Alignments for a candidate for aguB in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for aguB in Azospirillum brasilense Sp245

Align N-carbamoylputrescine amidase; Nitrilase-like protein 1; EC 3.5.1.53 (characterized)
to candidate AZOBR_RS08170 AZOBR_RS08170 carbon-nitrogen family hydrolase

Query= SwissProt::Q8VYF5
         (299 letters)



>FitnessBrowser__azobra:AZOBR_RS08170
          Length = 298

 Score =  405 bits (1041), Expect = e-118
 Identities = 198/290 (68%), Positives = 232/290 (80%), Gaps = 4/290 (1%)

Query: 8   REVVVSSLQFACSDDISTNVAAAERLVREAHAKGANIILIQELFEGYYFCQAQREDFFKR 67
           R V V++ Q AC  D   NV   ERLVR+A A+GA IIL QELFE  YFC+ Q++D F  
Sbjct: 7   RTVTVAATQMACGWDRDANVNGVERLVRDAAARGAQIILPQELFETPYFCKDQKQDLFAL 66

Query: 68  AKPYKNHPTIARMQKLAKELGVVIPVSFFEEANTAHYNSIAIIDADGTDLGIYRKSHIPD 127
           A P ++HP IARM  LA+EL VVIP SFFE A  A+YNS+A+IDADGT LG+YRKSHIPD
Sbjct: 67  AHPVEDHPVIARMSALARELSVVIPTSFFERARNAYYNSLAMIDADGTVLGVYRKSHIPD 126

Query: 128 GPGYQEKFYFNPGDTGFKVFQTKFAKIGVAICWDQWFPEAARAMVLQGAEILFYPTAIGS 187
           GPGYQEK+YFNPGDTGF+V++T++A IG AICWDQWFPE+ARAM L+GAEILFYPTAIGS
Sbjct: 127 GPGYQEKYYFNPGDTGFQVYKTRYAAIGCAICWDQWFPESARAMALKGAEILFYPTAIGS 186

Query: 188 EPQDQGLDSRDHWRRVMQGHAGANVVPLVASNRIGKEIIETEHGPSQITFYGTSFIAGPT 247
           EPQD  LDS+ HW RVMQGHAGAN++PLVASNRIG+E    E     ITFYG+SFIAGPT
Sbjct: 187 EPQDGALDSQAHWTRVMQGHAGANLMPLVASNRIGRE----EGDTCGITFYGSSFIAGPT 242

Query: 248 GEIVAEADDKSEAVLVAQFDLDMIKSKRQSWGVFRDRRPDLYKVLLTMDG 297
           GE+VA+AD  SE VL A FDLD I ++R SWG+FRDRRP+LY  LLT+DG
Sbjct: 243 GELVAQADRDSETVLTASFDLDRIAAQRASWGIFRDRRPELYGPLLTLDG 292


Lambda     K      H
   0.321    0.137    0.410 

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: 340
Number of extensions: 8
Number of successful extensions: 2
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: 299
Length of database: 298
Length adjustment: 27
Effective length of query: 272
Effective length of database: 271
Effective search space:    73712
Effective search space used:    73712
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: 48 (23.1 bits)

Align candidate AZOBR_RS08170 AZOBR_RS08170 (carbon-nitrogen family hydrolase)
to HMM TIGR03381 (aguB: N-carbamoylputrescine amidase (EC 3.5.1.53))

# 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/TIGR03381.hmm
# target sequence database:        /tmp/gapView.10574.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03381  [M=279]
Accession:   TIGR03381
Description: agmatine_aguB: N-carbamoylputrescine amidase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.8e-148  477.4   0.0   7.8e-148  477.2   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS08170  AZOBR_RS08170 carbon-nitrogen fa


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS08170  AZOBR_RS08170 carbon-nitrogen family hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  477.2   0.0  7.8e-148  7.8e-148       1     278 [.       9     286 ..       9     287 .. 0.99

  Alignments for each domain:
  == domain 1  score: 477.2 bits;  conditional E-value: 7.8e-148
                                 TIGR03381   1 vkvaavqlalsedveeniekaeklvreaaakGaqiillpelfeapyfckeqeeeyfelakpveehplik 69 
                                               v+vaa+q+a+ +d ++n++ +e+lvr+aaa+Gaqiil++elfe+pyfck+q+++ f+la+pve+hp+i+
  lcl|FitnessBrowser__azobra:AZOBR_RS08170   9 VTVAATQMACGWDRDANVNGVERLVRDAAARGAQIILPQELFETPYFCKDQKQDLFALAHPVEDHPVIA 77 
                                               79******************************************************************* PP

                                 TIGR03381  70 rlqklakelevvlpvsffekagnalynslavidadGevlgvyrkshiPdgpgyeekfyfkpGdtGfkvw 138
                                               r+++la+el vv+p+sffe+a na+ynsla+idadG+vlgvyrkshiPdgpgy+ek+yf+pGdtGf+v+
  lcl|FitnessBrowser__azobra:AZOBR_RS08170  78 RMSALARELSVVIPTSFFERARNAYYNSLAMIDADGTVLGVYRKSHIPDGPGYQEKYYFNPGDTGFQVY 146
                                               ********************************************************************* PP

                                 TIGR03381 139 dtryakiGvgicWdqWfpeaaralalkGaevllyPtaiGsePadaeldskehWqramqGhaaanvvpvv 207
                                               +trya iG +icWdqWfpe+ara+alkGae+l+yPtaiGseP+d +lds++hW+r+mqGha an++p+v
  lcl|FitnessBrowser__azobra:AZOBR_RS08170 147 KTRYAAIGCAICWDQWFPESARAMALKGAEILFYPTAIGSEPQDGALDSQAHWTRVMQGHAGANLMPLV 215
                                               ********************************************************************* PP

                                 TIGR03381 208 aanrigkeveaeleltfyGssfiadetGelvaeadrseeavlvaefdldeiakeraawGlfrdrrpely 276
                                               a+nrig+e+ +++ +tfyGssfia  tGelva+adr+ e+vl+a+fdld+ia++ra+wG+frdrrpely
  lcl|FitnessBrowser__azobra:AZOBR_RS08170 216 ASNRIGREEGDTCGITFYGSSFIAGPTGELVAQADRDSETVLTASFDLDRIAAQRASWGIFRDRRPELY 284
                                               ********************************************************************* PP

                                 TIGR03381 277 ek 278
                                                 
  lcl|FitnessBrowser__azobra:AZOBR_RS08170 285 GP 286
                                               86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (279 nodes)
Target sequences:                          1  (298 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 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 7.78
//
[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, or view the source code.

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