GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo3_N2E3:AO353_27735
          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:

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