Aligments for a candidate for speB in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Aligments for a candidate for speB in Azospirillum brasilense Sp245

Align agmatinase (EC 3.5.3.11) (characterized)
to candidate AZOBR_RS30775 AZOBR_RS30775 agmatinase

Query= BRENDA::W5PHZ9
         (361 letters)



>FitnessBrowser__azobra:AZOBR_RS30775
          Length = 351

 Score =  244 bits (624), Expect = 2e-69
 Identities = 137/318 (43%), Positives = 197/318 (61%), Gaps = 19/318 (5%)

Query: 44  QASDGPRNQPPSSEFVARSVGICSMMRLPMQ------ATPEGLDAALVGVPLDIGTSNRP 97
           Q S G R QP          G+ +++  P +      A   GLD AL+GVP+D+G +NR 
Sbjct: 34  QFSGGKRVQP--------FAGVSTLLDAPYRPDAADAADFGGLDIALIGVPMDLGVTNRA 85

Query: 98  GARFGPRRIREESVMLRTANPSTGAVPFQFLKVADLGDVNVNLYNLQDSCRL-IRADYQK 156
           GAR GPR +R     +     +   VP    K+AD+GDV ++     ++C   I A Y +
Sbjct: 86  GARLGPRAVRGME-RIGPYEHALRMVPAASCKLADVGDVPLSSRFSLEACHGDILAFYNR 144

Query: 157 IVAAGCVPLTLGGDHTITYPILQAIAEKHGPVGLVHVDAHMDTADKALGEKLYHGTPFRR 216
           ++ AG VPL++GGDH+ITY IL+A+  +  PVG++H DAH DT     G K +HG PFR+
Sbjct: 145 VMDAGVVPLSVGGDHSITYSILKALGRER-PVGMIHFDAHCDTGGPYEGAKFHHGGPFRQ 203

Query: 217 CVDEGLLDCKRVVQIGIRGSSTTLDTYRYSRSQGFRVVLAEDCWLKSLVPLMGEVRQQMG 276
            V +G+LD +R VQIGIRGS+  L  + +S   G  V+ AED   + +  ++   R+ +G
Sbjct: 204 AVLDGVLDPERTVQIGIRGSTEYL--WEFSYDSGMTVIHAEDIPERGIASVIETARKVVG 261

Query: 277 GRPIYISFDIDGLDPAYAPGTGTPEIAGLTPSQALEIIRGCQGLNVVGCDLVEVSPPYDP 336
             P+Y+SFD+D LDP +APGTGTPE+ GLT  +AL I+RG  GL+++G D+VEV+P YD 
Sbjct: 262 DGPVYVSFDVDCLDPVFAPGTGTPEVGGLTTREALAILRGLDGLDIIGGDVVEVAPQYDA 321

Query: 337 SGNTALVAANLLFEMLCV 354
           + NTA   A +LFE+LC+
Sbjct: 322 TTNTAHAGAQMLFEILCL 339


Lambda     K      H
   0.321    0.139    0.426 

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: 444
Number of extensions: 27
Number of successful extensions: 4
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: 361
Length of database: 351
Length adjustment: 29
Effective length of query: 332
Effective length of database: 322
Effective search space:   106904
Effective search space used:   106904
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: 49 (23.5 bits)

Align candidate AZOBR_RS30775 AZOBR_RS30775 (agmatinase)
to HMM TIGR01230 (speB: agmatinase (EC 3.5.3.11))

# 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/TIGR01230.hmm
# target sequence database:        /tmp/gapView.4695.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01230  [M=275]
Accession:   TIGR01230
Description: agmatinase: agmatinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    1.5e-58  184.6   0.0    1.8e-58  184.3   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS30775  AZOBR_RS30775 agmatinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS30775  AZOBR_RS30775 agmatinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.3   0.0   1.8e-58   1.8e-58      14     273 ..      69     337 ..      56     339 .. 0.89

  Alignments for each domain:
  == domain 1  score: 184.3 bits;  conditional E-value: 1.8e-58
                                 TIGR01230  14 evvivgiPydattsyrpGsrhgpeaireastnLeayseeld.rdlallkvvDagdlplaaG.daremve 80 
                                               ++ ++g+P+d  +  r+G+r gp a+r     +  y++ l  +  a  k++D+gd+pl    + ++  +
  lcl|FitnessBrowser__azobra:AZOBR_RS30775  69 DIALIGVPMDLGVTNRAGARLGPRAVRGME-RIGPYEHALRmVPAASCKLADVGDVPLSSRfSLEACHG 136
                                               67799**********************875.6778888887467777**********965325688899 PP

                                 TIGR01230  81 kieevveelleegkfvvaiGGeHsitlpvirAvkkkfeklavvqfDAHtDlrdefegeklshacvmrrv 149
                                                i +  ++++++g  ++++GG+Hsit+++++A  ++ +++ +++fDAH+D+   +eg k+ h  + r++
  lcl|FitnessBrowser__azobra:AZOBR_RS30775 137 DILAFYNRVMDAGVVPLSVGGDHSITYSILKALGRE-RPVGMIHFDAHCDTGGPYEGAKFHHGGPFRQA 204
                                               9*******************************9986.799**********************9988874 PP

                                 TIGR01230 150 lelg....lnvlqigiRsgikeeadlarennikvlk.relede.....iaevlakvldkpvyvtiDiDv 208
                                               +  g     +++qigiR  ++  +++  + ++ v++  ++ ++     i+++ + v d pvyv++D+D+
  lcl|FitnessBrowser__azobra:AZOBR_RS30775 205 VLDGvldpERTVQIGIRGSTEYLWEFSYDSGMTVIHaEDIPERgiasvIETARKVVGDGPVYVSFDVDC 273
                                               3322244459************************99777777676665888888899************ PP

                                 TIGR01230 209 lDPafaPGvgtpepgGltskellklfvlaekekkvvGlDvvEvaPvydssevtaltaaklalell 273
                                               lDP faPG+gtpe+gGlt++e+l+  +++     ++G DvvEvaP yd +  ta + a++  e+l
  lcl|FitnessBrowser__azobra:AZOBR_RS30775 274 LDPVFAPGTGTPEVGGLTTREALA-ILRGLDGLDIIGGDVVEVAPQYDATTNTAHAGAQMLFEIL 337
                                               ************************.889999******************************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (275 nodes)
Target sequences:                          1  (351 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 11.42
//
[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