GapMind for catabolism of small carbon sources

 

Aligments for a candidate for prpB in Pseudomonas fluorescens FW300-N2E3

Align isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate AO353_27735 AO353_27735 isocitrate lyase

Query= BRENDA::P9WKK7
         (428 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_27735 AO353_27735 isocitrate
           lyase
          Length = 441

 Score =  545 bits (1404), Expect = e-159
 Identities = 270/430 (62%), Positives = 333/430 (77%), Gaps = 14/430 (3%)

Query: 13  IQQEWDTNPRWKDVTRTYSAEDVVALQGSVVEEHTLARRGAEVLWEQLH---------DL 63
           ++++W  NPRWK VTRTYSA DVV L+GSV  EHT A+ GAE LW  +          + 
Sbjct: 12  LEKDWAENPRWKGVTRTYSAADVVRLRGSVQPEHTFAKMGAEKLWNLVTQGAKPAFRPEK 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+ I+ L +ARLAADVA  PT+++ARTDA AA L+TS
Sbjct: 192 HFEDQLASVKKCGHMGGKVLVPTQEAIQKLIAARLAADVAGTPTIILARTDANAADLLTS 251

Query: 240 DVDERDQPFITGERTREGFYRTKNGIEPCIARAKAYAPFADLIWMETGTPDLEAARQFSE 299
           D D  DQPF+TGERT+EGFY+ + G++  IAR  AYAP+ADLIW ET  PDL+ AR+F+E
Sbjct: 252 DCDPYDQPFVTGERTQEGFYKVRAGLDQAIARGLAYAPYADLIWCETAKPDLDEARRFAE 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 NLAHDYARNDMTAYVKLQEQEFADAAKGYTFVAHQQEVGTGYFDDMTTVIQGGSSSVTAL 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: 638
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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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