Alignments for a candidate for adiA in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for adiA in Pseudomonas fluorescens GW456-L13

Align Biosynthetic arginine decarboxylase (EC 4.1.1.19) (characterized)
to candidate PfGW456L13_43 Biosynthetic arginine decarboxylase (EC 4.1.1.19)

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



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_43
          Length = 637

 Score = 1248 bits (3229), Expect = 0.0
 Identities = 622/637 (97%), Positives = 631/637 (99%)

Query: 1   MSVRRTRKDDGSQWTVADSRSVYGIRHWGAGYFAINDAGRVEVRPNGPTSSPIDLFEQVD 60
           MSVRRTRKDDGSQWTVADSRSVYGIRHWGAGYFAINDAGRVEVRPNGP+SSPIDL+EQVD
Sbjct: 1   MSVRRTRKDDGSQWTVADSRSVYGIRHWGAGYFAINDAGRVEVRPNGPSSSPIDLYEQVD 60

Query: 61  QLRKSGLSLPLLVRFPDILQDRVRQLTGAFDANIERLEYQSKYTALYPIKVNQQEAVIEN 120
           QLRKSGLSLPLLVRFPDILQDRVRQLTGAFDANIERLEYQSKYTALYPIKVNQQEAVIEN
Sbjct: 61  QLRKSGLSLPLLVRFPDILQDRVRQLTGAFDANIERLEYQSKYTALYPIKVNQQEAVIEN 120

Query: 121 IIATQNVSIGLEAGSKPELLAVLALAPKGGTIVCNGYKDREFIRLALMGQKLGHNVFIVI 180
           IIATQNVSIGLEAGSKPELLAVLALAPKGGTIVCNGYKDREFIRLALMGQKLGHNVFIVI
Sbjct: 121 IIATQNVSIGLEAGSKPELLAVLALAPKGGTIVCNGYKDREFIRLALMGQKLGHNVFIVI 180

Query: 181 EKESEVGLVIEEAASLKVKPQVGLRVRLSSLASSKWADTGGEKSKFGLSAAQLLSVVERF 240
           EKESEVGLVIEEAASLKVKPQVGLRVRLSSLASSKWADTGGEKSKFGLSAAQLLSVVERF
Sbjct: 181 EKESEVGLVIEEAASLKVKPQVGLRVRLSSLASSKWADTGGEKSKFGLSAAQLLSVVERF 240

Query: 241 RAAGLDQGIRLLHFHMGSQIANLADYQHGFKEAIRYYGELRNLGLPVDHIDVGGGLGVDY 300
           RAAGLDQGIRLLHFHMGSQIANLADYQHGFKEAIRYYGELRNLGLPVDHIDVGGGLGVDY
Sbjct: 241 RAAGLDQGIRLLHFHMGSQIANLADYQHGFKEAIRYYGELRNLGLPVDHIDVGGGLGVDY 300

Query: 301 DGTHSRNASSINYDMDDYAGVVVGMLKEFCDAQSLPHPNIFSESGRSLTAHHAMLVVQVT 360
           DGTHSRNASSINYDMDDYAGVVVGMLKEFCDAQSLPHPNIFSESGRSLTAHHAMLV+QVT
Sbjct: 301 DGTHSRNASSINYDMDDYAGVVVGMLKEFCDAQSLPHPNIFSESGRSLTAHHAMLVIQVT 360

Query: 361 DVEKHNDDVPKIDNKEELPETVQWLVDLLGPTDIEMVTETYWRATHYMSDVATQYADGKL 420
           DVEKHNDDVP+I+NKE LPETVQWLVDLLGPTDIEMVTETYWRATHYMSDVA+QYADGKL
Sbjct: 361 DVEKHNDDVPQIENKEALPETVQWLVDLLGPTDIEMVTETYWRATHYMSDVASQYADGKL 420

Query: 421 TLAQKALAEQCYFAVCRRLHNSLKARQRSHRQVLDELNDKLADKYICNFSVFQSLPDTWA 480
           TLA+KALAEQCYFAVCRRLHNSLKARQRSHRQVLDELNDKLADKYICNFSVFQSLPDTWA
Sbjct: 421 TLAEKALAEQCYFAVCRRLHNSLKARQRSHRQVLDELNDKLADKYICNFSVFQSLPDTWA 480

Query: 481 IGQVLPILPLHRLDEEPLRRAVLQDLTCDSDGKIKQYVDEQSIETSLPVHGLNEGEDYLL 540
           I QVLPI+PLHRLDEEPLRRAVLQDLTCDSDGKI QYVDEQSIETSLPVH L EGEDYLL
Sbjct: 481 IDQVLPIIPLHRLDEEPLRRAVLQDLTCDSDGKINQYVDEQSIETSLPVHALKEGEDYLL 540

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

Query: 601 MTHYRDKCASARISAAERTQFLDALRLGLTRSSYLSS 637
           MTHYRDKCASARISA ERTQFLDALRLGLTRSSYLSS
Sbjct: 601 MTHYRDKCASARISATERTQFLDALRLGLTRSSYLSS 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: 1407
Number of extensions: 49
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 PfGW456L13_43 (Biosynthetic arginine decarboxylase (EC 4.1.1.19))
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.28942.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                             -----------
   1.5e-273  894.9   0.0   1.7e-273  894.7   0.0    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_43  Biosynthetic arginine decarboxyl


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_43  Biosynthetic arginine decarboxylase (EC 4.1.1.19)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  894.7   0.0  1.7e-273  1.7e-273       1     624 []      14     636 ..      14     636 .. 0.99

  Alignments for each domain:
  == domain 1  score: 894.7 bits;  conditional E-value: 1.7e-273
                                             TIGR01273   1 wsaeesakvYnikgWgagyfavnkeGevsvrpkgeetlkeidllelvkqveakglkl 57 
                                                           w++++s++vY+i++Wgagyfa+n++G+v+vrp+g + ++ idl+e v+q+++ gl+l
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_43  14 WTVADSRSVYGIRHWGAGYFAINDAGRVEVRPNGPS-SSPIDLYEQVDQLRKSGLSL 69 
                                                           88999***************************9888.99****************** PP

                                             TIGR01273  58 PllvrFpdilqkrikslnaaFkeaieeleYaskyqavyPiKvnqqrevveelvasgg 114
                                                           PllvrFpdilq+r+++l+ aF+++ie+leY+sky+a+yPiKvnqq++v+e+++a+++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_43  70 PLLVRFPDILQDRVRQLTGAFDANIERLEYQSKYTALYPIKVNQQEAVIENIIATQN 126
                                                           ********************************************************* PP

                                             TIGR01273 115 kslGLEaGsKpEllialalaekpkavivcnGyKDreyielaliarklglkvviviek 171
                                                            s+GLEaGsKpEll++lala  ++ +ivcnGyKDre+i+lal+++klg++v+iviek
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_43 127 VSIGLEAGSKPELLAVLALAP-KGGTIVCNGYKDREFIRLALMGQKLGHNVFIVIEK 182
                                                           *********************.8899******************************* PP

                                             TIGR01273 172 leEldlvieeakklgvkPklGlRvrLaskgsgkwassgGeksKFGLsasqvlevvkk 228
                                                           ++E+ lvieea++l+vkP++GlRvrL+s +s+kwa++gGeksKFGLsa+q+l+vv++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_43 183 ESEVGLVIEEAASLKVKPQVGLRVRLSSLASSKWADTGGEKSKFGLSAAQLLSVVER 239
                                                           ********************************************************* PP

                                             TIGR01273 229 lkeedlldslkllHfHlGsqianiddvkkgvrEaarlyvelrklGvkievvdvGGGL 285
                                                           +++++l++ ++llHfH+Gsqian++d+++g++Ea+r+y elr+lG++++++dvGGGL
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_43 240 FRAAGLDQGIRLLHFHMGSQIANLADYQHGFKEAIRYYGELRNLGLPVDHIDVGGGL 296
                                                           ********************************************************* PP

                                             TIGR01273 286 gvdYdGtksksdlsvnYsleeyaaavvaalkevceekgvpePviisEsGRaitahha 342
                                                           gvdYdGt+s++++s+nY++++ya  vv +lke+c+++++p+P+i+sEsGR++tahha
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_43 297 GVDYDGTHSRNASSINYDMDDYAGVVVGMLKEFCDAQSLPHPNIFSESGRSLTAHHA 353
                                                           ********************************************************* PP

                                             TIGR01273 343 vlvaevleveeeeeeeaeeile.eeapeevkeleellkeideesaeelledavqlle 398
                                                           +lv++v++ve+++++ +++i + e+ pe+v++l +ll+++d e+++e++++a+++++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_43 354 MLVIQVTDVEKHNDD-VPQIENkEALPETVQWLVDLLGPTDIEMVTETYWRATHYMS 409
                                                           *************99.6666554899******************************* PP

                                             TIGR01273 399 eavelfklGkldleeralaeqlalailkkvke.leakekshreildelqeklaekyl 454
                                                           ++++++++Gkl+l+e+alaeq++ a+++++++ l+a+++shr++ldel++kla+ky+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_43 410 DVASQYADGKLTLAEKALAEQCYFAVCRRLHNsLKARQRSHRQVLDELNDKLADKYI 466
                                                           ********************************************************* PP

                                             TIGR01273 455 vnlslFqslPDaWgidqlfPilPlerLdekpdrravllDltCDsDGkikkfveeqgi 511
                                                           +n+s+FqslPD+W+idq++Pi+Pl+rLde+p rravl+DltCDsDGki+++v+eq+i
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_43 467 CNFSVFQSLPDTWAIDQVLPIIPLHRLDEEPLRRAVLQDLTCDSDGKINQYVDEQSI 523
                                                           ********************************************************* PP

                                             TIGR01273 512 ektlplheldkdeeyllgfflvGAYqEiLgdvHnLFgdteavevvvkekgeveveai 568
                                                           e++lp+h+l++ e+yllg+flvGAYqEiLgd+HnLFgdt++v+++++++g+v+++ i
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_43 524 ETSLPVHALKEGEDYLLGVFLVGAYQEILGDMHNLFGDTDSVNIYQNADGSVYHAGI 580
                                                           ********************************************************* PP

                                             TIGR01273 569 eegdtvedvlkavqydpeellkalkqkvaeaklkaeekkqvlelleaglsgypYLs 624
                                                           e++dt+ed+l++v+++peel++++++k a+a+++a e++q+l++l+ gl++++YLs
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_43 581 ETHDTIEDMLRYVHLSPEELMTHYRDKCASARISATERTQFLDALRLGLTRSSYLS 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 10.34
//
[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