Alignments for a candidate for arg-monooxygenase in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for arg-monooxygenase in Pseudomonas putida KT2440

Align Arginine 2-monooxygenase (Decarboxylating); EC 1.13.12.3; SubName: Full=FAD-dependent oxidoreductase (characterized, see rationale)
to candidate PP_0383 PP_0383 Lysine 2-monooxygenase

Query= uniprot:A0A291T0Y3
         (569 letters)



>FitnessBrowser__Putida:PP_0383
          Length = 560

 Score =  729 bits (1883), Expect = 0.0
 Identities = 330/560 (58%), Positives = 430/560 (76%), Gaps = 3/560 (0%)

Query: 11  DQQEERALDALPPVTMFGPDFPYAYDDYLAHPAGLGQIPATEHGSEVAVVGGGLSGVVTA 70
           +++     D   P+T+FGPDFP+A+DD+L HPAGLG IPA  HG EVA+VG G++G+V A
Sbjct: 2   NKKNRHPADGKKPITIFGPDFPFAFDDWLEHPAGLGSIPAERHGEEVAIVGAGIAGLVAA 61

Query: 71  YELMKMGLRPVVYEADRIGGRLRTVGFDGCDDSLTAEMGAMRFPPSSTALQHYIDLVGLK 130
           YELMK+GL+PVVYEA ++GGRLR+  F+G D  + AE+G MRFP SSTA  HY+D +GL+
Sbjct: 62  YELMKLGLKPVVYEASKLGGRLRSQAFNGTD-GIVAELGGMRFPVSSTAFYHYVDKLGLE 120

Query: 131 TRPFPNPLAPDTPSTVVDLKGESHYARTIDDLPPVYREVADAWSACLEEGADFSDMNRAI 190
           T+PFPNPL P + STV+DL+G+++YA    DLP ++ EVADAW+  LE GA F+D+ +AI
Sbjct: 121 TKPFPNPLTPASGSTVIDLEGQTYYAEKPTDLPQLFHEVADAWADALESGAQFADIQQAI 180

Query: 191 RERDVPRIREIWSRLVEKLDNQTFYGFLCDSTAFT--SFRHREIFGQVGFGTGGWDTDFP 248
           R+RDVPR++E+W++LV   D++TFY F+  S +F   SF+HRE+FGQVGFGTGGWD+DFP
Sbjct: 181 RDRDVPRLKELWNKLVPLWDDRTFYDFVATSRSFAKLSFQHREVFGQVGFGTGGWDSDFP 240

Query: 249 NSILEILRVVYTEADDHHRGIVGGSQQLPLRLWEREPGKIVHWPQGTSLASLHGGAPRPA 308
           NS+LEI RVV T  DDH   +VGG +Q+P  +W   P + VHWP+GTSL++LHGGAPR  
Sbjct: 241 NSMLEIFRVVMTNCDDHQHLVVGGVEQVPQGIWRDVPERCVHWPEGTSLSTLHGGAPRTG 300

Query: 309 ATRLHRAAGDRVVVTDASGDIRSYRAVVFTAQSWMLLSQIDCDDSLFPIDHWTAIERTHY 368
             R+ RAA  R+ VTD  GD R Y AV+ T Q+W+L +QIDC++SLF    W A++RT Y
Sbjct: 301 VKRIARAADGRLAVTDNWGDTRHYSAVLATCQTWLLTTQIDCEESLFSQKMWMALDRTRY 360

Query: 369 MESSKLFVPVDRPFWLDEDETTGRDTMSMTLTDRMTRGTYLLDDGPDRPAVICLSYTWCD 428
           M+SSK FV VDRPFW D+D  TGRD +SMTLTDR+TRGTYL D+G D+P VICLSY+W  
Sbjct: 361 MQSSKTFVMVDRPFWKDKDPETGRDLLSMTLTDRLTRGTYLFDNGNDKPGVICLSYSWMS 420

Query: 429 DSLKWLPLSANERMEVMLKSLSEIYPNVDIRKHIIGSPITVSWENEPYFMGAFKANLPGH 488
           D+LK LP    +R+++ L +L +IYP  DI  HIIG PITVSWE +PYF+GAFK  LPGH
Sbjct: 421 DALKMLPHPVEKRVQLALDALKKIYPKTDIAGHIIGDPITVSWEADPYFLGAFKGALPGH 480

Query: 489 YRYQRRLFTHFMQDRLPADKRGVFLAGDDISWTAGWAEGAVQTALNAVWGVMHRFGGATD 548
           YRY +R++ HFMQ  +PA++RG+F+AGDD+SWT  W EGAVQT+LNAVWG+M+ FGG T 
Sbjct: 481 YRYNQRMYAHFMQQDMPAEQRGIFIAGDDVSWTPAWVEGAVQTSLNAVWGIMNHFGGHTH 540

Query: 549 PKNPGPGDLYEEIAPVELPE 568
           P NPGPGD++ EI P+ L +
Sbjct: 541 PDNPGPGDVFNEIGPIALAD 560


Lambda     K      H
   0.320    0.138    0.436 

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: 1136
Number of extensions: 44
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: 569
Length of database: 560
Length adjustment: 36
Effective length of query: 533
Effective length of database: 524
Effective search space:   279292
Effective search space used:   279292
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 (21.8 bits)
S2: 53 (25.0 bits)

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

Downloads

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

Related tools

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