Alignments for a candidate for adiA in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for adiA in Pseudomonas fluorescens FW300-N2E3

Align Biosynthetic arginine decarboxylase (EC 4.1.1.19) (characterized)
to candidate AO353_13720 AO353_13720 arginine decarboxylase

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



>FitnessBrowser__pseudo3_N2E3:AO353_13720
          Length = 637

 Score = 1250 bits (3234), Expect = 0.0
 Identities = 625/637 (98%), Positives = 633/637 (99%)

Query: 1   MSVRRTRKDDGSQWTVADSRSVYGIRHWGAGYFAINDAGRVEVRPNGPTSSPIDLFEQVD 60
           MSVRRTRKDDGSQWTVADSRSVYGIRHWGAGYFAI+DAGRVEVRPNGP+S+PIDLFEQV 
Sbjct: 1   MSVRRTRKDDGSQWTVADSRSVYGIRHWGAGYFAISDAGRVEVRPNGPSSAPIDLFEQVA 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
           DGTHSRNASSINYDMDDYAGVVVGMLKEFCDAQSLPHPNIFSESGRSLTAHHAMLVVQVT
Sbjct: 301 DGTHSRNASSINYDMDDYAGVVVGMLKEFCDAQSLPHPNIFSESGRSLTAHHAMLVVQVT 360

Query: 361 DVEKHNDDVPKIDNKEELPETVQWLVDLLGPTDIEMVTETYWRATHYMSDVATQYADGKL 420
           DVEKHNDDVP I+NKEELPETVQWLVDLLGPTDIEMVTETYWRATHYMSDVATQYADGKL
Sbjct: 361 DVEKHNDDVPMIENKEELPETVQWLVDLLGPTDIEMVTETYWRATHYMSDVATQYADGKL 420

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

Query: 481 IGQVLPILPLHRLDEEPLRRAVLQDLTCDSDGKIKQYVDEQSIETSLPVHGLNEGEDYLL 540
           IGQVLPILPLHRLDEEP+RRAVLQDLTCDSDGKIKQYVDEQSIETSLPVHGLN+GEDYLL
Sbjct: 481 IGQVLPILPLHRLDEEPMRRAVLQDLTCDSDGKIKQYVDEQSIETSLPVHGLNDGEDYLL 540

Query: 541 GIFLVGAYQEILGDMHNLFGDTDSVNIYQNADGSVYHAGIETHDTIEDMLRYVHLSPEEL 600
           GIFLVGAYQEILGDMHNLFGDTDSVNIYQNADGSVYHAGIETHDTIEDMLRYVHLSPEEL
Sbjct: 541 GIFLVGAYQEILGDMHNLFGDTDSVNIYQNADGSVYHAGIETHDTIEDMLRYVHLSPEEL 600

Query: 601 MTHYRDKCASARISAAERTQFLDALRLGLTRSSYLSS 637
           MTHYRDK ASARISA ERTQ+LDALRLGLTRSSYLSS
Sbjct: 601 MTHYRDKVASARISATERTQYLDALRLGLTRSSYLSS 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: 1415
Number of extensions: 44
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 AO353_13720 AO353_13720 (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.25667.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   2.2e-271  887.7   0.0   2.5e-271  887.5   0.0    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_13720  AO353_13720 arginine decarboxyla


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_13720  AO353_13720 arginine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  887.5   0.0  2.5e-271  2.5e-271       1     624 []      14     636 ..      14     636 .. 0.99

  Alignments for each domain:
  == domain 1  score: 887.5 bits;  conditional E-value: 2.5e-271
                                     TIGR01273   1 wsaeesakvYnikgWgagyfavnkeGevsvrpkgeetlkeidllelvkqveakglklPllvrFpd 65 
                                                   w++++s++vY+i++Wgagyfa+ ++G+v+vrp+g + ++ idl e v q+++ gl+lPllvrFpd
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_13720  14 WTVADSRSVYGIRHWGAGYFAISDAGRVEVRPNGPS-SAPIDLFEQVAQLRKSGLSLPLLVRFPD 77 
                                                   88999***************************9888.99************************** PP

                                     TIGR01273  66 ilqkrikslnaaFkeaieeleYaskyqavyPiKvnqqrevveelvasggkslGLEaGsKpEllia 130
                                                   ilq+r+++l+ aF+++ie+leY+sky+a+yPiKvnqq++v+e+++a+++ s+GLEaGsKpEll++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_13720  78 ILQDRVRQLTGAFDANIERLEYQSKYTALYPIKVNQQEAVIENIIATQNVSIGLEAGSKPELLAV 142
                                                   ***************************************************************** PP

                                     TIGR01273 131 lalaekpkavivcnGyKDreyielaliarklglkvviviekleEldlvieeakklgvkPklGlRv 195
                                                   lala  ++ +ivcnGyKDre+i+lal+++klg++v+iviek++E+ lvieea++l+vkP++GlRv
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_13720 143 LALAP-KGGTIVCNGYKDREFIRLALMGQKLGHNVFIVIEKESEVGLVIEEAASLKVKPQVGLRV 206
                                                   *****.8899******************************************************* PP

                                     TIGR01273 196 rLaskgsgkwassgGeksKFGLsasqvlevvkklkeedlldslkllHfHlGsqianiddvkkgvr 260
                                                   rL+s +s+kwa++gGeksKFGLsa+q+l+vv+++++++l++ ++llHfH+Gsqian++d+++g++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_13720 207 RLSSLASSKWADTGGEKSKFGLSAAQLLSVVERFRAAGLDQGIRLLHFHMGSQIANLADYQHGFK 271
                                                   ***************************************************************** PP

                                     TIGR01273 261 EaarlyvelrklGvkievvdvGGGLgvdYdGtksksdlsvnYsleeyaaavvaalkevceekgvp 325
                                                   Ea+r+y elr+lG++++++dvGGGLgvdYdGt+s++++s+nY++++ya  vv +lke+c+++++p
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_13720 272 EAIRYYGELRNLGLPVDHIDVGGGLGVDYDGTHSRNASSINYDMDDYAGVVVGMLKEFCDAQSLP 336
                                                   ***************************************************************** PP

                                     TIGR01273 326 ePviisEsGRaitahhavlvaevleveeeeeeeaeeileeeapeevkeleellkeideesaeell 390
                                                   +P+i+sEsGR++tahha+lv++v++ve+++++      +ee pe+v++l +ll+++d e+++e++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_13720 337 HPNIFSESGRSLTAHHAMLVVQVTDVEKHNDDVPMIENKEELPETVQWLVDLLGPTDIEMVTETY 401
                                                   ******************************99633334489************************ PP

                                     TIGR01273 391 edavqlleeavelfklGkldleeralaeqlalailkkvke.leakekshreildelqeklaekyl 454
                                                   ++a+++++++++++++Gkl+l+e+alaeq++ a+++++++ l+a+++shr++ldel++kla+ky+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_13720 402 WRATHYMSDVATQYADGKLTLAEKALAEQCYFAVCRRLHNsLKARQRSHRQVLDELNDKLADKYI 466
                                                   ***************************************************************** PP

                                     TIGR01273 455 vnlslFqslPDaWgidqlfPilPlerLdekpdrravllDltCDsDGkikkfveeqgiektlplhe 519
                                                   +n+s+FqslPD+W+i+q++PilPl+rLde+p rravl+DltCDsDGkik++v+eq+ie++lp+h 
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_13720 467 CNFSVFQSLPDTWAIGQVLPILPLHRLDEEPMRRAVLQDLTCDSDGKIKQYVDEQSIETSLPVHG 531
                                                   ***************************************************************** PP

                                     TIGR01273 520 ldkdeeyllgfflvGAYqEiLgdvHnLFgdteavevvvkekgeveveaieegdtvedvlkavqyd 584
                                                   l+  e+yllg+flvGAYqEiLgd+HnLFgdt++v+++++++g+v+++ ie++dt+ed+l++v+++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_13720 532 LNDGEDYLLGIFLVGAYQEILGDMHNLFGDTDSVNIYQNADGSVYHAGIETHDTIEDMLRYVHLS 596
                                                   ***************************************************************** PP

                                     TIGR01273 585 peellkalkqkvaeaklkaeekkqvlelleaglsgypYLs 624
                                                   peel++++++kva+a+++a e++q+l++l+ gl++++YLs
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_13720 597 PEELMTHYRDKVASARISATERTQYLDALRLGLTRSSYLS 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: 11.81
//
[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)
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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