Alignments for a candidate for davB in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Alignments for a candidate for davB in Pseudomonas fluorescens FW300-N2C3

Align lysine 2-monooxygenase (EC 1.13.12.2) (characterized)
to candidate AO356_14230 AO356_14230 amine oxidase

Query= reanno::pseudo5_N2C3_1:AO356_14230
         (560 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_14230
          Length = 560

 Score = 1168 bits (3022), Expect = 0.0
 Identities = 560/560 (100%), Positives = 560/560 (100%)

Query: 1   MNKNNRHPADGKKPITIFGPDFPFAFDDWIEHPAGLGSIPAHNHGTEVAIVGAGIAGLVA 60
           MNKNNRHPADGKKPITIFGPDFPFAFDDWIEHPAGLGSIPAHNHGTEVAIVGAGIAGLVA
Sbjct: 1   MNKNNRHPADGKKPITIFGPDFPFAFDDWIEHPAGLGSIPAHNHGTEVAIVGAGIAGLVA 60

Query: 61  AYELMKLGLKPVVYEASKMGGRLRSQAFNGAEGVIAELGGMRFPVSSTAFYHYVDKLGLE 120
           AYELMKLGLKPVVYEASKMGGRLRSQAFNGAEGVIAELGGMRFPVSSTAFYHYVDKLGLE
Sbjct: 61  AYELMKLGLKPVVYEASKMGGRLRSQAFNGAEGVIAELGGMRFPVSSTAFYHYVDKLGLE 120

Query: 121 TKPFPNPLTPASGSTVIDLEGQTYYAQKLADLPALFQEVADAWADALEDGSRFGDIQQAI 180
           TKPFPNPLTPASGSTVIDLEGQTYYAQKLADLPALFQEVADAWADALEDGSRFGDIQQAI
Sbjct: 121 TKPFPNPLTPASGSTVIDLEGQTYYAQKLADLPALFQEVADAWADALEDGSRFGDIQQAI 180

Query: 181 RDRDVPRLKELWNTLVPLWDDRTFYDFVATSKAFAKLSFQHREVFGQVGFGTGGWDSDFP 240
           RDRDVPRLKELWNTLVPLWDDRTFYDFVATSKAFAKLSFQHREVFGQVGFGTGGWDSDFP
Sbjct: 181 RDRDVPRLKELWNTLVPLWDDRTFYDFVATSKAFAKLSFQHREVFGQVGFGTGGWDSDFP 240

Query: 241 NSMLEIFRVVMTNCDDHQHLVVGGVEQVPHGIWNHVPERCAHWPEGTSLNSLHLGAPRSG 300
           NSMLEIFRVVMTNCDDHQHLVVGGVEQVPHGIWNHVPERCAHWPEGTSLNSLHLGAPRSG
Sbjct: 241 NSMLEIFRVVMTNCDDHQHLVVGGVEQVPHGIWNHVPERCAHWPEGTSLNSLHLGAPRSG 300

Query: 301 VKRIARSADGRFSVTDVWENTREYAAVLVTCQSWLLTTQIECEEALFSQKMWMALDRTRY 360
           VKRIARSADGRFSVTDVWENTREYAAVLVTCQSWLLTTQIECEEALFSQKMWMALDRTRY
Sbjct: 301 VKRIARSADGRFSVTDVWENTREYAAVLVTCQSWLLTTQIECEEALFSQKMWMALDRTRY 360

Query: 361 MQSSKTFVMVDRPFWKDKDPETGRDLMSMTLTDRLTRGTYLFDNGDDKPGVICLSYSWMS 420
           MQSSKTFVMVDRPFWKDKDPETGRDLMSMTLTDRLTRGTYLFDNGDDKPGVICLSYSWMS
Sbjct: 361 MQSSKTFVMVDRPFWKDKDPETGRDLMSMTLTDRLTRGTYLFDNGDDKPGVICLSYSWMS 420

Query: 421 DALKMLPHPVEKRVKLALDALKKIYPKVDIAARIIGDPITVSWEADPHFLGAFKGALPGH 480
           DALKMLPHPVEKRVKLALDALKKIYPKVDIAARIIGDPITVSWEADPHFLGAFKGALPGH
Sbjct: 421 DALKMLPHPVEKRVKLALDALKKIYPKVDIAARIIGDPITVSWEADPHFLGAFKGALPGH 480

Query: 481 YRYNQRMYAHFMQDDMPAEQRGIFIAGDDVSWTPAWVEGAVQTSLNAVWGIMKHFGGETH 540
           YRYNQRMYAHFMQDDMPAEQRGIFIAGDDVSWTPAWVEGAVQTSLNAVWGIMKHFGGETH
Sbjct: 481 YRYNQRMYAHFMQDDMPAEQRGIFIAGDDVSWTPAWVEGAVQTSLNAVWGIMKHFGGETH 540

Query: 541 AENPGPGDVFHEIGPIALPE 560
           AENPGPGDVFHEIGPIALPE
Sbjct: 541 AENPGPGDVFHEIGPIALPE 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: 1406
Number of extensions: 35
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 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

GapMind for catabolism of small carbon sources