GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aspA in Pseudomonas fluorescens FW300-N2E3

Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate AO353_09950 AO353_09950 aspartate ammonia-lyase

Query= BRENDA::Q9HTD7
         (474 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_09950 AO353_09950 aspartate
           ammonia-lyase
          Length = 474

 Score =  830 bits (2143), Expect = 0.0
 Identities = 427/474 (90%), Positives = 445/474 (93%)

Query: 1   MSPVASSRIEKDLLGTLEVPADAYYGIQTLRAVNNFRLSGVPLSHYPKLVVALAMVKQAA 60
           MS  AS R EKDLLG LEVPA AYYGIQTLRAVNNFRLSGVP+SHYPKLVV LAMVKQAA
Sbjct: 1   MSSAASFRTEKDLLGVLEVPAQAYYGIQTLRAVNNFRLSGVPISHYPKLVVGLAMVKQAA 60

Query: 61  ADANRQLGHLPEDKHAAISEACARLIRGDFHEQFVVDMIQGGAGTSTNMNANEVIANIAL 120
           ADANR+LGHL + KHAAISEACARLIRGDFHE+FVVDMIQGGAGTSTNMNANEVIANIAL
Sbjct: 61  ADANRELGHLSDVKHAAISEACARLIRGDFHEEFVVDMIQGGAGTSTNMNANEVIANIAL 120

Query: 121 EAMGHTKGEYKYLHPNNDVNMAQSTNDAYPTAIRLGLLLGHDTLLASLDSLIQAFAAKGV 180
           EAMGH+KGEY+YLHPNNDVNMAQSTNDAYPTAIRLGLLLGHD LLASLDSLIQ+FAAKG 
Sbjct: 121 EAMGHSKGEYQYLHPNNDVNMAQSTNDAYPTAIRLGLLLGHDALLASLDSLIQSFAAKGE 180

Query: 181 EFAGVLKMGRTQLQDAVPMTLGQEFHAFATTLGEDLDRLRRLAPELLTEVNLGGTAIGTG 240
           EF+ VLKMGRTQLQDAVPMTLGQEF AFATTL EDL RL+ LAPELLTEVNLGGTAIGTG
Sbjct: 181 EFSHVLKMGRTQLQDAVPMTLGQEFRAFATTLSEDLARLKTLAPELLTEVNLGGTAIGTG 240

Query: 241 INADPGYQKLAVERLAAISGQPLKPAADLIEATSDMGAFVLFSGMLKRTAVKLSKICNDL 300
           INADP YQ LAV+RLA ISGQPL PAADLIEATSDMGAFVLFSGMLKRTAVKLSKICNDL
Sbjct: 241 INADPRYQHLAVQRLALISGQPLVPAADLIEATSDMGAFVLFSGMLKRTAVKLSKICNDL 300

Query: 301 RLLSSGPRTGINEINLPPRQPGSSIMPGKVNPVIPEAVNQVAFEVIGNDLALTLAAEGGQ 360
           RLLSSGPRTGINEINLP RQPGSSIMPGKVNPVIPEAVNQVAF++IGNDLALT+AAEGGQ
Sbjct: 301 RLLSSGPRTGINEINLPARQPGSSIMPGKVNPVIPEAVNQVAFQIIGNDLALTIAAEGGQ 360

Query: 361 LQLNVMEPLIAYKIFDSIRLLQRAMDMLREHCITGITANVERCHELVEHSIGLVTALNPY 420
           LQLNVMEPLIA+KIFDSIRLLQRAMDMLREHCI GITAN  RC ELVEHSIGLVTALNPY
Sbjct: 361 LQLNVMEPLIAFKIFDSIRLLQRAMDMLREHCIVGITANEARCRELVEHSIGLVTALNPY 420

Query: 421 IGYENSTRIAKTALESGRGVLELVREEKLLDEATLADILLPENMIAPRLIPLRA 474
           IGYEN+TRIA+ ALESGRGVLELVREE LLDEA LADIL PENMIAPRL+PL+A
Sbjct: 421 IGYENATRIARIALESGRGVLELVREEGLLDEAMLADILRPENMIAPRLVPLKA 474


Lambda     K      H
   0.318    0.135    0.380 

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: 813
Number of extensions: 19
Number of successful extensions: 2
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: 474
Length of database: 474
Length adjustment: 33
Effective length of query: 441
Effective length of database: 441
Effective search space:   194481
Effective search space used:   194481
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: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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