GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praB in Rhizobium leguminosarum bv. trifolii WSM1325

Align aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate WP_012757758.1 RLEG_RS11275 aldehyde dehydrogenase family protein

Query= BRENDA::Q83XU8
         (485 letters)



>NCBI__GCF_000023185.1:WP_012757758.1
          Length = 795

 Score =  310 bits (795), Expect = 9e-89
 Identities = 180/444 (40%), Positives = 247/444 (55%), Gaps = 22/444 (4%)

Query: 25  PLNNAVIAKVHEAGRAEVDAAVAAAQAALKGAWGRMSLAQRVEVLYAVADGINRRFDDFL 84
           P    V+AK+   G A+VD AVAAA+ A + +W R+    R   LYA+A  I R      
Sbjct: 55  PATGKVLAKLANGGAADVDNAVAAARKA-QASWARLPGHARARHLYALARMIQRHARLIA 113

Query: 85  AAEVEDTGKPMSLARHVDIPRGAANFKIFADVVKNVPTEFFEMPTPDGVGAINYAVRRPV 144
             E  D GKP+   R +D+P  A +F   A   +   TEF              A   PV
Sbjct: 114 VVEAIDNGKPIRETRDLDVPLAARHFYHHAGWAQIQDTEF--------------ADHVPV 159

Query: 145 GVVGVICPWNLPLLLMTWKVGPALACGNTVVVKPSEETPQTAALLGEVMNTAGVPPGVYN 204
           GVVG I PWN P L++ WKV PALA GNTV++KP+E T  TA L  E+ + AG+PPGV N
Sbjct: 160 GVVGQIIPWNFPFLMLAWKVAPALALGNTVILKPAEFTSLTALLFAELASAAGLPPGVLN 219

Query: 205 VVHGFGPNSTGEFLTSHPDVNAITFTGETGTGEAIMKAAADGARPVSLELGGKNAAIVFA 264
           +V G G   TG  L  H D++ I FTG T  G  I +  A   + ++LELGGK+  +VF 
Sbjct: 220 IVTGEG--ETGALLVGHADIDKIAFTGSTEVGRVIRERTAGSGKSLTLELGGKSPFVVFD 277

Query: 265 DCDLDKAIEGTLRSCFANCGQVCLGTERVYVERPIFDRFVSRLKKGAEGMQLGRPEDLAT 324
           D D+D A+EG + + + N GQVC    R+ V+  I D F  RLK+  E +++G+P D   
Sbjct: 278 DADIDGAVEGVVDAIWFNQGQVCCAGSRLLVQEGIADLFHERLKRRMETLRVGQPLDKCI 337

Query: 325 GMGPLISQEHREKVLSYYKKAVEAGATVVTGGGVPEMPEALKGGAWVQPTIWTGLGDDSV 384
            MG +I+     ++ +  KK V  GAT+       ++P   KGG++  PT+ +G+   S+
Sbjct: 338 DMGAIIAPVQLTRIEALVKKGVSEGATL--HQAKIDLP---KGGSFYPPTLLSGVQPTSI 392

Query: 385 VAREEIFGPCALVMPFDSEEEVIRRANDNDYGLARRIWTTNLSRAHRVAGAIEVGIAWVN 444
           VA EEIFGP A+ M F + EE I+ AN   YGLA  +W+  +  A  VA  +  G+ WVN
Sbjct: 393 VATEEIFGPVAVSMTFRTPEEAIQLANHTRYGLAASVWSETIGLALNVAAKLAAGVVWVN 452

Query: 445 SWFLRDLRTAFGGSKQSGIGREGG 468
           +  L D    FGG ++SG GREGG
Sbjct: 453 ATNLFDAAVGFGGKRESGFGREGG 476



 Score = 92.8 bits (229), Expect = 4e-23
 Identities = 68/233 (29%), Positives = 109/233 (46%), Gaps = 9/233 (3%)

Query: 23  SSPLNNAVIAKVHEAGRAEVDAAVAAAQAALKGAWGRMSLAQRVEVLYAVADGINRRFDD 82
           +SP   A I +V E+ R ++  AV AAQAA   AW   +   R ++LY +A+ ++ R D+
Sbjct: 540 ASPKGKA-IGEVGESNRKDIRNAVVAAQAA--SAWSNATTHNRAQILYYIAENLSGRADE 596

Query: 83  FLAAEVEDTGKPMSLARHVDIPRGAANFKIFADVVKNVPTEFFEMPTPDGVGAINYAVRR 142
           F +     TG   + A + ++    +    +A           + P    +  +  A+  
Sbjct: 597 FASRITAMTGASAANA-NAEVDAAISRLFTYAAWADKYEGGIHQPP----LRGVALAMPE 651

Query: 143 PVGVVGVICPWNLPLLLMTWKVGPALACGNTVVVKPSEETPQTAALLGEVMNTAGVPPGV 202
            +GVVGVICP   PLL     + P +A GN VV  PSE  P +A     V+ T+ VP GV
Sbjct: 652 AIGVVGVICPPEAPLLGFISLIAPLIATGNRVVAVPSEAFPLSATDFYSVLETSDVPAGV 711

Query: 203 YNVVHGFGPNSTGEFLTSHPDVNAITFTGETGTGEAIMKAAADGARPVSLELG 255
            N+V G       + L +H DV+A+   G       + K ++   +   ++ G
Sbjct: 712 VNIVTG-SAIELAKILAAHNDVDALWAFGSAELSTTVEKLSSGNLKRTFVDNG 763


Lambda     K      H
   0.318    0.135    0.406 

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: 918
Number of extensions: 38
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 485
Length of database: 795
Length adjustment: 37
Effective length of query: 448
Effective length of database: 758
Effective search space:   339584
Effective search space used:   339584
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: 53 (25.0 bits)

This GapMind analysis is from Apr 09 2024. 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