Aligments for a candidate for davB in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Aligments for a candidate for davB in Pseudomonas simiae WCS417

Align Lysine 2-monooxygenase (EC 1.13.12.2) (characterized)
to candidate GFF5058 PS417_25910 amine oxidase

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1171
         (560 letters)



>lcl|FitnessBrowser__WCS417:GFF5058 PS417_25910 amine oxidase
          Length = 560

 Score = 1112 bits (2876), Expect = 0.0
 Identities = 531/560 (94%), Positives = 541/560 (96%)

Query: 1   MNKNNRHPADGKKPVTIFGPDFPFAFDDWIEHPAGLGSIPEHNHGAEVAIVGGGIAGLVA 60
           M+K NRHPADGKKP+TIFGPDFPFAFDDWIEHPAGLGSIP  NHGAEVAIVG GIAGLVA
Sbjct: 1   MSKTNRHPADGKKPITIFGPDFPFAFDDWIEHPAGLGSIPTANHGAEVAIVGAGIAGLVA 60

Query: 61  AYELMKLGLKPVVYEASKMGGRLRSQAFNGAEGIVAELGGMRFPVSSTAFYHYVDKLGLE 120
           AYELMKLGLKPVVYEASKMGGRLRSQAF GAEGI+AELGGMRFPVSSTAFYHYVDKLGLE
Sbjct: 61  AYELMKLGLKPVVYEASKMGGRLRSQAFEGAEGIIAELGGMRFPVSSTAFYHYVDKLGLE 120

Query: 121 TKPFPNPLTPASGSTVIDLEGQTHYAQKLSDLPALFQEVADAWADALEAGSQFSDIQQAI 180
           TKPFPNPLTPASGSTVIDLEGQTHYAQKLSDLP LFQEVADAWADALEAGSQF DIQQAI
Sbjct: 121 TKPFPNPLTPASGSTVIDLEGQTHYAQKLSDLPVLFQEVADAWADALEAGSQFGDIQQAI 180

Query: 181 RDRDVPRLKELWNTLVPLWDDRTFYDFVATSKAFAKLSFHHREVFGQVGFGTGGWDSDFP 240
           RDRDVPRLKELWN LVPLWDDRTFYDFVATSKAFAKLSFHHREVFGQVGFGTGGWDSDFP
Sbjct: 181 RDRDVPRLKELWNKLVPLWDDRTFYDFVATSKAFAKLSFHHREVFGQVGFGTGGWDSDFP 240

Query: 241 NSMLEIFRVVMTNCDDHQHLVVGGVEQVPQGIWRHVPERCAHWPAGTSLSSLHNGAPRTG 300
           NSMLEIFRVVMTNCDDHQHLVVGGV QVP GIWRHVPERCAHWPAGTSLSSLH GAPR G
Sbjct: 241 NSMLEIFRVVMTNCDDHQHLVVGGVAQVPMGIWRHVPERCAHWPAGTSLSSLHRGAPRAG 300

Query: 301 VKKIAHAPGGRFAVTDNWGDTREYAAVLTTCQSWLLTTQIECDETLFSQKMWMALDRTRY 360
           VK+IAHA  GRFAVTDN+GDTREYAAVLTTCQSWLLTTQIECDETLFSQKMWMALDRTRY
Sbjct: 301 VKRIAHAADGRFAVTDNYGDTREYAAVLTTCQSWLLTTQIECDETLFSQKMWMALDRTRY 360

Query: 361 MQSSKTFVMVDRPFWKDKDPETGRDLMSMTLTDRLTRGTYLFDNGDDKPGVICLSYSWMS 420
           MQSSKTFVMVDRPFWKDKDPETGRDLMSMTLTDRLTRGTYLFDNGDDKPGVICLSYSWMS
Sbjct: 361 MQSSKTFVMVDRPFWKDKDPETGRDLMSMTLTDRLTRGTYLFDNGDDKPGVICLSYSWMS 420

Query: 421 DALKMLPQPVEKRVKLALDALKKIYPKVDIAARIIGDPITVSWEADPHFLGAFKGALPGH 480
           DALKMLPQP++KRVKLALDALKKIYPKVDI ARIIGDPITVSWEADPHFLGAFKGALPGH
Sbjct: 421 DALKMLPQPIDKRVKLALDALKKIYPKVDIKARIIGDPITVSWEADPHFLGAFKGALPGH 480

Query: 481 YRYNQRMYAHFMQDDMPAEQRGIFIAGDDVSWTPAWVEGAVQTSLNAVWGIMKHFGGATH 540
           YRYNQRMYAHFMQ DMPAEQRGIFIAGDDVSWTPAWVEGAVQTSLNAVWGIM HFGG+TH
Sbjct: 481 YRYNQRMYAHFMQKDMPAEQRGIFIAGDDVSWTPAWVEGAVQTSLNAVWGIMTHFGGSTH 540

Query: 541 AENPGPGDVFNEIGPIALPE 560
            ENPGPGDVF+EIGPIAL +
Sbjct: 541 PENPGPGDVFDEIGPIALAD 560


Lambda     K      H
   0.320    0.137    0.438 

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: 1358
Number of extensions: 41
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: 560
Length of database: 560
Length adjustment: 36
Effective length of query: 524
Effective length of database: 524
Effective search space:   274576
Effective search space used:   274576
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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