Alignments for a candidate for adiA in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for adiA in Pseudomonas putida KT2440

Align Biosynthetic arginine decarboxylase (EC 4.1.1.19) (characterized)
to candidate PP_0567 PP_0567 Biosynthetic arginine decarboxylase

Query= reanno::pseudo1_N1B4:Pf1N1B4_1296
         (637 letters)



>FitnessBrowser__Putida:PP_0567
          Length = 637

 Score = 1211 bits (3134), Expect = 0.0
 Identities = 600/637 (94%), Positives = 620/637 (97%)

Query: 1   MSVRRTRKDDGSQWTVADSRSVYGIRHWGAGYFAINDAGRVEVRPNGPTSSPIDLFEQVD 60
           MSVRRTRKDDGSQWTVADSRSVYGIRHWGAGYFAIN+AGRVEVRPNGP S+PIDLFEQVD
Sbjct: 1   MSVRRTRKDDGSQWTVADSRSVYGIRHWGAGYFAINEAGRVEVRPNGPQSAPIDLFEQVD 60

Query: 61  QLRKSGLSLPLLVRFPDILQDRVRQLTGAFDANIERLEYQSKYTALYPIKVNQQEAVIEN 120
           +LR+SGLSLPLLVRFPDILQDRVRQLTGAFDANI RLEYQS+YTALYPIKVNQQEAV+EN
Sbjct: 61  ELRQSGLSLPLLVRFPDILQDRVRQLTGAFDANIARLEYQSQYTALYPIKVNQQEAVVEN 120

Query: 121 IIATQNVSIGLEAGSKPELLAVLALAPKGGTIVCNGYKDREFIRLALMGQKLGHNVFIVI 180
           IIATQNVSIGLEAGSKPELLAVLALAPKGGTIVCNGYKDREFIRLALMGQKLGHNVFIVI
Sbjct: 121 IIATQNVSIGLEAGSKPELLAVLALAPKGGTIVCNGYKDREFIRLALMGQKLGHNVFIVI 180

Query: 181 EKESEVGLVIEEAASLKVKPQVGLRVRLSSLASSKWADTGGEKSKFGLSAAQLLSVVERF 240
           EKESEV LVIEEAA LKVKPQVGLRVRLSSLASSKWADTGGEKSKFGLSAAQLLSVV+RF
Sbjct: 181 EKESEVALVIEEAAELKVKPQVGLRVRLSSLASSKWADTGGEKSKFGLSAAQLLSVVQRF 240

Query: 241 RAAGLDQGIRLLHFHMGSQIANLADYQHGFKEAIRYYGELRNLGLPVDHIDVGGGLGVDY 300
           R AGLDQGIRLLHFHMGSQIANLADYQHGFKEAIRYYGELR LGLPVDHIDVGGGLGVDY
Sbjct: 241 RDAGLDQGIRLLHFHMGSQIANLADYQHGFKEAIRYYGELRALGLPVDHIDVGGGLGVDY 300

Query: 301 DGTHSRNASSINYDMDDYAGVVVGMLKEFCDAQSLPHPNIFSESGRSLTAHHAMLVVQVT 360
           DGTHSRNASSINYDMDDYAGVVVGMLKEFCDAQ LPHP+IFSESGRSLTAHHAMLV+QVT
Sbjct: 301 DGTHSRNASSINYDMDDYAGVVVGMLKEFCDAQGLPHPHIFSESGRSLTAHHAMLVIQVT 360

Query: 361 DVEKHNDDVPKIDNKEELPETVQWLVDLLGPTDIEMVTETYWRATHYMSDVATQYADGKL 420
           DVEKHNDDVP I+NKE LPETVQWLVDLLGPTDIEMVTETYWRATHYM DVA QYADGKL
Sbjct: 361 DVEKHNDDVPTIENKEALPETVQWLVDLLGPTDIEMVTETYWRATHYMGDVAAQYADGKL 420

Query: 421 TLAQKALAEQCYFAVCRRLHNSLKARQRSHRQVLDELNDKLADKYICNFSVFQSLPDTWA 480
           +L +KALAEQCYFAVCRRLHNSLKARQRSHRQVLDELNDKLADKYICNFSVFQSLPDTWA
Sbjct: 421 SLGEKALAEQCYFAVCRRLHNSLKARQRSHRQVLDELNDKLADKYICNFSVFQSLPDTWA 480

Query: 481 IGQVLPILPLHRLDEEPLRRAVLQDLTCDSDGKIKQYVDEQSIETSLPVHGLNEGEDYLL 540
           IGQVLPI+PLHRLDEEP+RRAVLQDLTCDSDGKI QYVDEQSIETS+PVH + EGEDYLL
Sbjct: 481 IGQVLPIIPLHRLDEEPMRRAVLQDLTCDSDGKINQYVDEQSIETSMPVHAVKEGEDYLL 540

Query: 541 GIFLVGAYQEILGDMHNLFGDTDSVNIYQNADGSVYHAGIETHDTIEDMLRYVHLSPEEL 600
           G+FLVGAYQEILGDMHNLFGDTDSVNIYQNADGSVYHAGIETHDTIEDMLRYVHLSPEEL
Sbjct: 541 GVFLVGAYQEILGDMHNLFGDTDSVNIYQNADGSVYHAGIETHDTIEDMLRYVHLSPEEL 600

Query: 601 MTHYRDKCASARISAAERTQFLDALRLGLTRSSYLSS 637
           MTHYRDK ASA+I+A ERTQ+LDALRLGLTRSSYLSS
Sbjct: 601 MTHYRDKVASAKITARERTQYLDALRLGLTRSSYLSS 637


Lambda     K      H
   0.319    0.136    0.396 

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: 1376
Number of extensions: 43
Number of successful extensions: 1
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: 637
Length of database: 637
Length adjustment: 38
Effective length of query: 599
Effective length of database: 599
Effective search space:   358801
Effective search space used:   358801
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: 54 (25.4 bits)

Align candidate PP_0567 PP_0567 (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.22376.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   5.7e-273  892.9   0.0   6.5e-273  892.8   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_0567  PP_0567 Biosynthetic arginine de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_0567  PP_0567 Biosynthetic arginine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  892.8   0.0  6.5e-273  6.5e-273       1     624 []      14     636 ..      14     636 .. 0.99

  Alignments for each domain:
  == domain 1  score: 892.8 bits;  conditional E-value: 6.5e-273
                           TIGR01273   1 wsaeesakvYnikgWgagyfavnkeGevsvrpkgeetlkeidllelvkqveakglklPllvrFpdilqkriksln 75 
                                         w++++s++vY+i++Wgagyfa+n++G+v+vrp+g + ++ idl e v+++++ gl+lPllvrFpdilq+r+++l+
  lcl|FitnessBrowser__Putida:PP_0567  14 WTVADSRSVYGIRHWGAGYFAINEAGRVEVRPNGPQ-SAPIDLFEQVDELRQSGLSLPLLVRFPDILQDRVRQLT 87 
                                         88999***************************9998.99************************************ PP

                           TIGR01273  76 aaFkeaieeleYaskyqavyPiKvnqqrevveelvasggkslGLEaGsKpEllialalaekpkavivcnGyKDre 150
                                          aF+++i +leY+s+y+a+yPiKvnqq++vve+++a+++ s+GLEaGsKpEll++lala  ++ +ivcnGyKDre
  lcl|FitnessBrowser__Putida:PP_0567  88 GAFDANIARLEYQSQYTALYPIKVNQQEAVVENIIATQNVSIGLEAGSKPELLAVLALAP-KGGTIVCNGYKDRE 161
                                         ************************************************************.8899********** PP

                           TIGR01273 151 yielaliarklglkvviviekleEldlvieeakklgvkPklGlRvrLaskgsgkwassgGeksKFGLsasqvlev 225
                                         +i+lal+++klg++v+iviek++E++lvieea++l+vkP++GlRvrL+s +s+kwa++gGeksKFGLsa+q+l+v
  lcl|FitnessBrowser__Putida:PP_0567 162 FIRLALMGQKLGHNVFIVIEKESEVALVIEEAAELKVKPQVGLRVRLSSLASSKWADTGGEKSKFGLSAAQLLSV 236
                                         *************************************************************************** PP

                           TIGR01273 226 vkklkeedlldslkllHfHlGsqianiddvkkgvrEaarlyvelrklGvkievvdvGGGLgvdYdGtksksdlsv 300
                                         v+++++++l++ ++llHfH+Gsqian++d+++g++Ea+r+y elr lG++++++dvGGGLgvdYdGt+s++++s+
  lcl|FitnessBrowser__Putida:PP_0567 237 VQRFRDAGLDQGIRLLHFHMGSQIANLADYQHGFKEAIRYYGELRALGLPVDHIDVGGGLGVDYDGTHSRNASSI 311
                                         *************************************************************************** PP

                           TIGR01273 301 nYsleeyaaavvaalkevceekgvpePviisEsGRaitahhavlvaevleveeeeeeeaeeile.eeapeevkel 374
                                         nY++++ya  vv +lke+c+++g+p+P+i+sEsGR++tahha+lv++v++ve+++++  + i + e+ pe+v++l
  lcl|FitnessBrowser__Putida:PP_0567 312 NYDMDDYAGVVVGMLKEFCDAQGLPHPHIFSESGRSLTAHHAMLVIQVTDVEKHNDDV-PTIENkEALPETVQWL 385
                                         *******************************************************995.444443899******* PP

                           TIGR01273 375 eellkeideesaeelledavqlleeavelfklGkldleeralaeqlalailkkvke.leakekshreildelqek 448
                                          +ll+++d e+++e++++a++++ ++++++++Gkl+l e+alaeq++ a+++++++ l+a+++shr++ldel++k
  lcl|FitnessBrowser__Putida:PP_0567 386 VDLLGPTDIEMVTETYWRATHYMGDVAAQYADGKLSLGEKALAEQCYFAVCRRLHNsLKARQRSHRQVLDELNDK 460
                                         *************************************************************************** PP

                           TIGR01273 449 laekylvnlslFqslPDaWgidqlfPilPlerLdekpdrravllDltCDsDGkikkfveeqgiektlplheldkd 523
                                         la+ky++n+s+FqslPD+W+i+q++Pi+Pl+rLde+p rravl+DltCDsDGki+++v+eq+ie+++p+h++++ 
  lcl|FitnessBrowser__Putida:PP_0567 461 LADKYICNFSVFQSLPDTWAIGQVLPIIPLHRLDEEPMRRAVLQDLTCDSDGKINQYVDEQSIETSMPVHAVKEG 535
                                         *************************************************************************** PP

                           TIGR01273 524 eeyllgfflvGAYqEiLgdvHnLFgdteavevvvkekgeveveaieegdtvedvlkavqydpeellkalkqkvae 598
                                         e+yllg+flvGAYqEiLgd+HnLFgdt++v+++++++g+v+++ ie++dt+ed+l++v+++peel++++++kva+
  lcl|FitnessBrowser__Putida:PP_0567 536 EDYLLGVFLVGAYQEILGDMHNLFGDTDSVNIYQNADGSVYHAGIETHDTIEDMLRYVHLSPEELMTHYRDKVAS 610
                                         *************************************************************************** PP

                           TIGR01273 599 aklkaeekkqvlelleaglsgypYLs 624
                                         ak++a+e++q+l++l+ gl++++YLs
  lcl|FitnessBrowser__Putida:PP_0567 611 AKITARERTQYLDALRLGLTRSSYLS 636
                                         ************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (624 nodes)
Target sequences:                          1  (637 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: 00:00:00.04
# Mc/sec: 9.30
//
[ok]

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

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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