Alignments for a candidate for hutF in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutF in Herbaspirillum seropedicae SmR1

Align Formiminoglutamic iminohydrolase (EC 3.5.3.13) (characterized)
to candidate HSERO_RS11455 HSERO_RS11455 N-formimino-L-glutamate deiminase

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



>FitnessBrowser__HerbieS:HSERO_RS11455
          Length = 458

 Score =  489 bits (1258), Expect = e-142
 Identities = 252/448 (56%), Positives = 302/448 (67%), Gaps = 3/448 (0%)

Query: 9   LFAADALLPTGWARDVLVAWDGAGRITAVTPNAQPNGAAVAPGPLLPGMPNLHSHAFQRA 68
           LF   ALLP GW  DVL+ WDGAGR+T VTP++    AA+A GP+LPGMPNLHSHAFQRA
Sbjct: 1   LFCPLALLPQGWRSDVLLRWDGAGRLTHVTPDSARGSAALASGPVLPGMPNLHSHAFQRA 60

Query: 69  FAGLTEYRGESQDSFWSWRNLMYRFAARITPESLEAIATWLYVEMLEAGYTSVCEFHYVH 128
            AGL E  G   DSFWSWR LMYRFA R+ P  LEAIA   Y+EML+AGYTSVCEFHY+H
Sbjct: 61  MAGLAETMGSPADSFWSWRELMYRFAQRLQPRQLEAIARQTYIEMLKAGYTSVCEFHYLH 120

Query: 129 HDQDGRPYADDATLSLALLRAAKSAGIGITLLPVLYQTSGFGAKPPRADQARFIRSTDNM 188
           H  DG PYAD A ++  LL+AA  +GIG+TLLPVLYQ  G G +P  A+Q RF+ +   +
Sbjct: 121 HAPDGAPYADPAEMAWPLLQAAGQSGIGMTLLPVLYQQGGLGGRPVSAEQRRFVAAPSWL 180

Query: 189 LSLLERLAPATRALG-GILGLAPHSLRAVPPDSLAAAVQGLTAL--NPQAPIHIHIAEQT 245
           L L ERL            G+APHSLRAV P  L   + GL        APIHIH+AEQ 
Sbjct: 181 LGLRERLLQHMPENDMRRYGVAPHSLRAVAPTGLEELLSGLAGQPGGSDAPIHIHVAEQL 240

Query: 246 QEVEDCIAWSGQRPVQWLLEHAPVDERWCLVHATHMTPQEYADAARTGAVAGICPTTEAN 305
           +EVEDC+AWSGQRPVQWLL   PVD RWCLVHATHM  +EY   A +GAV G+CPTTEAN
Sbjct: 241 REVEDCLAWSGQRPVQWLLSSQPVDARWCLVHATHMDDEEYRAVAGSGAVVGLCPTTEAN 300

Query: 306 LGDGIFDMPLWLQHGGRWGVGSDSHACVNAAEELLMLEYGQRLSLRQRNVLASRSQAEVA 365
           LGDG+ D P  +    RWG+GSDS+  ++   EL +LEY QRL  R+RNVLA      VA
Sbjct: 301 LGDGVIDAPRLIDSAARWGIGSDSNIAISLRAELRLLEYAQRLHHRRRNVLAVIDAPAVA 360

Query: 366 TAMTLQAVQGGAQASGRSVSGLAVGQQADLVALDARHVALAGLPAPSMLSSHVFGSHRTS 425
             +  QA+ GGAQA+GR+V+GL  GQ+ADLV LD  HV LA   +  +LS+ VF  H   
Sbjct: 361 DRLFCQALAGGAQAAGRAVAGLMPGQRADLVVLDPDHVNLAQRSSTQLLSALVFCEHDGP 420

Query: 426 AIDSLWVAGVLRVAQGRHALHDAAAQAF 453
            I  ++V G   V +GRHAL D A + +
Sbjct: 421 MIGDVYVGGRQVVKEGRHALDDRAREDY 448


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: 734
Number of extensions: 38
Number of successful extensions: 3
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: 458
Length adjustment: 33
Effective length of query: 431
Effective length of database: 425
Effective search space:   183175
Effective search space used:   183175
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 HSERO_RS11455 HSERO_RS11455 (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.2829.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   3.2e-182  592.2   0.3   3.6e-182  592.1   0.3    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS11455  HSERO_RS11455 N-formimino-L-glut


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS11455  HSERO_RS11455 N-formimino-L-glutamate deiminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  592.1   0.3  3.6e-182  3.6e-182       5     454 ..       2     456 ..       1     457 [. 0.96

  Alignments for each domain:
  == domain 1  score: 592.1 bits;  conditional E-value: 3.6e-182
                                  TIGR02022   5 faerallpdgwaegvrlavaedGrilavetgvsaaedaerlsgvvlpglanlHsHAFqralaGlaeva 72 
                                                f+  allp+gw ++v l  + +Gr++ v  +++    a++ sg+vlpg++nlHsHAFqra+aGlae++
  lcl|FitnessBrowser__HerbieS:HSERO_RS11455   2 FCPLALLPQGWRSDVLLRWDGAGRLTHVTPDSA-RGSAALASGPVLPGMPNLHSHAFQRAMAGLAETM 68 
                                                7889************************88887.677888999************************* PP

                                  TIGR02022  73 gsgaDsFWtWRevmYrlverldPeqleaiarqlyvemlkaGftrvgEFHYlHHaadGtpYadpaelae 140
                                                gs+aDsFW+WRe+mYr+++rl+P qleaiarq+y+emlkaG+t+v EFHYlHHa+dG+pYadpae+a 
  lcl|FitnessBrowser__HerbieS:HSERO_RS11455  69 GSPADSFWSWRELMYRFAQRLQPRQLEAIARQTYIEMLKAGYTSVCEFHYLHHAPDGAPYADPAEMAW 136
                                                ******************************************************************** PP

                                  TIGR02022 141 riaaAAadaGigltlLpvlYahagFGgaaanegqrrfiddveaflrlvealrkelaaqeearlGlaiH 208
                                                 +++AA ++Gig+tlLpvlY + g Gg + +++qrrf+  +   l l e+l +++ +++  r G+a+H
  lcl|FitnessBrowser__HerbieS:HSERO_RS11455 137 PLLQAAGQSGIGMTLLPVLYQQGGLGGRPVSAEQRRFVAAPSWLLGLRERLLQHMPENDMRRYGVAPH 204
                                                ******************************************************************** PP

                                  TIGR02022 209 slRAvtaeelaavlqaserq.....lPvHiHvaEqqkEvddClaasgrrPvewLldhaevdarwclvH 271
                                                slRAv +  l+++l+  + q     +P+HiHvaEq +Ev+dCla+sg+rPv+wLl  ++vdarwclvH
  lcl|FitnessBrowser__HerbieS:HSERO_RS11455 205 SLRAVAPTGLEELLSGLAGQpggsdAPIHIHVAEQLREVEDCLAWSGQRPVQWLLSSQPVDARWCLVH 272
                                                *************9954432222338****************************************** PP

                                  TIGR02022 272 atHltdeevkllaksgavaglCpttEanLgDGifpaadfvaaggrlgiGsDshvvvdvleElRllEyg 339
                                                atH++dee +++a sgav+glCpttEanLgDG++ a  ++   +r+giGsDs++++++  ElRllEy+
  lcl|FitnessBrowser__HerbieS:HSERO_RS11455 273 ATHMDDEEYRAVAGSGAVVGLCPTTEANLGDGVIDAPRLIDSAARWGIGSDSNIAISLRAELRLLEYA 340
                                                ******************************************************************** PP

                                  TIGR02022 340 qRLrdraRnvlaageeasvaralydaAlaggaqalGlaegeleaGarADlltldledpslagakgdal 407
                                                qRL++r+Rnvla  + ++va++l+ +Alaggaqa+G+a  +l  G+rADl++ld ++++la++++ +l
  lcl|FitnessBrowser__HerbieS:HSERO_RS11455 341 QRLHHRRRNVLAVIDAPAVADRLFCQALAGGAQAAGRAVAGLMPGQRADLVVLDPDHVNLAQRSSTQL 408
                                                ******************************************************************** PP

                                  TIGR02022 408 ldsllfaaeka.avrdvvvaGrkvvrdgrHaleeeierafakvlrall 454
                                                l +l+f  ++   + dv+v+Gr+vv++grHal +++ + + ++l all
  lcl|FitnessBrowser__HerbieS:HSERO_RS11455 409 LSALVFCEHDGpMIGDVYVGGRQVVKEGRHALDDRAREDYRHALAALL 456
                                                ******987652799**************************9999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (458 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: 7.76
//
[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