Aligments for a candidate for arg-monooxygenase in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Aligments for a candidate for arg-monooxygenase in Pseudomonas fluorescens GW456-L13

Align Arginine 2-monooxygenase (Decarboxylating); EC 1.13.12.3; SubName: Full=FAD-dependent oxidoreductase (characterized, see rationale)
to candidate PfGW456L13_1171 Lysine 2-monooxygenase (EC 1.13.12.2)

Query= uniprot:A0A291T0Y3
         (569 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1171 Lysine
           2-monooxygenase (EC 1.13.12.2)
          Length = 560

 Score =  731 bits (1886), Expect = 0.0
 Identities = 331/552 (59%), Positives = 426/552 (77%), Gaps = 3/552 (0%)

Query: 19  DALPPVTMFGPDFPYAYDDYLAHPAGLGQIPATEHGSEVAVVGGGLSGVVTAYELMKMGL 78
           D   PVT+FGPDFP+A+DD++ HPAGLG IP   HG+EVA+VGGG++G+V AYELMK+GL
Sbjct: 10  DGKKPVTIFGPDFPFAFDDWIEHPAGLGSIPEHNHGAEVAIVGGGIAGLVAAYELMKLGL 69

Query: 79  RPVVYEADRIGGRLRTVGFDGCDDSLTAEMGAMRFPPSSTALQHYIDLVGLKTRPFPNPL 138
           +PVVYEA ++GGRLR+  F+G +  + AE+G MRFP SSTA  HY+D +GL+T+PFPNPL
Sbjct: 70  KPVVYEASKMGGRLRSQAFNGAE-GIVAELGGMRFPVSSTAFYHYVDKLGLETKPFPNPL 128

Query: 139 APDTPSTVVDLKGESHYARTIDDLPPVYREVADAWSACLEEGADFSDMNRAIRERDVPRI 198
            P + STV+DL+G++HYA+ + DLP +++EVADAW+  LE G+ FSD+ +AIR+RDVPR+
Sbjct: 129 TPASGSTVIDLEGQTHYAQKLSDLPALFQEVADAWADALEAGSQFSDIQQAIRDRDVPRL 188

Query: 199 REIWSRLVEKLDNQTFYGFLCDSTAFT--SFRHREIFGQVGFGTGGWDTDFPNSILEILR 256
           +E+W+ LV   D++TFY F+  S AF   SF HRE+FGQVGFGTGGWD+DFPNS+LEI R
Sbjct: 189 KELWNTLVPLWDDRTFYDFVATSKAFAKLSFHHREVFGQVGFGTGGWDSDFPNSMLEIFR 248

Query: 257 VVYTEADDHHRGIVGGSQQLPLRLWEREPGKIVHWPQGTSLASLHGGAPRPAATRLHRAA 316
           VV T  DDH   +VGG +Q+P  +W   P +  HWP GTSL+SLH GAPR    ++  A 
Sbjct: 249 VVMTNCDDHQHLVVGGVEQVPQGIWRHVPERCAHWPAGTSLSSLHNGAPRTGVKKIAHAP 308

Query: 317 GDRVVVTDASGDIRSYRAVVFTAQSWMLLSQIDCDDSLFPIDHWTAIERTHYMESSKLFV 376
           G R  VTD  GD R Y AV+ T QSW+L +QI+CD++LF    W A++RT YM+SSK FV
Sbjct: 309 GGRFAVTDNWGDTREYAAVLTTCQSWLLTTQIECDETLFSQKMWMALDRTRYMQSSKTFV 368

Query: 377 PVDRPFWLDEDETTGRDTMSMTLTDRMTRGTYLLDDGPDRPAVICLSYTWCDDSLKWLPL 436
            VDRPFW D+D  TGRD MSMTLTDR+TRGTYL D+G D+P VICLSY+W  D+LK LP 
Sbjct: 369 MVDRPFWKDKDPETGRDLMSMTLTDRLTRGTYLFDNGDDKPGVICLSYSWMSDALKMLPQ 428

Query: 437 SANERMEVMLKSLSEIYPNVDIRKHIIGSPITVSWENEPYFMGAFKANLPGHYRYQRRLF 496
              +R+++ L +L +IYP VDI   IIG PITVSWE +P+F+GAFK  LPGHYRY +R++
Sbjct: 429 PVEKRVKLALDALKKIYPKVDIAARIIGDPITVSWEADPHFLGAFKGALPGHYRYNQRMY 488

Query: 497 THFMQDRLPADKRGVFLAGDDISWTAGWAEGAVQTALNAVWGVMHRFGGATDPKNPGPGD 556
            HFMQD +PA++RG+F+AGDD+SWT  W EGAVQT+LNAVWG+M  FGGAT  +NPGPGD
Sbjct: 489 AHFMQDDMPAEQRGIFIAGDDVSWTPAWVEGAVQTSLNAVWGIMKHFGGATHAENPGPGD 548

Query: 557 LYEEIAPVELPE 568
           ++ EI P+ LPE
Sbjct: 549 VFNEIGPIALPE 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: 1125
Number of extensions: 42
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.

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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 preprint 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

GapMind for catabolism of small carbon sources