Alignments for a candidate for hutF in Cereibacter sphaeroides ATCC 17029

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutF in Cereibacter sphaeroides ATCC 17029

Align Formiminoglutamic iminohydrolase (EC 3.5.3.13) (characterized)
to candidate WP_011841109.1 RSPH17029_RS07980 formimidoylglutamate deiminase

Query= reanno::Phaeo:GFF3581
         (455 letters)



>NCBI__GCF_000015985.1:WP_011841109.1
          Length = 455

 Score =  457 bits (1175), Expect = e-133
 Identities = 239/452 (52%), Positives = 298/452 (65%), Gaps = 2/452 (0%)

Query: 1   MQTIFAQHARMPQGWVTDLRLTIEAGKIATLEPGAAVQPQDHRVGALVPALANLHSHSFQ 60
           MQ I A+ A +P+GW  D+ + IE GKIA++ PG A   +  RVG L+PA  NLHSH+FQ
Sbjct: 1   MQLIHAEEALLPEGWARDVTIRIEGGKIASVLPGTAAGAEAVRVGCLLPAPVNLHSHAFQ 60

Query: 61  RAMAGMTETR-VSGRDSFWSWRKLMYQFVDHLTPEQYEAIAALVFMEMLEAGYASVGEFH 119
           RAMAG+TE R   G+DSFW+WR+LM++F++ LTP++ EAIAA   +EMLEAG+A+V EFH
Sbjct: 61  RAMAGLTEGRGPDGQDSFWTWRRLMFRFLESLTPDEVEAIAAFAQIEMLEAGFAAVAEFH 120

Query: 120 YVHHQPGGQPYEVLGELSHRVFAAADLTGIGLTHLPVLYTYGGAGQAPLGGGQQRFGNDV 179
           Y+HH+P G+ Y    E++ R+ AA++ +G+GLT LPVLY  GG     L  GQ RFG+D 
Sbjct: 121 YLHHRPDGRAYADPAEMAARICAASETSGLGLTLLPVLYQQGGCDGRALAPGQVRFGSDP 180

Query: 180 TRYANLLSDCRTTARELLPMDARVGIAPHSLRATAPDELAEVLTLRAESPVHIHIAEQPQ 239
           T YA LL   R  A   LP DA +G+APHSLRA +P+ L   + L    P+H+H+AEQ  
Sbjct: 181 TSYAGLLDGARR-ALAGLPADATLGVAPHSLRAVSPEGLEAAVALAGSGPIHMHLAEQAA 239

Query: 240 EVADIGGWLGERPVQWLLNNCAVDKDWCLIHATHMTEQETHDLARSGAVAGLCPITEANL 299
           EV ++   LG RPV WLL++  VD  WCLIH T M   ET  LAR+ AVAGLCP+TEANL
Sbjct: 240 EVEEVEAGLGARPVSWLLDHQPVDARWCLIHCTQMQPAETDRLARTSAVAGLCPVTEANL 299

Query: 300 GDGPFNGVLFQNNGGRFGVGSDSNIRISLSEELRLLEYSQRLRDLARNVMVPEEGSVGAA 359
           GDG F+G  +   GGRFG+GSDSNIRI+ SEELR L+YSQRLRD  R        S G  
Sbjct: 300 GDGIFDGARYMAAGGRFGIGSDSNIRIAFSEELRQLDYSQRLRDRVRAPFATAGRSSGRV 359

Query: 360 LYLGAACGGAQALGRDAGRLEVGALADLMAFDTTDVTLCALRPDQFLDGLCFAADDSVVR 419
           L+  A  GGAQA GR +G L  G  ADL+A D   V L     D  LD   FA  D +  
Sbjct: 360 LHEAALAGGAQAAGRASGALAPGLWADLLALDRGAVDLEGRSGDGLLDAWIFAGSDRMAS 419

Query: 420 DVWSAGRHVVSGGRHANREQIIARYNSAVAAL 451
           +VWSAGRHVVSGGRH  R  I A Y   +A L
Sbjct: 420 EVWSAGRHVVSGGRHVARSPIEAGYRRVMARL 451


Lambda     K      H
   0.321    0.136    0.413 

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: 632
Number of extensions: 28
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: 455
Length of database: 455
Length adjustment: 33
Effective length of query: 422
Effective length of database: 422
Effective search space:   178084
Effective search space used:   178084
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 WP_011841109.1 RSPH17029_RS07980 (formimidoylglutamate 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.458111.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.1e-168  546.7   2.2   2.4e-168  546.5   2.2    1.0  1  NCBI__GCF_000015985.1:WP_011841109.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000015985.1:WP_011841109.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  546.5   2.2  2.4e-168  2.4e-168       1     454 [.       1     452 [.       1     453 [. 0.97

  Alignments for each domain:
  == domain 1  score: 546.5 bits;  conditional E-value: 2.4e-168
                             TIGR02022   1 akvyfaerallpdgwaegvrlavaedGrilavetgvsaaedaerlsgvvlpglanlHsHAFqralaGlaevag 73 
                                           ++ ++ae+allp+gwa++v + ++ +G+i++v  g++a+ +a r++  +lp+ +nlHsHAFqra+aGl+e +g
  NCBI__GCF_000015985.1:WP_011841109.1   1 MQLIHAEEALLPEGWARDVTIRIE-GGKIASVLPGTAAGAEAVRVG-CLLPAPVNLHSHAFQRAMAGLTEGRG 71 
                                           5789*******************9.88********99766666665.*************************9 PP

                             TIGR02022  74 sg.aDsFWtWRevmYrlverldPeqleaiarqlyvemlkaGftrvgEFHYlHHaadGtpYadpaelaeriaaA 145
                                              +DsFWtWR +m+r++e+l+P+++eaia+ +++eml+aGf++v+EFHYlHH +dG  Yadpae+a+ri aA
  NCBI__GCF_000015985.1:WP_011841109.1  72 PDgQDSFWTWRRLMFRFLESLTPDEVEAIAAFAQIEMLEAGFAAVAEFHYLHHRPDGRAYADPAEMAARICAA 144
                                           644********************************************************************** PP

                             TIGR02022 146 AadaGigltlLpvlYahagFGgaaanegqrrfiddveaflrlvealrkelaaqe.earlGlaiHslRAvtaee 217
                                            +++G+gltlLpvlY + g  g a  +gq rf  d+ +++ l++  r++la+ + +a+lG+a+HslRAv++e 
  NCBI__GCF_000015985.1:WP_011841109.1 145 SETSGLGLTLLPVLYQQGGCDGRALAPGQVRFGSDPTSYAGLLDGARRALAGLPaDATLGVAPHSLRAVSPEG 217
                                           ***************************************************9973689*************** PP

                             TIGR02022 218 laavlqaserqlPvHiHvaEqqkEvddClaasgrrPvewLldhaevdarwclvHatHltdeevkllaksgava 290
                                           l+a ++++ +  P+H+H+aEq +Ev++  a  g rPv wLldh++vdarwcl+H t +++ e+ +la++ ava
  NCBI__GCF_000015985.1:WP_011841109.1 218 LEAAVALAGS-GPIHMHLAEQAAEVEEVEAGLGARPVSWLLDHQPVDARWCLIHCTQMQPAETDRLARTSAVA 289
                                           **99988776.5************************************************************* PP

                             TIGR02022 291 glCpttEanLgDGifpaadfvaaggrlgiGsDshvvvdvleElRllEygqRLrdraRnvlaageeasvaraly 363
                                           glCp+tEanLgDGif  a ++aaggr+giGsDs++ +   eElR+l+y+qRLrdr R+ +a+  ++s++r l+
  NCBI__GCF_000015985.1:WP_011841109.1 290 GLCPVTEANLGDGIFDGARYMAAGGRFGIGSDSNIRIAFSEELRQLDYSQRLRDRVRAPFAT-AGRSSGRVLH 361
                                           *************************************************************7.779******* PP

                             TIGR02022 364 daAlaggaqalGlaegeleaGarADlltldledpslagakgdalldsllfaaekaavrdvvvaGrkvvrdgrH 436
                                           +aAlaggaqa+G+a+g+l+ G  ADll ld   + l g++gd lld+++fa++++   +v+ aGr+vv++grH
  NCBI__GCF_000015985.1:WP_011841109.1 362 EAALAGGAQAAGRASGALAPGLWADLLALDRGAVDLEGRSGDGLLDAWIFAGSDRMASEVWSAGRHVVSGGRH 434
                                           ************************************************************************* PP

                             TIGR02022 437 aleeeierafakvlrall 454
                                            ++  ie  + +v+ +l+
  NCBI__GCF_000015985.1:WP_011841109.1 435 VARSPIEAGYRRVMARLR 452
                                           ************998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (455 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 20.50
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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