GapMind for catabolism of small carbon sources

 

Alignments for a candidate for amaB in Sinorhizobium meliloti 1021

Align L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale)
to candidate SMa2213 SMa2213 aldehyde dehydrogenase

Query= uniprot:Q88CC3
         (496 letters)



>FitnessBrowser__Smeli:SMa2213
          Length = 494

 Score =  194 bits (492), Expect = 8e-54
 Identities = 143/460 (31%), Positives = 227/460 (49%), Gaps = 24/460 (5%)

Query: 39  GKAETIAR-IDQAQSAFEA--WRSVPAPRRGELVRLFGEVLREHKADLGELVSIEAGKIT 95
           G AE   R +  A  AF    W  +    RG +++ F  ++ EH   L ++   + G++ 
Sbjct: 41  GNAEDADRAVRAAHRAFSQGPWGKMHPTERGRIIQRFAALIEEHADALADIEVRDNGRLL 100

Query: 96  QEGLGEVQEMIDICDFAVGLSRQLYGLTIASERPGHHMRETWHPLGVVGVISAFNFPVAV 155
            E   +++ +     +  G + ++ G     ++P         PLGV   I  +N P+ +
Sbjct: 101 AEMTHQIRYIPRWYHYYAGFADKIEGTLHPCDKPALSFSRH-EPLGVCVGIVPWNAPLLL 159

Query: 156 WAWNTALALVAGNSVVWKPSEKTPLTALACQALFEKALKAFGDAPAGLAQLVIG-GREAG 214
           ++   A AL AGN++V KP+E T  TAL    L EKA       P G+  +V G G E G
Sbjct: 160 FSLKAAPALAAGNTLVMKPAEFTSATALKLMELVEKA-----GFPTGVINVVTGYGPEVG 214

Query: 215 EAMVDDPRVPLVSATGSTRMGREVGPRVAARFGRSILELGGNNAMILAPSADLDLAVRGI 274
           E +V  P    V  TGST+ G  +    A    R  LELGG +  I+   ADLD AVRG+
Sbjct: 215 EPLVTHPLTRHVGFTGSTKTGAHLYSLAAKDVKRVSLELGGKSPNIVFGDADLDNAVRGV 274

Query: 275 LFSAVGTAGQRCTTLRRLIVHRSIKDEVVARVKAAYGKVRIGDPRK-DNLVGPLIDKQSF 333
           +    G  GQ C    RL+VHRSI DE + ++       RIGDPRK +  +GP+ +   F
Sbjct: 275 VGGIFGAVGQTCIAGSRLLVHRSIHDEFLEKLAVFTKTARIGDPRKVETQIGPIANSMQF 334

Query: 334 DAMQGALAKARDEGGQ-VFGGERQLADQYPNAYYVSPAI-AEMPAQSDVVRHETFAPILY 391
           + + G +  AR EG + + GG R   ++    Y++ P I A +     + R E F P+L 
Sbjct: 335 EKVLGYIDIARREGAELILGGGRPDLEECGTGYFIEPTIFAGVSNDMRIAREEVFGPVLS 394

Query: 392 VLAYDDFEEALRLNNEVPQGLSSCIFTTDIREA----ERFQSASGSDCGIANVNIGTSGA 447
            + +D+ EEAL + N+   GL + ++T+D+R A    ER ++ S       +++  T   
Sbjct: 395 AIVFDEPEEALAIANDSEFGLGAGVWTSDMRLALKMSERLEAGSVWVNTYRDISYTT--- 451

Query: 448 EIGGAFGGEKETGGGRESGSDAWKGYMRRQTNTVNYSREL 487
                FGG K++G GRE+G      Y++ +   ++ + E+
Sbjct: 452 ----PFGGYKKSGIGRENGVAGIYEYLQTKAVWLSTAEEI 487


Lambda     K      H
   0.318    0.135    0.396 

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: 558
Number of extensions: 23
Number of successful extensions: 6
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: 496
Length of database: 494
Length adjustment: 34
Effective length of query: 462
Effective length of database: 460
Effective search space:   212520
Effective search space used:   212520
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: 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