Alignments for a candidate for aguA in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for aguA in Pseudomonas fluorescens GW456-L13

Align agmatine deiminase (EC 3.5.3.12) (characterized)
to candidate PfGW456L13_3370 Agmatine deiminase (EC 3.5.3.12)

Query= BRENDA::Q9I6J9
         (368 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3370
          Length = 374

 Score =  382 bits (980), Expect = e-110
 Identities = 183/361 (50%), Positives = 244/361 (67%), Gaps = 4/361 (1%)

Query: 6   STPRADGFRMPAEWEPHEQTWMVWPERPDNWRNGGKPAQAAFAAVAKAIARFEPVTVCAS 65
           +TP+ DGFR+P E+E     W+ WPER D WRNG KPAQ  +  +  AI+  EPVTVCAS
Sbjct: 7   TTPKQDGFRLPGEFEAKSGCWLGWPERTDVWRNGAKPAQKVWVQIVTAISMSEPVTVCAS 66

Query: 66  AGQYENARARLDDGNIRVVEISSDDAWVRDTGPTFVIDD-KGDVRGVDWGFNAWGGFEGG 124
           A Q+  AR +L    +RVVE++ +D W RD+GP FV++D +G+VRGVD+ FNA+GG +GG
Sbjct: 67  AAQFATARRQLPP-QVRVVEMTCNDTWFRDSGPCFVVNDQRGEVRGVDFEFNAYGGLDGG 125

Query: 125 LYFPWQRDDQVARKILEIERRARYRTDDFVLEGGSIHVDGEGTLITTEECLLNHNRNPHL 184
           LY+PW +DDQ+A KILEIER  RYR    + E G I  DG+G+++TTE+CLLN NRN HL
Sbjct: 126 LYYPWDKDDQIAGKILEIERFDRYRAP-LIAELGGIQSDGQGSILTTEQCLLNRNRNQHL 184

Query: 185 SQAEIERTLRDYLAVESIIWLPNGLYNDETDGHVDNFCCYARPGEVLLAWTDDQDDPNYL 244
            + E+ R L DYL  E +IWLP G   DETDGHVD+  C+ RPGEV+L WTD++DDP + 
Sbjct: 185 GKDEVTRRLTDYLGAEQVIWLPRGCKFDETDGHVDDLACFVRPGEVVLQWTDNRDDPQWE 244

Query: 245 RCQAALRVLEESRDAKGRKLVVHKMPIPGPLYATQEECDGVDIVEGSQPRDPSIRLAGSY 304
             Q A  +L  +RD++GR+L+VHK+P P  L  T EE +G+D  + +  R    ++  SY
Sbjct: 245 IYQEAYDILRSTRDSRGRELIVHKLPQPDVLEWTAEEAEGLDRQDSTHTRQAGTKICASY 304

Query: 305 VNFLIVNGGIIAPSFDDPKDAEARAILQRVFPEHEVVMVP-GREILLGGGNIHCITQQQP 363
           +N+   N  I+ P F D  D  A A L  +FP+H +V +   REILLGGGN+ CIT  Q 
Sbjct: 305 INYYAGNSSIVVPLFGDRNDKVALATLAELFPQHSIVGIENSREILLGGGNVACITMPQY 364

Query: 364 A 364
           A
Sbjct: 365 A 365


Lambda     K      H
   0.319    0.138    0.439 

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: 477
Number of extensions: 20
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: 368
Length of database: 374
Length adjustment: 30
Effective length of query: 338
Effective length of database: 344
Effective search space:   116272
Effective search space used:   116272
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate PfGW456L13_3370 (Agmatine deiminase (EC 3.5.3.12))
to HMM TIGR03380 (aguA: agmatine deiminase (EC 3.5.3.12))

# 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/TIGR03380.hmm
# target sequence database:        /tmp/gapView.20304.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03380  [M=357]
Accession:   TIGR03380
Description: agmatine_aguA: agmatine 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-167  542.6   0.0   2.2e-167  542.4   0.0    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3370  Agmatine deiminase (EC 3.5.3.12)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3370  Agmatine deiminase (EC 3.5.3.12)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  542.4   0.0  2.2e-167  2.2e-167       1     356 [.       7     364 ..       7     365 .. 0.99

  Alignments for each domain:
  == domain 1  score: 542.4 bits;  conditional E-value: 2.2e-167
                                               TIGR03380   1 ttpkedgfrlPaefekqkevwliWPerpDnWregakpaqkafaevakaiakvepv 55 
                                                             ttpk+dgfrlP+efe+++ +wl WPer+D Wr+gakpaqk+++++++ai+ +epv
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3370   7 TTPKQDGFRLPGEFEAKSGCWLGWPERTDVWRNGAKPAQKVWVQIVTAISMSEPV 61 
                                                             69***************************************************** PP

                                               TIGR03380  56 tvlvskeqyenarkalpeeirvvemssnDawirDvGPtfvvndk.gelrgvdwef 109
                                                             tv++s++q++ ar++lp ++rvvem++nD+w+rD+GP fvvnd+ ge+rgvd+ef
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3370  62 TVCASAAQFATARRQLPPQVRVVEMTCNDTWFRDSGPCFVVNDQrGEVRGVDFEF 116
                                                             ******************************************9769********* PP

                                               TIGR03380 110 nawgglkdGlyfpWdkDdkvarkvleleridryradlvleggsihvDGeGtlltt 164
                                                             na+ggl++Gly pWdkDd++a k+le+er dryra+l+ e g+i++DG+G +ltt
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3370 117 NAYGGLDGGLYYPWDKDDQIAGKILEIERFDRYRAPLIAELGGIQSDGQGSILTT 171
                                                             ******************************************************* PP

                                               TIGR03380 165 eeclLsegrnpelskeeieeklkeylgvekviWlkeGlyldetnGhvDnllnfvr 219
                                                             e+clL+++rn++l k+e++++l +ylg+e+viWl++G++ det+GhvD+l++fvr
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3370 172 EQCLLNRNRNQHLGKDEVTRRLTDYLGAEQVIWLPRGCKFDETDGHVDDLACFVR 226
                                                             ******************************************************* PP

                                               TIGR03380 220 PGevvlswtddesdPqyeiskealevLenetDakGrklkvhklklpeplllteee 274
                                                             PGevvl+wtd+++dPq+ei +ea+++L++++D++Gr+l vhkl++p+ l++t+ee
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3370 227 PGEVVLQWTDNRDDPQWEIYQEAYDILRSTRDSRGRELIVHKLPQPDVLEWTAEE 281
                                                             ******************************************************* PP

                                               TIGR03380 275 akgvdavegtlpreagerlaasyvnyliankaiilPlfddekDkeakkllqelfP 329
                                                             a+g+d+ ++t++r+ag++++asy+ny++ n++i++Plf+d++Dk+a ++l+elfP
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3370 282 AEGLDRQDSTHTRQAGTKICASYINYYAGNSSIVVPLFGDRNDKVALATLAELFP 336
                                                             ******************************************************* PP

                                               TIGR03380 330 drkvvgv.kareillgGGnihcitqqip 356
                                                             ++++vg+ ++reillgGGn++cit+ ++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3370 337 QHSIVGIeNSREILLGGGNVACITMPQY 364
                                                             *******899**************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (357 nodes)
Target sequences:                          1  (374 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: 00:00:00.01
# Mc/sec: 7.58
//
[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