Alignments for a candidate for aguA in Shewanella sp. ANA-3

GapMind for catabolism of small carbon sources

Alignments for a candidate for aguA in Shewanella sp. ANA-3

Align agmatine deiminase (EC 3.5.3.12) (characterized)
to candidate 7026323 Shewana3_3465 agmatine deiminase (RefSeq)

Query= BRENDA::Q9I6J9
         (368 letters)



>FitnessBrowser__ANA3:7026323
          Length = 370

 Score =  419 bits (1076), Expect = e-122
 Identities = 207/361 (57%), Positives = 251/361 (69%), Gaps = 5/361 (1%)

Query: 5   TSTPRADGFRMPAEWEPHEQTWMVWPERPDNWRNGGKPAQAAFAAVAKAIARFEPVTVCA 64
           T+ P  DGF MPAEW   +  WM+WP RPDNWR+ G  AQA FA VA AI    PV +  
Sbjct: 12  TTKPSEDGFYMPAEWAAQQAVWMIWPYRPDNWRSAGAYAQATFAKVADAIGGATPVYMGV 71

Query: 65  SAGQYENARARLDDGNIRVVEISSDDAWVRDTGPTFVIDDKGDVRGVDWGFNAWGGFEGG 124
                  A+  +   ++ +VEI S+D W RDTGPT V++ +G+ RGVDWGFNAWGG  GG
Sbjct: 72  PQAFLAEAQTVMPS-HVTLVEIDSNDCWARDTGPTVVVNAEGECRGVDWGFNAWGGHNGG 130

Query: 125 LYFPWQRDDQVARKILEIERRARYRTDDFVLEGGSIHVDGEGTLITTEECLLNHNRNPHL 184
           LYFPW +D+QVA ++L+    ARY     +LEGGSIHVDGEGT +TT ECLLN NRNP L
Sbjct: 131 LYFPWDKDEQVAAQMLKQHGFARYSAP-LILEGGSIHVDGEGTCMTTAECLLNANRNPDL 189

Query: 185 SQAEIERTLRDYLAVESIIWLPNGLYNDETDGHVDNFCCYARPGEVLLAWTDDQDDPNYL 244
           ++ +IE  LRDYL V+  IWL  G+Y DETDGH+DN CC+ARPGEV+L WTDD+ DP Y 
Sbjct: 190 TKEQIEALLRDYLNVKQFIWLEEGVYMDETDGHIDNMCCFARPGEVILHWTDDETDPQYP 249

Query: 245 RCQAALRVLEESRDAKGRKLVVHKMPIPGPLYATQEECDGVDIVEGS-QPRDPSIRLAGS 303
           R +AAL VL+ + DA+GRKL +H +P PGPLY T+EE  GV   EG+  PR    RLAGS
Sbjct: 250 RSKAALDVLQNTVDAQGRKLKIHLLPQPGPLYCTEEESKGV--TEGTGVPRTAGERLAGS 307

Query: 304 YVNFLIVNGGIIAPSFDDPKDAEARAILQRVFPEHEVVMVPGREILLGGGNIHCITQQQP 363
           YVNFLI N  I+ P  D   D  A   LQ +FPEH++V VP REILLGGGNIHCITQQ P
Sbjct: 308 YVNFLITNDRIVFPLLDPATDDIAAQKLQEIFPEHKIVGVPAREILLGGGNIHCITQQIP 367

Query: 364 A 364
           +
Sbjct: 368 S 368


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: 529
Number of extensions: 21
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: 368
Length of database: 370
Length adjustment: 30
Effective length of query: 338
Effective length of database: 340
Effective search space:   114920
Effective search space used:   114920
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 7026323 Shewana3_3465 (agmatine deiminase (RefSeq))
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.19645.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.1e-178  579.6   0.0   1.2e-178  579.4   0.0    1.0  1  lcl|FitnessBrowser__ANA3:7026323  Shewana3_3465 agmatine deiminase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7026323  Shewana3_3465 agmatine deiminase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  579.4   0.0  1.2e-178  1.2e-178       1     356 [.      13     367 ..      13     368 .. 1.00

  Alignments for each domain:
  == domain 1  score: 579.4 bits;  conditional E-value: 1.2e-178
                         TIGR03380   1 ttpkedgfrlPaefekqkevwliWPerpDnWregakpaqkafaevakaiakvepvtvlvskeqyenarkalpeeirv 77 
                                       t+p+edgf++Pae+++q++vw+iWP+rpDnWr+++ +aq++fa+va+ai  ++pv++ v+++++++a++++p+++++
  lcl|FitnessBrowser__ANA3:7026323  13 TKPSEDGFYMPAEWAAQQAVWMIWPYRPDNWRSAGAYAQATFAKVADAIGGATPVYMGVPQAFLAEAQTVMPSHVTL 89 
                                       579************************************************************************** PP

                         TIGR03380  78 vemssnDawirDvGPtfvvndkgelrgvdwefnawgglkdGlyfpWdkDdkvarkvleleridryradlvleggsih 154
                                       ve++snD+w rD+GPt+vvn +ge+rgvdw fnawgg+++GlyfpWdkD++va ++l+ ++ +ry+a+l+leggsih
  lcl|FitnessBrowser__ANA3:7026323  90 VEIDSNDCWARDTGPTVVVNAEGECRGVDWGFNAWGGHNGGLYFPWDKDEQVAAQMLKQHGFARYSAPLILEGGSIH 166
                                       ***************************************************************************** PP

                         TIGR03380 155 vDGeGtlltteeclLsegrnpelskeeieeklkeylgvekviWlkeGlyldetnGhvDnllnfvrPGevvlswtdde 231
                                       vDGeGt++tt+eclL+ +rnp+l+ke+ie+ l++yl+v+++iWl+eG+y+det+Gh+Dn+++f+rPGev+l+wtdde
  lcl|FitnessBrowser__ANA3:7026323 167 VDGEGTCMTTAECLLNANRNPDLTKEQIEALLRDYLNVKQFIWLEEGVYMDETDGHIDNMCCFARPGEVILHWTDDE 243
                                       ***************************************************************************** PP

                         TIGR03380 232 sdPqyeiskealevLenetDakGrklkvhklklpeplllteeeakgvdavegtlpreagerlaasyvnyliankaii 308
                                       +dPqy +sk+al+vL+n++Da+Grklk+h l++p+pl++teee+kgv++ +g +pr+agerla+syvn+li+n++i+
  lcl|FitnessBrowser__ANA3:7026323 244 TDPQYPRSKAALDVLQNTVDAQGRKLKIHLLPQPGPLYCTEEESKGVTEGTG-VPRTAGERLAGSYVNFLITNDRIV 319
                                       ****************************************************.************************ PP

                         TIGR03380 309 lPlfddekDkeakkllqelfPdrkvvgvkareillgGGnihcitqqip 356
                                       +Pl+d ++D++a+++lqe+fP++k+vgv+areillgGGnihcitqqip
  lcl|FitnessBrowser__ANA3:7026323 320 FPLLDPATDDIAAQKLQEIFPEHKIVGVPAREILLGGGNIHCITQQIP 367
                                       **********************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (357 nodes)
Target sequences:                          1  (370 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: 00:00:00.01
# Mc/sec: 9.02
//
[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