GapMind for catabolism of small carbon sources

 

Aligments for a candidate for nbaE in Herbaspirillum seropedicae SmR1

Align aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate HSERO_RS04810 HSERO_RS04810 aldehyde dehydrogenase

Query= BRENDA::Q83XU8
         (485 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS04810 HSERO_RS04810 aldehyde
           dehydrogenase
          Length = 504

 Score =  283 bits (725), Expect = 7e-81
 Identities = 166/461 (36%), Positives = 248/461 (53%), Gaps = 12/461 (2%)

Query: 24  SPLNNAVIAKVHEAGRAEVDAAVAAAQAALKGAWGRMSLAQRVEVLYAVADGINRRFDDF 83
           +P          + G A V+AA  AAQ A +  W  +S A R   LYAV   I    +  
Sbjct: 43  NPATGRASLSYRDGGAAAVEAAAVAAQRAQR-QWWALSHAARGRALYAVGAVIRAEAEPL 101

Query: 84  LAAEVEDTGKPMSLARHVDIPRGAANFKIFADVVKNVPTEFFEMPTPDGVGAINYAVRRP 143
              E   +GKP+   R  ++ + A  F+ +A        E   +P+      +NY  R P
Sbjct: 102 ARLEAISSGKPIRDCR-AEMQKVAEMFEYYAGWADKFYGEVIPVPSSH----LNYTRREP 156

Query: 144 VGVVGVICPWNLPLLLMTWKVGPALACGNTVVVKPSEETPQTAALLGEVMNTAGVPPGVY 203
            G V  + PWN P     W++GPALA GN V++KPSE TP ++  +  +   AG+P G+ 
Sbjct: 157 YGTVLQMTPWNAPAFTCGWQLGPALATGNAVLLKPSELTPFSSLAIARLGEQAGLPAGLV 216

Query: 204 NVVHGFGPNSTGEFLTSHPDVNAITFTGETGTGEAIMKAAADGARPVSLELGGKNAAIVF 263
           NV+ G G     + + +   V  + F G   TG  I KAAA    P  LELGGK+A I+F
Sbjct: 217 NVLAGLGQTMVPQAMATWT-VKKVIFVGSPATGALIAKAAAARVMPCVLELGGKSANIIF 275

Query: 264 ADCDLDKAIEGTLRSCFANCGQVCLGTERVYVERPIFDRFVSRLKKGAEGMQLGRPEDLA 323
            D DL  A  G   + F+  GQ C+   R+ V+R ++DRFV  +  GAE ++LG P D +
Sbjct: 276 EDADLRLAAFGAQAAIFSGAGQSCVAGSRLLVQRKVYDRFVETVAAGAEKIRLGAPLDDS 335

Query: 324 TGMGPLISQEHREKVLSYYKKAVEAGATVVTGGGVPEMPEALKGGAWVQPTIWTGLGDDS 383
           T +GP+ +++  E +     + +EAGAT+  G          + G +V+PT+     +  
Sbjct: 336 TEVGPINNRKQYEHIQRMVARGLEAGATLAAGH-----TRYGEEGYFVRPTLLAHASNAM 390

Query: 384 VVAREEIFGPCALVMPFDSEEEVIRRANDNDYGLARRIWTTNLSRAHRVAGAIEVGIAWV 443
            VAR EIFGP A+ +PF+ EEE I  AND+++GLA  +WT +++RAHRVA ++  G  WV
Sbjct: 391 EVARSEIFGPVAVAIPFEDEEEAIAIANDSEFGLAGAVWTRDVARAHRVAASVNAGTFWV 450

Query: 444 NSWFLRDLRTAFGGSKQSGIGREGGVHSLEFYTELKNVCIK 484
           NS+   ++ + FGG  +SG GR  G+ +L  YT+ K+V ++
Sbjct: 451 NSYKTINVASPFGGFNRSGYGRSSGMEALYDYTQTKSVWVE 491


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: 573
Number of extensions: 18
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: 485
Length of database: 504
Length adjustment: 34
Effective length of query: 451
Effective length of database: 470
Effective search space:   211970
Effective search space used:   211970
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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