GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuC in Sinorhizobium meliloti 1021

Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate SMa2213 SMa2213 aldehyde dehydrogenase

Query= metacyc::MONOMER-11560
         (497 letters)



>FitnessBrowser__Smeli:SMa2213
          Length = 494

 Score =  361 bits (926), Expect = e-104
 Identities = 203/475 (42%), Positives = 283/475 (59%), Gaps = 5/475 (1%)

Query: 23  FINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAK 82
           +I+G++    SGE  E + P   R  A V   +  DA+RAV  A   F+ G W ++ P +
Sbjct: 10  YIDGQWVAPASGEYIETVDPFTARPWALVPRGNAEDADRAVRAAHRAFSQGPWGKMHPTE 69

Query: 83  RKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDEV 142
           R   + RFA L+ ++ + LA +E  D G+ + + +   I    +  H+ A   DK+   +
Sbjct: 70  RGRIIQRFAALIEEHADALADIEVRDNGRLLAEMTH-QIRYIPRWYHYYAGFADKIEGTL 128

Query: 143 APTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAIR 202
            P     L     EP+GV   IVPWN PLL+   K  PALA GN++V+KP+E +  TA++
Sbjct: 129 HPCDKPALSFSRHEPLGVCVGIVPWNAPLLLFSLKAAPALAAGNTLVMKPAEFTSATALK 188

Query: 203 IAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESNMK 262
           + +L  +AG P GV+NV+ GYG  VG+ L  H     + FTGSTK    L   A + ++K
Sbjct: 189 LMELVEKAGFPTGVINVVTGYGPEVGEPLVTHPLTRHVGFTGSTKTGAHLYSLAAK-DVK 247

Query: 263 RIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKFLPMV 322
           R+ LE GGKSPNIVF DA DL  A       I    G+ C AGSRLLV RSI D+FL  +
Sbjct: 248 RVSLELGGKSPNIVFGDA-DLDNAVRGVVGGIFGAVGQTCIAGSRLLVHRSIHDEFLEKL 306

Query: 323 VEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRT-LEETG-G 380
               K  + G+P   +T +G + ++ Q   VL YI+   ++GA+L+ GG R  LEE G G
Sbjct: 307 AVFTKTARIGDPRKVETQIGPIANSMQFEKVLGYIDIARREGAELILGGGRPDLEECGTG 366

Query: 381 TYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTSDISK 440
            ++EPTIF GV+N MRIA+EE+FGPVLS I FD  EEA+AIAND+ +GL AG+WTSD+  
Sbjct: 367 YFIEPTIFAGVSNDMRIAREEVFGPVLSAIVFDEPEEALAIANDSEFGLGAGVWTSDMRL 426

Query: 441 AHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELKATWI 495
           A K +  + AGSVWVN Y     T PFGG+K+SG GR+  +  + +Y + KA W+
Sbjct: 427 ALKMSERLEAGSVWVNTYRDISYTTPFGGYKKSGIGRENGVAGIYEYLQTKAVWL 481


Lambda     K      H
   0.316    0.132    0.390 

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: 673
Number of extensions: 29
Number of successful extensions: 5
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: 497
Length of database: 494
Length adjustment: 34
Effective length of query: 463
Effective length of database: 460
Effective search space:   212980
Effective search space used:   212980
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: 52 (24.6 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