Aligments for a candidate for prpB in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Aligments for a candidate for prpB in Pseudomonas fluorescens FW300-N2C3

Align isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate AO356_22080 AO356_22080 isocitrate lyase

Query= BRENDA::P9WKK7
         (428 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22080 AO356_22080
           isocitrate lyase
          Length = 441

 Score =  541 bits (1395), Expect = e-158
 Identities = 268/430 (62%), Positives = 331/430 (76%), Gaps = 14/430 (3%)

Query: 13  IQQEWDTNPRWKDVTRTYSAEDVVALQGSVVEEHTLARRGAEVLWEQLH---------DL 63
           ++++W  NPRWK V R YSA DVV L+GSV  EHT A+ GAE LW  +          + 
Sbjct: 12  LEKDWAENPRWKGVKRNYSAADVVRLRGSVQPEHTFAKMGAEKLWNLVTQGAKPAFRPEK 71

Query: 64  EWVNALGALTGNMAVQQVRAGLKAIYLSGWQVAGDANLSGHTYPDQSLYPANSVPQVVRR 123
           ++VN +GALTG  AVQQV+AG++AIYLSGWQVA D N +   YPDQSLYP +SVP VV+R
Sbjct: 72  DFVNCMGALTGGQAVQQVKAGIQAIYLSGWQVAADNNSAESMYPDQSLYPVDSVPTVVKR 131

Query: 124 INNALQRADQI----AKIEGDTSVENWLAPIVADGEAGFGGALNVYELQKALIAAGVAGS 179
           INN+ +RADQI     K  GD    ++ APIVAD EAGFGG LN YEL K++I AG AG 
Sbjct: 132 INNSFRRADQIQWKAGKNPGDEGYIDYFAPIVADAEAGFGGVLNAYELMKSMIEAGAAGV 191

Query: 180 HWEDQLASEKKCGHLGGKVLIPTQQHIRTLTSARLAADVADVPTVVIARTDAEAATLITS 239
           H+EDQLAS KKCGH+GGKVL+PTQ+ ++ LT+ARLAADVA VPT+++ARTDA AA L+TS
Sbjct: 192 HFEDQLASVKKCGHMGGKVLVPTQEAVQKLTAARLAADVAGVPTIILARTDANAADLLTS 251

Query: 240 DVDERDQPFITGERTREGFYRTKNGIEPCIARAKAYAPFADLIWMETGTPDLEAARQFSE 299
           D D  DQPF+TG RT+EGFY+ + G++  IAR  AYAP+ADLIW ET  PDL+ AR+F+E
Sbjct: 252 DCDPYDQPFVTGTRTQEGFYKVRAGLDQAIARGLAYAPYADLIWCETAKPDLDEARRFAE 311

Query: 300 AVKAEYPDQMLAYNCSPSFNWKKHLDDATIAKFQKELAAMGFKFQFITLAGFHALNYSMF 359
           A+K EYPDQ+L+YNCSPSFNWKK+LDDATIAKFQ+EL+AMG+K QFITLAG H + +SMF
Sbjct: 312 AIKKEYPDQLLSYNCSPSFNWKKNLDDATIAKFQRELSAMGYKHQFITLAGIHNMWHSMF 371

Query: 360 DLAYGYAQNQMSAYVELQEREFAAEERGYTATKHQREVGAGYFDRIATTVD-PNSSTTAL 418
           +LA+ YA+N M+AYV+LQE+EFA   +GYT   HQ+EVG GYFD + T +    SS TAL
Sbjct: 372 NLAHDYARNDMTAYVKLQEQEFADAAKGYTFVAHQQEVGTGYFDDMTTVIQGGTSSVTAL 431

Query: 419 TGSTEEGQFH 428
           TGSTEE QFH
Sbjct: 432 TGSTEEEQFH 441


Lambda     K      H
   0.316    0.130    0.384 

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: 632
Number of extensions: 14
Number of successful extensions: 4
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: 428
Length of database: 441
Length adjustment: 32
Effective length of query: 396
Effective length of database: 409
Effective search space:   161964
Effective search space used:   161964
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 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