GapMind for catabolism of small carbon sources

 

Aligments for a candidate for davB in Pseudomonas putida KT2440

Align lysine 2-monooxygenase (EC 1.13.12.2) (characterized)
to candidate PP_0383 PP_0383 Lysine 2-monooxygenase

Query= BRENDA::Q88QV1
         (560 letters)



>lcl|FitnessBrowser__Putida:PP_0383 PP_0383 Lysine 2-monooxygenase
          Length = 560

 Score = 1172 bits (3031), Expect = 0.0
 Identities = 560/560 (100%), Positives = 560/560 (100%)

Query: 1   MNKKNRHPADGKKPITIFGPDFPFAFDDWLEHPAGLGSIPAERHGEEVAIVGAGIAGLVA 60
           MNKKNRHPADGKKPITIFGPDFPFAFDDWLEHPAGLGSIPAERHGEEVAIVGAGIAGLVA
Sbjct: 1   MNKKNRHPADGKKPITIFGPDFPFAFDDWLEHPAGLGSIPAERHGEEVAIVGAGIAGLVA 60

Query: 61  AYELMKLGLKPVVYEASKLGGRLRSQAFNGTDGIVAELGGMRFPVSSTAFYHYVDKLGLE 120
           AYELMKLGLKPVVYEASKLGGRLRSQAFNGTDGIVAELGGMRFPVSSTAFYHYVDKLGLE
Sbjct: 61  AYELMKLGLKPVVYEASKLGGRLRSQAFNGTDGIVAELGGMRFPVSSTAFYHYVDKLGLE 120

Query: 121 TKPFPNPLTPASGSTVIDLEGQTYYAEKPTDLPQLFHEVADAWADALESGAQFADIQQAI 180
           TKPFPNPLTPASGSTVIDLEGQTYYAEKPTDLPQLFHEVADAWADALESGAQFADIQQAI
Sbjct: 121 TKPFPNPLTPASGSTVIDLEGQTYYAEKPTDLPQLFHEVADAWADALESGAQFADIQQAI 180

Query: 181 RDRDVPRLKELWNKLVPLWDDRTFYDFVATSRSFAKLSFQHREVFGQVGFGTGGWDSDFP 240
           RDRDVPRLKELWNKLVPLWDDRTFYDFVATSRSFAKLSFQHREVFGQVGFGTGGWDSDFP
Sbjct: 181 RDRDVPRLKELWNKLVPLWDDRTFYDFVATSRSFAKLSFQHREVFGQVGFGTGGWDSDFP 240

Query: 241 NSMLEIFRVVMTNCDDHQHLVVGGVEQVPQGIWRDVPERCVHWPEGTSLSTLHGGAPRTG 300
           NSMLEIFRVVMTNCDDHQHLVVGGVEQVPQGIWRDVPERCVHWPEGTSLSTLHGGAPRTG
Sbjct: 241 NSMLEIFRVVMTNCDDHQHLVVGGVEQVPQGIWRDVPERCVHWPEGTSLSTLHGGAPRTG 300

Query: 301 VKRIARAADGRLAVTDNWGDTRHYSAVLATCQTWLLTTQIDCEESLFSQKMWMALDRTRY 360
           VKRIARAADGRLAVTDNWGDTRHYSAVLATCQTWLLTTQIDCEESLFSQKMWMALDRTRY
Sbjct: 301 VKRIARAADGRLAVTDNWGDTRHYSAVLATCQTWLLTTQIDCEESLFSQKMWMALDRTRY 360

Query: 361 MQSSKTFVMVDRPFWKDKDPETGRDLLSMTLTDRLTRGTYLFDNGNDKPGVICLSYSWMS 420
           MQSSKTFVMVDRPFWKDKDPETGRDLLSMTLTDRLTRGTYLFDNGNDKPGVICLSYSWMS
Sbjct: 361 MQSSKTFVMVDRPFWKDKDPETGRDLLSMTLTDRLTRGTYLFDNGNDKPGVICLSYSWMS 420

Query: 421 DALKMLPHPVEKRVQLALDALKKIYPKTDIAGHIIGDPITVSWEADPYFLGAFKGALPGH 480
           DALKMLPHPVEKRVQLALDALKKIYPKTDIAGHIIGDPITVSWEADPYFLGAFKGALPGH
Sbjct: 421 DALKMLPHPVEKRVQLALDALKKIYPKTDIAGHIIGDPITVSWEADPYFLGAFKGALPGH 480

Query: 481 YRYNQRMYAHFMQQDMPAEQRGIFIAGDDVSWTPAWVEGAVQTSLNAVWGIMNHFGGHTH 540
           YRYNQRMYAHFMQQDMPAEQRGIFIAGDDVSWTPAWVEGAVQTSLNAVWGIMNHFGGHTH
Sbjct: 481 YRYNQRMYAHFMQQDMPAEQRGIFIAGDDVSWTPAWVEGAVQTSLNAVWGIMNHFGGHTH 540

Query: 541 PDNPGPGDVFNEIGPIALAD 560
           PDNPGPGDVFNEIGPIALAD
Sbjct: 541 PDNPGPGDVFNEIGPIALAD 560


Lambda     K      H
   0.320    0.138    0.441 

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: 1407
Number of extensions: 53
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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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 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