GapMind for catabolism of small carbon sources

 

Alignments for a candidate for arg-monooxygenase in Pseudomonas fluorescens FW300-N2C3

Align Arginine 2-monooxygenase (Decarboxylating); EC 1.13.12.3; SubName: Full=FAD-dependent oxidoreductase (characterized, see rationale)
to candidate AO356_14230 AO356_14230 amine oxidase

Query= uniprot:A0A291T0Y3
         (569 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_14230
          Length = 560

 Score =  716 bits (1848), Expect = 0.0
 Identities = 325/552 (58%), Positives = 426/552 (77%), Gaps = 3/552 (0%)

Query: 19  DALPPVTMFGPDFPYAYDDYLAHPAGLGQIPATEHGSEVAVVGGGLSGVVTAYELMKMGL 78
           D   P+T+FGPDFP+A+DD++ HPAGLG IPA  HG+EVA+VG G++G+V AYELMK+GL
Sbjct: 10  DGKKPITIFGPDFPFAFDDWIEHPAGLGSIPAHNHGTEVAIVGAGIAGLVAAYELMKLGL 69

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

Query: 139 APDTPSTVVDLKGESHYARTIDDLPPVYREVADAWSACLEEGADFSDMNRAIRERDVPRI 198
            P + STV+DL+G+++YA+ + DLP +++EVADAW+  LE+G+ F D+ +AIR+RDVPR+
Sbjct: 129 TPASGSTVIDLEGQTYYAQKLADLPALFQEVADAWADALEDGSRFGDIQQAIRDRDVPRL 188

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

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

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

Query: 377 PVDRPFWLDEDETTGRDTMSMTLTDRMTRGTYLLDDGPDRPAVICLSYTWCDDSLKWLPL 436
            VDRPFW D+D  TGRD MSMTLTDR+TRGTYL D+G D+P VICLSY+W  D+LK LP 
Sbjct: 369 MVDRPFWKDKDPETGRDLMSMTLTDRLTRGTYLFDNGDDKPGVICLSYSWMSDALKMLPH 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  FGG T  +NPGPGD
Sbjct: 489 AHFMQDDMPAEQRGIFIAGDDVSWTPAWVEGAVQTSLNAVWGIMKHFGGETHAENPGPGD 548

Query: 557 LYEEIAPVELPE 568
           ++ EI P+ LPE
Sbjct: 549 VFHEIGPIALPE 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: 1117
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.

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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:

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