GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Sinorhizobium meliloti 1021

Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate SM_b21185 SM_b21185 succinate-semialdehyde dehydrogenase (NAD(P)+) protein

Query= BRENDA::P25553
         (479 letters)



>FitnessBrowser__Smeli:SM_b21185
          Length = 491

 Score =  329 bits (844), Expect = 1e-94
 Identities = 177/448 (39%), Positives = 263/448 (58%), Gaps = 2/448 (0%)

Query: 25  DVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERASWLRKISAGIRERAS 84
           DV NP+T  +++ +PD   +DAR AIDAA  AQP W   PA +R+  LR+    I E A 
Sbjct: 36  DVSNPSTGELLATLPDMGIDDARTAIDAAALAQPLWAGKPAKDRSIILRRWHDLIVEHAD 95

Query: 85  EISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQSDRPGENILLFKRALG 144
           +++A++  E GK    A+ EV   A Y+++ AE A+R  GE   +      +L+ K+ +G
Sbjct: 96  DLAAILTAEMGKPVGEAKGEVLHAASYVEWYAEEAKRVYGETFPAPANDRRMLVIKQPVG 155

Query: 145 VTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAFAKIVDEIGLPRGVFNL 204
           V   I PWNFP  ++ARK++PAL  G TIV+KP+E TP  A A   + ++ G P GV NL
Sbjct: 156 VVGTITPWNFPASMVARKISPALAAGCTIVLKPAEQTPLVAGAMFVLAEKAGFPEGVLNL 215

Query: 205 V-LGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKVCLELGGKAPAIVMDD 263
           +    G  +G+EL GNPKV  +S TGS   G  +M   +  I KV LELGG AP IV DD
Sbjct: 216 LYASEGAPIGRELCGNPKVRKISFTGSTEVGRLLMRQCSDQIKKVSLELGGNAPFIVFDD 275

Query: 264 ADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEAMQAVQFGNPAERNDI 323
           AD++ AV   V ++  N+GQ C  A R+YVQ  ++D F  +    ++ +  G+     D+
Sbjct: 276 ADIDEAVDGAVQAKFRNAGQTCVSANRIYVQSAVHDAFAEKFVTRVRELTVGD-GFAPDV 334

Query: 324 AMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGYYYPPTLLLDVRQEMSIMHEE 383
           A+GP+I+A A++++E  VA AV +GA+V  GG  +   G ++ PT+L  +  +M I  EE
Sbjct: 335 AIGPMIDAHAIDKIEAHVADAVAKGAQVRSGGSRIGTTGTFFEPTVLTGISHDMRIAQEE 394

Query: 384 TFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAIKGLKFGETYINRENFE 443
           TFGP+ P++ F+T E  ++ AND+ YGL +  Y +NL       + L++G   IN     
Sbjct: 395 TFGPIAPIIRFETAEQVVAEANDTIYGLAAYFYAENLKRVWHVAEALEYGMVGINTGRMS 454

Query: 444 AMQGFHAGWRKSGIGGADGKHGLHEYLQ 471
           +      G ++SGIG    +HGL +YL+
Sbjct: 455 SEAAPFGGIKQSGIGREGSRHGLEDYLE 482


Lambda     K      H
   0.318    0.135    0.392 

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: 550
Number of extensions: 19
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: 479
Length of database: 491
Length adjustment: 34
Effective length of query: 445
Effective length of database: 457
Effective search space:   203365
Effective search space used:   203365
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