Alignments for a candidate for adiA in Marinobacter adhaerens HP15

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.22126.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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 10.01
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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