GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpB in Dyella japonica UNC79MFTsu3.2

Align isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate N515DRAFT_4123 N515DRAFT_4123 isocitrate lyase

Query= BRENDA::P9WKK7
         (428 letters)



>FitnessBrowser__Dyella79:N515DRAFT_4123
          Length = 433

 Score =  591 bits (1523), Expect = e-173
 Identities = 282/421 (66%), Positives = 347/421 (82%), Gaps = 2/421 (0%)

Query: 9   SAEQIQQEWDTNPRWKDVTRTYSAEDVVALQGSVVEEHTLARRGAEVLWEQLHDLEWVNA 68
           +AEQI  +W  NPRW  V R Y+A DVV L+G+V  EH++AR GAE LW+ L   ++VNA
Sbjct: 7   TAEQITLDWQNNPRWNGVRRNYTAADVVRLRGTVPVEHSIARHGAERLWKSLQQEDFVNA 66

Query: 69  LGALTGNMAVQQVRAGLKAIYLSGWQVAGDANLSGHTYPDQSLYPANSVPQVVRRINNAL 128
           LGALTGN A+QQV+AGLKAIYLSGWQVA DANL+G  YPDQSLYPANSVPQVV+RINN L
Sbjct: 67  LGALTGNQAMQQVKAGLKAIYLSGWQVAADANLAGEMYPDQSLYPANSVPQVVKRINNTL 126

Query: 129 QRADQIAKIEGDTSVENWLAPIVADGEAGFGGALNVYELQKALIAAGVAGSHWEDQLASE 188
            RADQ+   EG+  ++ W+ PIVAD EAGFGG LN +EL KA+I AG +G H+EDQLAS 
Sbjct: 127 LRADQLHHAEGNDEID-WMVPIVADAEAGFGGVLNAFELMKAMIEAGASGVHFEDQLASV 185

Query: 189 KKCGHLGGKVLIPTQQHIRTLTSARLAADVADVPTVVIARTDAEAATLITSDVDERDQPF 248
           KKCGH+GGKVL+PT++ +  LT+ARLAADV  VPT+++ARTDA+AA L+TSD+D+ D+PF
Sbjct: 186 KKCGHMGGKVLVPTREAVDKLTAARLAADVLGVPTLLVARTDADAADLLTSDIDDNDRPF 245

Query: 249 ITGERTREGFYRTKNGIEPCIARAKAYAPFADLIWMETGTPDLEAARQFSEAVKAEYPDQ 308
           +TGERT EGF+R + G++  I+R  AYAP+ADL+W ET  P+LE AR+F+EA+ A++P +
Sbjct: 246 VTGERTVEGFFRVRPGLDQAISRGLAYAPYADLVWCETSKPNLEEARRFAEAIHAQFPGK 305

Query: 309 MLAYNCSPSFNWKKHLDDATIAKFQKELAAMGFKFQFITLAGFHALNYSMFDLAYGYAQN 368
           +LAYNCSPSFNWKK+LDDATIA+FQ+EL AMG+KFQFITLAGFH+LNY MFDLA+GYA+ 
Sbjct: 306 LLAYNCSPSFNWKKNLDDATIARFQRELGAMGYKFQFITLAGFHSLNYGMFDLAHGYARR 365

Query: 369 QMSAYVELQEREFAAEERGYTATKHQREVGAGYFDRIATTVDP-NSSTTALTGSTEEGQF 427
           QMSA+VELQEREFAA ERG+TA KHQREVG GYFD++   +    SSTTAL GSTEE QF
Sbjct: 366 QMSAFVELQEREFAAAERGFTAVKHQREVGTGYFDQVTQAIQQGQSSTTALKGSTEEAQF 425

Query: 428 H 428
           H
Sbjct: 426 H 426


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: 621
Number of extensions: 21
Number of successful extensions: 3
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: 433
Length adjustment: 32
Effective length of query: 396
Effective length of database: 401
Effective search space:   158796
Effective search space used:   158796
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