Alignments for a candidate for hutI in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutI in Azospirillum brasilense Sp245

Align Imidazolonepropionase (EC 3.5.2.7) (characterized)
to candidate AZOBR_RS21725 AZOBR_RS21725 imidazolonepropionase

Query= reanno::Cup4G11:RR42_RS16905
         (420 letters)



>FitnessBrowser__azobra:AZOBR_RS21725
          Length = 404

 Score =  514 bits (1323), Expect = e-150
 Identities = 262/397 (65%), Positives = 298/397 (75%), Gaps = 2/397 (0%)

Query: 12  DGVWHRCHLLPDGDPAKAIRDAALVVQQGRIVWLGMQAELPQAYAALPRHDAGSAWITPG 71
           D +W   H      P   +RDA + V+ GRI W+G   + P   AA   HD G  W+TPG
Sbjct: 4   DSLWFNGHAATMA-PGGVVRDAVIAVKDGRIAWIGAAKDRPAGRAA-EEHDLGGRWVTPG 61

Query: 72  LVDCHTHLVYGGQRADEFAMRLAGAGYEEIARAGGGIVSTVRATRAADEDTLFALAAARL 131
           L+DCHTHLV+GG RA EF MRL GA YEEIARAGGGI STV ATRAADED L A AA RL
Sbjct: 62  LIDCHTHLVFGGNRAREFEMRLEGATYEEIARAGGGIASTVAATRAADEDGLIASAAVRL 121

Query: 132 APLLAEGVTTLEIKSGYGLDLASERKQLRVARRLGDAFGVTVHTTFLGAHALPPEYAGRA 191
             LLAEGVT +E+KSGYGLDLA+ER+ LR AR LG+ F VTV  T L AHALPPE+AGRA
Sbjct: 122 QRLLAEGVTMVEVKSGYGLDLATERRMLRAARALGERFPVTVRMTGLAAHALPPEFAGRA 181

Query: 192 DDYITLVCETMMPVLADEGLIDAVDAFCESVGFSLAQTERVFQAAERHGLRVKLHAEQLS 251
           DDYI LVCE ++P LA EGL+DAVDAFCE + FS  QT RVF  A+R GL VKLHA+QLS
Sbjct: 182 DDYIALVCEDILPALAAEGLLDAVDAFCERIAFSPEQTARVFDTAQRLGLPVKLHADQLS 241

Query: 252 NLGGTALAARYRALSADHLEHLDEAGVVAMAGSGTVAVLLPGAYYFLRDTNLPPIDLLRR 311
           + GG ALAARY+ALSADH+EH  E G  AMA +GTVAVLLPGA+Y LR+T LPPI+L RR
Sbjct: 242 DGGGAALAARYKALSADHVEHTGEEGARAMADAGTVAVLLPGAFYTLRETKLPPIELFRR 301

Query: 312 HGVPMAISTDHNPGTSPVTSLLLMMNMACTLFRLTVPEVLAGVTTHAARALGAADRHGLL 371
           HGVPMA+STD NPGTSP  SLLLM+NMACTLFRLT  E LAGVT +AA+ALG A  HG L
Sbjct: 302 HGVPMAVSTDCNPGTSPAVSLLLMLNMACTLFRLTPQEALAGVTRNAAQALGMAATHGTL 361

Query: 372 AAGRAADFVLWNVDSPAELAYWFGRNPAAAVVRQGKV 408
             G+AAD  +WNV  PAEL YW G NP AAVVR G++
Sbjct: 362 EPGKAADLAVWNVGDPAELCYWLGANPCAAVVRGGRL 398


Lambda     K      H
   0.321    0.134    0.402 

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: 596
Number of extensions: 22
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: 420
Length of database: 404
Length adjustment: 31
Effective length of query: 389
Effective length of database: 373
Effective search space:   145097
Effective search space used:   145097
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: 50 (23.9 bits)

Align candidate AZOBR_RS21725 AZOBR_RS21725 (imidazolonepropionase)
to HMM TIGR01224 (hutI: imidazolonepropionase (EC 3.5.2.7))

# 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/TIGR01224.hmm
# target sequence database:        /tmp/gapView.21347.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01224  [M=377]
Accession:   TIGR01224
Description: hutI: imidazolonepropionase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.4e-151  488.0   0.0   9.6e-151  487.8   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS21725  AZOBR_RS21725 imidazolonepropion


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS21725  AZOBR_RS21725 imidazolonepropionase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  487.8   0.0  9.6e-151  9.6e-151       2     376 ..      22     397 ..      21     398 .. 0.99

  Alignments for each domain:
  == domain 1  score: 487.8 bits;  conditional E-value: 9.6e-151
                                 TIGR01224   2 edaailveegkiaaigqkaalpgeeaakiidleGklvvPGlvDpHtHlvfagdRvkefelklqGasYle 70 
                                                da+i+v++g+ia+ig  ++ p+  aa+++dl+G+ v+PGl+D+HtHlvf+g+R++efe++l+Ga+Y+e
  lcl|FitnessBrowser__azobra:AZOBR_RS21725  22 RDAVIAVKDGRIAWIGAAKDRPAGRAAEEHDLGGRWVTPGLIDCHTHLVFGGNRAREFEMRLEGATYEE 90 
                                               5899***************************************************************** PP

                                 TIGR01224  71 ilaeGgGilstvratraAseeellkeaeerlkkllrsGtttlEvKsGYGLdleaElkmLrvikalkeel 139
                                               i+++GgGi stv atraA+e+ l+++a  rl++ll++G+t +EvKsGYGLdl +E +mLr+++al e++
  lcl|FitnessBrowser__azobra:AZOBR_RS21725  91 IARAGGGIASTVAATRAADEDGLIASAAVRLQRLLAEGVTMVEVKSGYGLDLATERRMLRAARALGERF 159
                                               ********************************************************************* PP

                                 TIGR01224 140 pvdvvttflgaHavPkevqededeyvdaileelipkvaeeklaeavDvFcekgvFsveqsrrilkaaqe 208
                                               pv v  t l+aHa+P+e+ ++ d+y++ ++e+++p+ a e l +avD+Fce+ +Fs+eq+ r+++ aq 
  lcl|FitnessBrowser__azobra:AZOBR_RS21725 160 PVTVRMTGLAAHALPPEFAGRADDYIALVCEDILPALAAEGLLDAVDAFCERIAFSPEQTARVFDTAQR 228
                                               ********************************************************************* PP

                                 TIGR01224 209 aGlavklHaeelkalggaelaaklgavsadHleeasdedikalaeagtvavlLPgtaflLr.eaappar 276
                                                Gl+vklHa++l+  gga+laa+ +a+sadH+e++ +e+++a+a+agtvavlLPg++++Lr ++ pp++
  lcl|FitnessBrowser__azobra:AZOBR_RS21725 229 LGLPVKLHADQLSDGGGAALAARYKALSADHVEHTGEEGARAMADAGTVAVLLPGAFYTLReTKLPPIE 297
                                               *************************************************************8889**** PP

                                 TIGR01224 277 klidekvivalatDlnPgsspllslqlilslavtllkltaeealaaatvnaAqalglgeekGtleeGkd 345
                                                ++ ++v++a++tD nPg+sp  sl l+l++a+tl++lt++eala++t naAqalg+++++Gtle Gk 
  lcl|FitnessBrowser__azobra:AZOBR_RS21725 298 LFRRHGVPMAVSTDCNPGTSPAVSLLLMLNMACTLFRLTPQEALAGVTRNAAQALGMAATHGTLEPGKA 366
                                               ********************************************************************* PP

                                 TIGR01224 346 adlvvlsaesyeeiaYrlgvnvveaviknGe 376
                                               adl+v+++ +++e+ Y+lg+n  +av+  G 
  lcl|FitnessBrowser__azobra:AZOBR_RS21725 367 ADLAVWNVGDPAELCYWLGANPCAAVVRGGR 397
                                               ***********************99998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (377 nodes)
Target sequences:                          1  (404 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 7.64
//
[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