Alignments for a candidate for aguA in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Alignments for a candidate for aguA in Shewanella amazonensis SB2B

Align agmatine deiminase (EC 3.5.3.12) (characterized)
to candidate 6938402 Sama_2521 agmatine deiminase (RefSeq)

Query= BRENDA::Q9I6J9
         (368 letters)



>FitnessBrowser__SB2B:6938402
          Length = 375

 Score =  432 bits (1110), Expect = e-126
 Identities = 211/359 (58%), Positives = 257/359 (71%), Gaps = 3/359 (0%)

Query: 6   STPRADGFRMPAEWEPHEQTWMVWPERPDNWRNGGKPAQAAFAAVAKAIARFEPVTVCAS 65
           STP ADGF MPAEW   +  WM+WP RPDNWR  G+ AQA FA VA AI    PV +   
Sbjct: 18  STPAADGFTMPAEWAHQQAVWMIWPYRPDNWREAGRFAQATFAKVADAIGGATPVFMGVP 77

Query: 66  AGQYENARARLDDGNIRVVEISSDDAWVRDTGPTFVIDDKGDVRGVDWGFNAWGGFEGGL 125
           A   + ARA +   ++ +VE++SDD W RDTGPT V +  G+ RG+DWGFNAWGG +GGL
Sbjct: 78  AEFMDKARAIMP-AHVTLVEMNSDDCWARDTGPTVVTNGAGECRGIDWGFNAWGGHKGGL 136

Query: 126 YFPWQRDDQVARKILEIERRARYRTDDFVLEGGSIHVDGEGTLITTEECLLNHNRNPHLS 185
           YFPW +D++VA ++L      RY     +LEGGSIHVDGEGT +TT ECLLN NRNPHL+
Sbjct: 137 YFPWDQDEKVAAQMLAQHGMDRYAAP-LILEGGSIHVDGEGTCMTTAECLLNENRNPHLT 195

Query: 186 QAEIERTLRDYLAVESIIWLPNGLYNDETDGHVDNFCCYARPGEVLLAWTDDQDDPNYLR 245
           + +IE  LRDYL V S IWL +G+Y DETDGH+DN CC+ RPGEV L WTDD +DP Y R
Sbjct: 196 KEQIEAHLRDYLGVTSFIWLGDGVYMDETDGHIDNICCFVRPGEVALHWTDDVNDPQYER 255

Query: 246 CQAALRVLEESRDAKGRKLVVHKMPIPGPLYATQEECDGVDIVEGSQPRDPSIRLAGSYV 305
             AAL++LE + DAKGRKL V K+P PGPLY T+EE  GV+   G  PR+   RLAGSYV
Sbjct: 256 SVAALKLLEAAVDAKGRKLKVWKLPQPGPLYCTEEESAGVESGTG-VPREAEGRLAGSYV 314

Query: 306 NFLIVNGGIIAPSFDDPKDAEARAILQRVFPEHEVVMVPGREILLGGGNIHCITQQQPA 364
           NFLI N  I+ P  D+  D EA+ IL+ +FPE++V+ VP REILLGGGNIHCITQQ P+
Sbjct: 315 NFLITNDRIVYPLLDEATDGEAQRILEDIFPEYQVIGVPAREILLGGGNIHCITQQIPS 373


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: 554
Number of extensions: 17
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: 375
Length adjustment: 30
Effective length of query: 338
Effective length of database: 345
Effective search space:   116610
Effective search space used:   116610
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 6938402 Sama_2521 (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.27048.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.2e-175  568.8   0.0   2.5e-175  568.6   0.0    1.0  1  lcl|FitnessBrowser__SB2B:6938402  Sama_2521 agmatine deiminase (Re


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6938402  Sama_2521 agmatine deiminase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  568.6   0.0  2.5e-175  2.5e-175       1     356 [.      18     372 ..      18     373 .. 1.00

  Alignments for each domain:
  == domain 1  score: 568.6 bits;  conditional E-value: 2.5e-175
                         TIGR03380   1 ttpkedgfrlPaefekqkevwliWPerpDnWregakpaqkafaevakaiakvepvtvlvskeqyenarkalpeeirv 77 
                                       +tp++dgf +Pae+++q++vw+iWP+rpDnWre+++ aq++fa+va+ai  ++pv++ v++e++++ar+ +p+++++
  lcl|FitnessBrowser__SB2B:6938402  18 STPAADGFTMPAEWAHQQAVWMIWPYRPDNWREAGRFAQATFAKVADAIGGATPVFMGVPAEFMDKARAIMPAHVTL 94 
                                       58*************************************************************************** PP

                         TIGR03380  78 vemssnDawirDvGPtfvvndkgelrgvdwefnawgglkdGlyfpWdkDdkvarkvleleridryradlvleggsih 154
                                       vem+s+D+w rD+GPt+v+n +ge+rg+dw fnawgg+k+GlyfpWd+D+kva ++l+ +++dry a+l+leggsih
  lcl|FitnessBrowser__SB2B:6938402  95 VEMNSDDCWARDTGPTVVTNGAGECRGIDWGFNAWGGHKGGLYFPWDQDEKVAAQMLAQHGMDRYAAPLILEGGSIH 171
                                       ***************************************************************************** PP

                         TIGR03380 155 vDGeGtlltteeclLsegrnpelskeeieeklkeylgvekviWlkeGlyldetnGhvDnllnfvrPGevvlswtdde 231
                                       vDGeGt++tt+eclL+e+rnp+l+ke+ie++l++ylgv+++iWl +G+y+det+Gh+Dn+++fvrPGev+l+wtdd 
  lcl|FitnessBrowser__SB2B:6938402 172 VDGEGTCMTTAECLLNENRNPHLTKEQIEAHLRDYLGVTSFIWLGDGVYMDETDGHIDNICCFVRPGEVALHWTDDV 248
                                       ***************************************************************************** PP

                         TIGR03380 232 sdPqyeiskealevLenetDakGrklkvhklklpeplllteeeakgvdavegtlpreagerlaasyvnyliankaii 308
                                       +dPqye+s +al++Le+++DakGrklkv+kl++p+pl++teee++gv++ +g +prea+ rla+syvn+li+n++i+
  lcl|FitnessBrowser__SB2B:6938402 249 NDPQYERSVAALKLLEAAVDAKGRKLKVWKLPQPGPLYCTEEESAGVESGTG-VPREAEGRLAGSYVNFLITNDRIV 324
                                       ***************************************************9.************************ PP

                         TIGR03380 309 lPlfddekDkeakkllqelfPdrkvvgvkareillgGGnihcitqqip 356
                                       +Pl+d+++D ea+++l+++fP+++v+gv+areillgGGnihcitqqip
  lcl|FitnessBrowser__SB2B:6938402 325 YPLLDEATDGEAQRILEDIFPEYQVIGVPAREILLGGGNIHCITQQIP 372
                                       **********************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (357 nodes)
Target sequences:                          1  (375 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: 8.64
//
[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