Alignments for a candidate for hutF in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutF in Azospirillum brasilense Sp245

Align formimidoylglutamate deiminase (EC 3.5.3.13) (characterized)
to candidate AZOBR_RS23505 AZOBR_RS23505 N-formimino-L-glutamate deiminase

Query= BRENDA::Q9HU77
         (453 letters)



>FitnessBrowser__azobra:AZOBR_RS23505
          Length = 462

 Score =  528 bits (1360), Expect = e-154
 Identities = 270/452 (59%), Positives = 321/452 (71%), Gaps = 9/452 (1%)

Query: 1   MSAIFAERALLPEGWARNVRFEISADGVLAEIRPDANADGAERLGGAVLPGMPNLHSHAF 60
           M+ +F ERALLPEGWA NV     A G L  +  DA++DG  R  G V+PGMPNLHSHAF
Sbjct: 1   MNGLFCERALLPEGWASNVALRFDARGTLTAVERDASSDGLPRAAGPVIPGMPNLHSHAF 60

Query: 61  QRAMAGLAEVAGNPNDSFWTWRELMYRMVARLSPEQIEVIACQLYIEMLKAGYTAVAEFH 120
           QRAMAGL E AG   DSFWTWR+ MY  V R++PE  E +A  LY+EM K GYTAVAEFH
Sbjct: 61  QRAMAGLTEYAGASEDSFWTWRDAMYGFVRRMTPEAAEAVAALLYMEMAKQGYTAVAEFH 120

Query: 121 YVHHDLDGRSYADPAELSLRISRAASAAGIGLTLLPVLYSHAGFGGQPASEGQRRFINGS 180
           Y+HH  DGR YAD AE+S RI  AA  AGIGLT LPVLY+H+GFGG+P S+GQ+RFIN  
Sbjct: 121 YLHHSADGRPYADRAEMSRRILAAADTAGIGLTHLPVLYAHSGFGGKPPSDGQKRFINDV 180

Query: 181 EAYLELLQRLRAPL--EAAGHSLGLCFHSLRAVTPQQIATVLAAGHDDL----PVHIHIA 234
           +  L ++  +   +  E AG   GL  HSLRAVTP+++   L  G D L    P+HIHIA
Sbjct: 181 DGLLSIVSAMEKAMGAERAGRRAGLALHSLRAVTPEEMRDAL-TGLDALDPGAPIHIHIA 239

Query: 235 EQQKEVDDCQAWSGRRPLQWLYENVAVDQRWCLVHATHADPAEVAAMARSGAVAGLCLST 294
           EQ  EVDDC AWS +RP++WL EN  V  RWCLVHATH  PAEV  MA SGAVAGLCL+T
Sbjct: 240 EQTAEVDDCVAWSSKRPVEWLLENAPVGPRWCLVHATHVTPAEVDGMAASGAVAGLCLTT 299

Query: 295 EANLGDGIFPATDFLAQGGRLGIGSDSHVSLSVVEELRWLEYGQRLRDRKRNRLYRDDQP 354
           EANLGDG+FPA  FLAQGGR G+GSDSH+S+S  EELR LEYGQRL  R+RN L   D P
Sbjct: 300 EANLGDGLFPAIPFLAQGGRFGVGSDSHISVSAAEELRLLEYGQRLVQRRRNVLRIGDCP 359

Query: 355 MIGRTLYDAALAGGAQALGQPI--GSLAVGRRADLLVLDGNDPYLASAEGDALLNRWLFA 412
            IG  LY AA+AGGAQALGQP+  G + VG+ ADL+VLD ++P L S   D+LL+ ++FA
Sbjct: 360 SIGGGLYRAAVAGGAQALGQPVTGGGVQVGQPADLVVLDADNPKLLSRTDDSLLDAYVFA 419

Query: 413 GGDRQVRDVMVAGRWVVRDGRHAGEERSARAF 444
                VRDV+ AGR VVR+GRH  E+    A+
Sbjct: 420 SDGHAVRDVIAAGRTVVREGRHVREDAIRAAY 451


Lambda     K      H
   0.321    0.136    0.415 

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: 665
Number of extensions: 29
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: 453
Length of database: 462
Length adjustment: 33
Effective length of query: 420
Effective length of database: 429
Effective search space:   180180
Effective search space used:   180180
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 (21.9 bits)
S2: 51 (24.3 bits)

Align candidate AZOBR_RS23505 AZOBR_RS23505 (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.31626.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.9e-198  645.7   1.3   2.2e-198  645.5   1.3    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS23505  AZOBR_RS23505 N-formimino-L-glut


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS23505  AZOBR_RS23505 N-formimino-L-glutamate deiminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  645.5   1.3  2.2e-198  2.2e-198       3     454 ..       3     459 ..       1     460 [. 0.97

  Alignments for each domain:
  == domain 1  score: 645.5 bits;  conditional E-value: 2.2e-198
                                 TIGR02022   3 vyfaerallpdgwaegvrlavaedGrilavetgvsaaedaerlsgvvlpglanlHsHAFqralaGlaev 71 
                                                +f+erallp+gwa++v+l  ++ G ++ave+++s +++  r +g+v+pg++nlHsHAFqra+aGl+e+
  lcl|FitnessBrowser__azobra:AZOBR_RS23505   3 GLFCERALLPEGWASNVALRFDARGTLTAVERDAS-SDGLPRAAGPVIPGMPNLHSHAFQRAMAGLTEY 70 
                                               689*******************************9.9******************************** PP

                                 TIGR02022  72 agsgaDsFWtWRevmYrlverldPeqleaiarqlyvemlkaGftrvgEFHYlHHaadGtpYadpaelae 140
                                               ag ++DsFWtWR++mY +v r++Pe +ea+a+ ly+em+k G+t+v+EFHYlHH+adG pYad+ae+++
  lcl|FitnessBrowser__azobra:AZOBR_RS23505  71 AGASEDSFWTWRDAMYGFVRRMTPEAAEAVAALLYMEMAKQGYTAVAEFHYLHHSADGRPYADRAEMSR 139
                                               ********************************************************************* PP

                                 TIGR02022 141 riaaAAadaGigltlLpvlYahagFGgaaanegqrrfiddveaflrlvealrkel.aaqeearlGlaiH 208
                                               ri+aAA++aGiglt+LpvlYah+gFGg+++++gq+rfi+dv+  l  v+a++k++ a+++  r Gla+H
  lcl|FitnessBrowser__azobra:AZOBR_RS23505 140 RILAAADTAGIGLTHLPVLYAHSGFGGKPPSDGQKRFINDVDGLLSIVSAMEKAMgAERAGRRAGLALH 208
                                               ****************************************************99834567899****** PP

                                 TIGR02022 209 slRAvtaeelaavlq...aserqlPvHiHvaEqqkEvddClaasgrrPvewLldhaevdarwclvHatH 274
                                               slRAvt+ee+++ l+   a +  +P+HiH+aEq++EvddC+a+s +rPvewLl++a+v+ rwclvHatH
  lcl|FitnessBrowser__azobra:AZOBR_RS23505 209 SLRAVTPEEMRDALTgldALDPGAPIHIHIAEQTAEVDDCVAWSSKRPVEWLLENAPVGPRWCLVHATH 277
                                               **********98765444777889********************************************* PP

                                 TIGR02022 275 ltdeevkllaksgavaglCpttEanLgDGifpaadfvaaggrlgiGsDshvvvdvleElRllEygqRLr 343
                                               +t+ ev  +a sgavaglC+ttEanLgDG+fpa  f+a+ggr+g+GsDsh++v+++eElRllEygqRL 
  lcl|FitnessBrowser__azobra:AZOBR_RS23505 278 VTPAEVDGMAASGAVAGLCLTTEANLGDGLFPAIPFLAQGGRFGVGSDSHISVSAAEELRLLEYGQRLV 346
                                               ********************************************************************* PP

                                 TIGR02022 344 draRnvlaageeasvaralydaAlaggaqalGlae..geleaGarADlltldledpslagakgdallds 410
                                               +r+Rnvl  g+ +s++  ly+aA+aggaqalG+    g++++G++ADl++ld+++p+l+ +++d+lld+
  lcl|FitnessBrowser__azobra:AZOBR_RS23505 347 QRRRNVLRIGDCPSIGGGLYRAAVAGGAQALGQPVtgGGVQVGQPADLVVLDADNPKLLSRTDDSLLDA 415
                                               *********************************987899****************************** PP

                                 TIGR02022 411 llfaaekaavrdvvvaGrkvvrdgrHaleeeierafakvlrall 454
                                               ++fa++++avrdv+ aGr+vvr+grH +e++i  a+ ++++ l+
  lcl|FitnessBrowser__azobra:AZOBR_RS23505 416 YVFASDGHAVRDVIAAGRTVVREGRHVREDAIRAAYRRAIEGLR 459
                                               **************************************998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (462 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: 10.20
//
[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