GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adiA in Marinobacter adhaerens HP15

Align arginine decarboxylase (EC 4.1.1.19) (characterized)
to candidate GFF273 HP15_272 biosynthetic arginine decarboxylase

Query= BRENDA::Q8ZHG8
         (659 letters)



>FitnessBrowser__Marino:GFF273
          Length = 636

 Score =  695 bits (1793), Expect = 0.0
 Identities = 354/638 (55%), Positives = 447/638 (70%), Gaps = 8/638 (1%)

Query: 27  MNDRNASKMLSTYNVAYWGGNYYDVNELGHISVCPDPDIREARVDLAQLVKKMQLEQGQR 86
           M++ +A+     YN+A+W   Y  VN+ G + + PD     AR++L +L + +  E G +
Sbjct: 1   MSEASATPAHKVYNIAHWSDGYIGVNDQGQVLIRPDRGHSPARINLPELTRTLT-ESGVQ 59

Query: 87  LPALFCFPQILQHRLRSINAAFKRARESFGYEGGYFLVYPIKVNQHRRVIESLVNSGEP- 145
           LP L  F  IL  R+  +  AF +  E   Y+GGY  VYPIKVNQ RRV+E L+ + EP 
Sbjct: 60  LPVLVRFVDILHDRVNKLCNAFNKVAEEHAYQGGYTAVYPIKVNQQRRVVEELL-AAEPA 118

Query: 146 -----LGLEAGSKAEMMAVLAHAGMTRSVIVCNGYKDREYIRLALIGEKLGHKVYLVIEK 200
                +GLEAGSK E+MAVLA +    SVIVCNGYKDREYIRLALIG+ LGH+V++V+EK
Sbjct: 119 ASNGQIGLEAGSKPELMAVLAMSQQPGSVIVCNGYKDREYIRLALIGQTLGHRVFIVVEK 178

Query: 201 MSEIKMVLEEAERLNVVPRLGVRARLASQGSGKWQASGGEKSKFGLSATQVLQLVDMLRE 260
            SE+ ++LEEA+ L V P +GVRARLA+ G G WQ +GGEKSKFGLSA+QVL +VD LRE
Sbjct: 179 KSELPLILEEAKSLGVSPLIGVRARLATIGKGNWQNTGGEKSKFGLSASQVLDVVDTLRE 238

Query: 261 ANSLESLQLLHFHLGSQLSNIRDISTGVRESARFYVELHKLGVNIQCFDVGGGLGVDYEG 320
           A +L++LQLLHFHLGSQ++NIRDI TG+RE ARFY EL ++G  I   D+GGGLGVDYEG
Sbjct: 239 AGALDTLQLLHFHLGSQIANIRDIQTGLRECARFYSELRQMGAPIGTVDIGGGLGVDYEG 298

Query: 321 TRSQSDCSVNYGLNEYANNVIWGIGDACNEHGLPHPTVITESGRAVTAHHTVLVSNVIGV 380
           TRS+S CS+NY + EYA NV+  +   C+ HG PHP +I+ESGRA+TAHH+VLV+NVI  
Sbjct: 299 TRSRSSCSMNYSVYEYAYNVVHVLQAECDRHGTPHPDLISESGRALTAHHSVLVTNVIDH 358

Query: 381 ERNEFCEPQPPEAGAPRALESLWDTWQEMQEPENRRSLREWLHDSQMDLHDVHTQYAHGM 440
           E  E   PQ P A A   L  LW   + +Q+    RSL E  HD    + DVH Q+AHG+
Sbjct: 359 EAPENRTPQQPGATASAPLHDLWRDLESLQDTNTPRSLAEIYHDVLHAMADVHAQFAHGV 418

Query: 441 LDLTHRAWAEQLYLSICNEIQKQLDPSNRAHRPIIDELQERMADKLYVNFSLFQSMPDAW 500
           L L  RA AE LY   C  ++ QLD SNRAHR IIDEL E++A+KL+VNFSLFQS+PD W
Sbjct: 419 LSLQERADAETLYTRCCRLLRDQLDSSNRAHREIIDELNEKLAEKLFVNFSLFQSLPDVW 478

Query: 501 GIDQLFPVLPLEGLDKPPERRAVLLDITCDSDGTIDHYIDGDGVATTMPMPPYDPENPPL 560
           GIDQ+FPV+P+ GLD+P  RRAV+ DITCDSDG ID Y+DG G  TT+P+P      P L
Sbjct: 479 GIDQIFPVMPINGLDRPLNRRAVIQDITCDSDGRIDRYVDGQGTETTLPLPEERSGEPLL 538

Query: 561 LGFFMVGAYQEILGNMHNLFGDTAAVDVYVFPDGTVEVEQTDEGDTVADMLEYVQLNPEK 620
           +GFFM GAYQEILG+MHNLFGDT +VDV + P+G  E+     GDTVA +L YV   PE 
Sbjct: 539 MGFFMTGAYQEILGDMHNLFGDTHSVDVRLTPEGGYEISAPITGDTVAKVLRYVNFEPEA 598

Query: 621 LLEHFRGQVKETDLDTELQAQFLEEFEAGLYGYTYLED 658
           L+E +RG+   + L  E QA  + E  AGL GYTYLE+
Sbjct: 599 LMEAYRGKFAASALAAETQAALMAELAAGLDGYTYLEE 636


Lambda     K      H
   0.318    0.136    0.406 

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: 1125
Number of extensions: 38
Number of successful extensions: 3
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: 659
Length of database: 636
Length adjustment: 38
Effective length of query: 621
Effective length of database: 598
Effective search space:   371358
Effective search space used:   371358
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)

Align candidate GFF273 HP15_272 (biosynthetic arginine decarboxylase)
to HMM TIGR01273 (speA: arginine decarboxylase (EC 4.1.1.19))

# 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/TIGR01273.hmm
# target sequence database:        /tmp/gapView.8268.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01273  [M=624]
Accession:   TIGR01273
Description: speA: arginine decarboxylase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   4.4e-255  833.8   0.0   5.1e-255  833.6   0.0    1.0  1  lcl|FitnessBrowser__Marino:GFF273  HP15_272 biosynthetic arginine d


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF273  HP15_272 biosynthetic arginine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  833.6   0.0  5.1e-255  5.1e-255       5     624 .]       8     635 ..       4     635 .. 0.97

  Alignments for each domain:
  == domain 1  score: 833.6 bits;  conditional E-value: 5.1e-255
                          TIGR01273   5 esakvYnikgWgagyfavnkeGevsvrpkgeetlkeidllelvkqveakglklPllvrFpdilqkrikslnaaFke 80 
                                         ++kvYni++W++gy  vn++G+v +rp+  ++ ++i+l+el  ++++ g++lP+lvrF dil++r+++l++aF++
  lcl|FitnessBrowser__Marino:GFF273   8 PAHKVYNIAHWSDGYIGVNDQGQVLIRPDRGHSPARINLPELTRTLTESGVQLPVLVRFVDILHDRVNKLCNAFNK 83 
                                        5789*************************99999****************************************** PP

                          TIGR01273  81 aieeleYaskyqavyPiKvnqqrevveelvasg....gkslGLEaGsKpEllialalaekpkavivcnGyKDreyi 152
                                          ee  Y++ y+avyPiKvnqqr+vveel+a +    + ++GLEaGsKpEl+++la++++p++vivcnGyKDreyi
  lcl|FitnessBrowser__Marino:GFF273  84 VAEEHAYQGGYTAVYPIKVNQQRRVVEELLAAEpaasNGQIGLEAGSKPELMAVLAMSQQPGSVIVCNGYKDREYI 159
                                        ******************************9988777889************************************ PP

                          TIGR01273 153 elaliarklglkvviviekleEldlvieeakklgvkPklGlRvrLaskgsgkwassgGeksKFGLsasqvlevvkk 228
                                        +lali++ lg+ v+iv+ek++El l++eeak+lgv+P +G+R+rLa+ g g+w+++gGeksKFGLsasqvl+vv++
  lcl|FitnessBrowser__Marino:GFF273 160 RLALIGQTLGHRVFIVVEKKSELPLILEEAKSLGVSPLIGVRARLATIGKGNWQNTGGEKSKFGLSASQVLDVVDT 235
                                        **************************************************************************** PP

                          TIGR01273 229 lkeedlldslkllHfHlGsqianiddvkkgvrEaarlyvelrklGvkievvdvGGGLgvdYdGtksksdlsvnYsl 304
                                        l+e++ ld+l+llHfHlGsqiani+d+++g+rE ar+y elr++G++i +vd+GGGLgvdY+Gt+s+s++s+nYs+
  lcl|FitnessBrowser__Marino:GFF273 236 LREAGALDTLQLLHFHLGSQIANIRDIQTGLRECARFYSELRQMGAPIGTVDIGGGLGVDYEGTRSRSSCSMNYSV 311
                                        **************************************************************************** PP

                          TIGR01273 305 eeyaaavvaalkevceekgvpePviisEsGRaitahhavlvaevleveeeeeeeaeeileeeapeevk...eleel 377
                                         eya +vv +l+  c+++g+p+P++isEsGRa+tahh+vlv++v++ e+ e+++ +++ + +++++ +   +le l
  lcl|FitnessBrowser__Marino:GFF273 312 YEYAYNVVHVLQAECDRHGTPHPDLISESGRALTAHHSVLVTNVIDHEAPENRTPQQPGATASAPLHDlwrDLESL 387
                                        *************************************************999998888875555544455588888 PP

                          TIGR01273 378 lkeideesaeelledavqlleeavelfklGkldleeralaeqlalailkkvke.leakekshreildelqeklaek 452
                                        + + + +s+ e+++d+ + +++++++f++G+l+l+era ae+l+++ ++ +++ l++ +++hrei+del+eklaek
  lcl|FitnessBrowser__Marino:GFF273 388 QDTNTPRSLAEIYHDVLHAMADVHAQFAHGVLSLQERADAETLYTRCCRLLRDqLDSSNRAHREIIDELNEKLAEK 463
                                        88999999********************************************99********************** PP

                          TIGR01273 453 ylvnlslFqslPDaWgidqlfPilPlerLdekpdrravllDltCDsDGkikkfveeqgiektlplheldkdeeyll 528
                                         +vn+slFqslPD+Wgidq+fP++P+++Ld   +rrav++D+tCDsDG+i+++v++qg+e+tlpl+e ++ e+ l+
  lcl|FitnessBrowser__Marino:GFF273 464 LFVNFSLFQSLPDVWGIDQIFPVMPINGLDRPLNRRAVIQDITCDSDGRIDRYVDGQGTETTLPLPEERSGEPLLM 539
                                        **************************************************************************** PP

                          TIGR01273 529 gfflvGAYqEiLgdvHnLFgdteavevvvkekgeveveaieegdtvedvlkavqydpeellkalkqkvaeaklkae 604
                                        gff++GAYqEiLgd+HnLFgdt++v+v ++ +g++e++a  +gdtv++vl++v+++pe l++a++ k a+++l+ae
  lcl|FitnessBrowser__Marino:GFF273 540 GFFMTGAYQEILGDMHNLFGDTHSVDVRLTPEGGYEISAPITGDTVAKVLRYVNFEPEALMEAYRGKFAASALAAE 615
                                        *******************************************************************9999***** PP

                          TIGR01273 605 ekkqvlelleaglsgypYLs 624
                                        ++++++++l+agl gy+YL+
  lcl|FitnessBrowser__Marino:GFF273 616 TQAALMAELAAGLDGYTYLE 635
                                        ******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (624 nodes)
Target sequences:                          1  (636 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: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.04
# Mc/sec: 8.13
//
[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