglCpttEanLgDGifpaadfvaaggrlgiGsDshvv 326
                                                   +vd+rwclvHatH++++e+ +la+sgavaglC+ttEanLgDG+fpa++++ a gr+g+GsDsh+ 
  lcl|FitnessBrowser__Burk376:H281DRAFT_04868 270 FDVDSRWCLVHATHVDANETLALARSGAVAGLCLTTEANLGDGLFPAQEYLDAKGRIGVGSDSHIG 335
                                                  ****************************************************************** PP

                                    TIGR02022 327 vdvleElRllEygqRLrdraRnvlaageeasvaralydaAlaggaqalGlaegeleaGarADlltl 392
                                                  vd   ElRllEygqRL++r+Rnvla+ + + va++l+daAl ggaqa G+a+g+l++G rAD+l+l
  lcl|FitnessBrowser__Burk376:H281DRAFT_04868 336 VDWRAELRLLEYGQRLTRRQRNVLASAQTPYVADRLFDAALEGGAQATGRATGALQVGHRADWLVL 401
                                                  ****************************************************************** PP

                                    TIGR02022 393 dledpslagakgdalldsllfaae.kaavrdvvvaGrkvvrdgrHaleeeierafakvlrall 454
                                                  d +++s+a+  ++a l  ++f  + ++ +rdv+ +G kvv ++rH++ee +  ++  +l +ll
  lcl|FitnessBrowser__Burk376:H281DRAFT_04868 402 DPNHASIAEHAPSAWLSGVVFCEHgETPIRDVYAGGDKVVDNRRHRDEEGAYARYRVALADLL 464
                                                  *********************9761567***************************99998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (465 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: 9.18
//
[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