GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dpkA in Sinorhizobium meliloti 1021

Align 1-piperideine-2-carboxylate/1-pyrroline-2-carboxylate reductase (NADPH) (EC 1.5.1.21) (characterized)
to candidate SMa1871 SMa1871 cyclodeaminase

Query= BRENDA::Q9QYU4
         (313 letters)



>FitnessBrowser__Smeli:SMa1871
          Length = 330

 Score =  137 bits (345), Expect = 3e-37
 Identities = 97/316 (30%), Positives = 158/316 (50%), Gaps = 20/316 (6%)

Query: 8   LSADEVQDHLRSSSLLIPPLEAALANFSKGPDGGVMQPVRTVVPVAKHRGFLGVMPAYSA 67
           L  DEV+  L   + +I  +E A   FS      V QP    +     RG +     Y  
Sbjct: 6   LKKDEVR-RLIGMAEVIGAVEEAYKAFSSDQ---VEQPDYIGIHHPSLRGEIDFKLGYYK 61

Query: 68  AEDALTTKLVT--FYEGHSNNAVPSHQASVLLFDPSNGSLLAVMDGNVITAKRTAAVSAI 125
           A + ++ K  +  F    + + VP+   ++LLFD  + +L+ +MDG++IT  RT A  A+
Sbjct: 62  ANEIISMKAHSGGFTNNPAEHGVPNSIGTILLFDARSCALICIMDGSLITGLRTGASGAV 121

Query: 126 ATKFLKPPGSDVLCILGAGVQAYSHYEIFTEQFSFKEVRMWNRTRENAEKFASSVQGD-- 183
           + K L    +  +  +G G QA        E    +++  W+RT E+  ++ + +Q +  
Sbjct: 122 SVKALARKNARTVASIGTGNQARMQIRAVNEIMKIEKIHAWSRTPESLSRYKTDIQREFG 181

Query: 184 --VRVCSSVQEAVTGADVIITVTMATEPILFGEWVKPGAHINAVGASRPDWRELDDELMK 241
             V V SS +EAV  AD++IT T     ++  +WVKPG HI A+G  +   +ELD E+ +
Sbjct: 182 IPVIVASSKKEAVEQADILITTTRGKGSLVEADWVKPGTHIVAIGTDQRGKQELDPEIFR 241

Query: 242 QAVLYVDSREAALKESGDV-------LLSGADIFAELGEVVSGAKPA--YCEKTTVFKSL 292
            A + VDS  A   E G+        +++  DI  E+GEV+ G KP     ++ T+F S 
Sbjct: 242 NAKVVVDS-VAQCTEKGETWHPLNKNIITKDDIHGEIGEVLLGRKPGRESDDEITIFDST 300

Query: 293 GMAVEDLVAAKLVYDS 308
           GMA++D   A  +Y +
Sbjct: 301 GMAIQDNTTASKIYQN 316


Lambda     K      H
   0.317    0.131    0.377 

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: 227
Number of extensions: 12
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: 313
Length of database: 330
Length adjustment: 28
Effective length of query: 285
Effective length of database: 302
Effective search space:    86070
Effective search space used:    86070
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 (21.7 bits)
S2: 48 (23.1 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