GapMind for catabolism of small carbon sources

 

Aligments for a candidate for adiA in Pseudomonas fluorescens FW300-N2C3

Align Biosynthetic arginine decarboxylase (EC 4.1.1.19) (characterized)
to candidate AO356_08155 AO356_08155 arginine decarboxylase

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



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_08155 AO356_08155 arginine
           decarboxylase
          Length = 637

 Score = 1248 bits (3229), Expect = 0.0
 Identities = 625/637 (98%), Positives = 631/637 (99%)

Query: 1   MSVRRTRKDDGSQWTVADSRSVYGIRHWGAGYFAINDAGRVEVRPNGPTSSPIDLFEQVD 60
           MSVRRTRKDDGSQWTVADSRSVYGIRHWGAGYFAIN+AGRVEVRPNGP SSPIDLFEQVD
Sbjct: 1   MSVRRTRKDDGSQWTVADSRSVYGIRHWGAGYFAINEAGRVEVRPNGPGSSPIDLFEQVD 60

Query: 61  QLRKSGLSLPLLVRFPDILQDRVRQLTGAFDANIERLEYQSKYTALYPIKVNQQEAVIEN 120
           QLR+SGLSLPLLVRFPDILQDRVRQLTGAFD+NI RLEYQSKYTALYPIKVNQQEAVIEN
Sbjct: 61  QLRQSGLSLPLLVRFPDILQDRVRQLTGAFDSNIARLEYQSKYTALYPIKVNQQEAVIEN 120

Query: 121 IIATQNVSIGLEAGSKPELLAVLALAPKGGTIVCNGYKDREFIRLALMGQKLGHNVFIVI 180
           IIATQNVSIGLEAGSKPELLAVLALAPKGGTIVCNGYKDREFIRLALMGQKLGHNVFIVI
Sbjct: 121 IIATQNVSIGLEAGSKPELLAVLALAPKGGTIVCNGYKDREFIRLALMGQKLGHNVFIVI 180

Query: 181 EKESEVGLVIEEAASLKVKPQVGLRVRLSSLASSKWADTGGEKSKFGLSAAQLLSVVERF 240
           EKESEVGLVIEEAA LKVKPQVGLRVRLSSLASSKWADTGGEKSKFGLSAAQLLSVVERF
Sbjct: 181 EKESEVGLVIEEAAVLKVKPQVGLRVRLSSLASSKWADTGGEKSKFGLSAAQLLSVVERF 240

Query: 241 RAAGLDQGIRLLHFHMGSQIANLADYQHGFKEAIRYYGELRNLGLPVDHIDVGGGLGVDY 300
           RAAGLDQGIRLLHFHMGSQIANLADYQHGFKEAIRYYGELRNLGLPVDHIDVGGGLGVDY
Sbjct: 241 RAAGLDQGIRLLHFHMGSQIANLADYQHGFKEAIRYYGELRNLGLPVDHIDVGGGLGVDY 300

Query: 301 DGTHSRNASSINYDMDDYAGVVVGMLKEFCDAQSLPHPNIFSESGRSLTAHHAMLVVQVT 360
           DGTHSRNASSINYDMDDYAGVVVGMLKEFCDAQSLPHP+IFSESGRSLTAHHAMLVVQVT
Sbjct: 301 DGTHSRNASSINYDMDDYAGVVVGMLKEFCDAQSLPHPHIFSESGRSLTAHHAMLVVQVT 360

Query: 361 DVEKHNDDVPKIDNKEELPETVQWLVDLLGPTDIEMVTETYWRATHYMSDVATQYADGKL 420
           DVEKHNDDVP IDNK+ELPETVQWLVDLLGPTDIEMVTETYWRATHYMSDVATQYADGKL
Sbjct: 361 DVEKHNDDVPVIDNKQELPETVQWLVDLLGPTDIEMVTETYWRATHYMSDVATQYADGKL 420

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

Query: 481 IGQVLPILPLHRLDEEPLRRAVLQDLTCDSDGKIKQYVDEQSIETSLPVHGLNEGEDYLL 540
           IGQVLPILPLHRLDEEPLRRAVLQDLTCDSDGKIKQYVDEQSIETSLPVH LN GEDYLL
Sbjct: 481 IGQVLPILPLHRLDEEPLRRAVLQDLTCDSDGKIKQYVDEQSIETSLPVHALNPGEDYLL 540

Query: 541 GIFLVGAYQEILGDMHNLFGDTDSVNIYQNADGSVYHAGIETHDTIEDMLRYVHLSPEEL 600
           GIFLVGAYQEILGDMHNLFGDTDSVNIYQNADGSVYHAGIETHDTIEDMLRYVHLSPEEL
Sbjct: 541 GIFLVGAYQEILGDMHNLFGDTDSVNIYQNADGSVYHAGIETHDTIEDMLRYVHLSPEEL 600

Query: 601 MTHYRDKCASARISAAERTQFLDALRLGLTRSSYLSS 637
           MTHYRDKCASARISAAERTQFLDALRLGLTRSSYLSS
Sbjct: 601 MTHYRDKCASARISAAERTQFLDALRLGLTRSSYLSS 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: 47
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 AO356_08155 AO356_08155 (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.5555.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   6.1e-271  886.2   0.0   6.9e-271  886.1   0.0    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_08155  AO356_08155 arginine decarboxyla


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_08155  AO356_08155 arginine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  886.1   0.0  6.9e-271  6.9e-271       1     624 []      14     636 ..      14     636 .. 0.99

  Alignments for each domain:
  == domain 1  score: 886.1 bits;  conditional E-value: 6.9e-271
                                       TIGR01273   1 wsaeesakvYnikgWgagyfavnkeGevsvrpkgeetlkeidllelvkqveakglklPllvrF 63 
                                                     w++++s++vY+i++Wgagyfa+n++G+v+vrp+g   ++ idl e v+q+++ gl+lPllvrF
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_08155  14 WTVADSRSVYGIRHWGAGYFAINEAGRVEVRPNGPG-SSPIDLFEQVDQLRQSGLSLPLLVRF 75 
                                                     88999***************************9988.99************************ PP

                                       TIGR01273  64 pdilqkrikslnaaFkeaieeleYaskyqavyPiKvnqqrevveelvasggkslGLEaGsKpE 126
                                                     pdilq+r+++l+ aF+++i +leY+sky+a+yPiKvnqq++v+e+++a+++ s+GLEaGsKpE
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_08155  76 PDILQDRVRQLTGAFDSNIARLEYQSKYTALYPIKVNQQEAVIENIIATQNVSIGLEAGSKPE 138
                                                     *************************************************************** PP

                                       TIGR01273 127 llialalaekpkavivcnGyKDreyielaliarklglkvviviekleEldlvieeakklgvkP 189
                                                     ll++lala  ++ +ivcnGyKDre+i+lal+++klg++v+iviek++E+ lvieea+ l+vkP
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_08155 139 LLAVLALAP-KGGTIVCNGYKDREFIRLALMGQKLGHNVFIVIEKESEVGLVIEEAAVLKVKP 200
                                                     *********.8899************************************************* PP

                                       TIGR01273 190 klGlRvrLaskgsgkwassgGeksKFGLsasqvlevvkklkeedlldslkllHfHlGsqiani 252
                                                     ++GlRvrL+s +s+kwa++gGeksKFGLsa+q+l+vv+++++++l++ ++llHfH+Gsqian+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_08155 201 QVGLRVRLSSLASSKWADTGGEKSKFGLSAAQLLSVVERFRAAGLDQGIRLLHFHMGSQIANL 263
                                                     *************************************************************** PP

                                       TIGR01273 253 ddvkkgvrEaarlyvelrklGvkievvdvGGGLgvdYdGtksksdlsvnYsleeyaaavvaal 315
                                                     +d+++g++Ea+r+y elr+lG++++++dvGGGLgvdYdGt+s++++s+nY++++ya  vv +l
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_08155 264 ADYQHGFKEAIRYYGELRNLGLPVDHIDVGGGLGVDYDGTHSRNASSINYDMDDYAGVVVGML 326
                                                     *************************************************************** PP

                                       TIGR01273 316 kevceekgvpePviisEsGRaitahhavlvaevleveeeeeee.aeeileeeapeevkeleel 377
                                                     ke+c+++++p+P+i+sEsGR++tahha+lv++v++ve+++++  + + + +e pe+v++l +l
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_08155 327 KEFCDAQSLPHPHIFSESGRSLTAHHAMLVVQVTDVEKHNDDVpVIDNK-QELPETVQWLVDL 388
                                                     ****************************************997444544.599********** PP

                                       TIGR01273 378 lkeideesaeelledavqlleeavelfklGkldleeralaeqlalailkkvke.leakekshr 439
                                                     l+++d e+++e++++a+++++++++++++Gkl+l+e+alaeq++ a+++++++ l+a+++shr
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_08155 389 LGPTDIEMVTETYWRATHYMSDVATQYADGKLTLAEKALAEQCYFAVCRRLHNsLKARQRSHR 451
                                                     *************************************************************** PP

                                       TIGR01273 440 eildelqeklaekylvnlslFqslPDaWgidqlfPilPlerLdekpdrravllDltCDsDGki 502
                                                     ++ldel++kla+ky++n+s+FqslPD+W+i+q++PilPl+rLde+p rravl+DltCDsDGki
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_08155 452 QVLDELNDKLADKYICNFSVFQSLPDTWAIGQVLPILPLHRLDEEPLRRAVLQDLTCDSDGKI 514
                                                     *************************************************************** PP

                                       TIGR01273 503 kkfveeqgiektlplheldkdeeyllgfflvGAYqEiLgdvHnLFgdteavevvvkekgevev 565
                                                     k++v+eq+ie++lp+h+l++ e+yllg+flvGAYqEiLgd+HnLFgdt++v+++++++g+v++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_08155 515 KQYVDEQSIETSLPVHALNPGEDYLLGIFLVGAYQEILGDMHNLFGDTDSVNIYQNADGSVYH 577
                                                     *************************************************************** PP

                                       TIGR01273 566 eaieegdtvedvlkavqydpeellkalkqkvaeaklkaeekkqvlelleaglsgypYLs 624
                                                     + ie++dt+ed+l++v+++peel++++++k a+a+++a+e++q+l++l+ gl++++YLs
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_08155 578 AGIETHDTIEDMLRYVHLSPEELMTHYRDKCASARISAAERTQFLDALRLGLTRSSYLS 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: 00:00:00.03
# Mc/sec: 10.86
//
[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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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