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.555558.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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 27.57
//
[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:

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:

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:

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:

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