GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__HerbieS:HSERO_RS04810
          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 (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