GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patA in Stutzerimonas stutzeri A1501

Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate WP_011911296.1 PST_RS00235 aspartate aminotransferase family protein

Query= BRENDA::P42588
         (459 letters)



>NCBI__GCF_000013785.1:WP_011911296.1
          Length = 439

 Score =  187 bits (476), Expect = 5e-52
 Identities = 128/393 (32%), Positives = 196/393 (49%), Gaps = 39/393 (9%)

Query: 79  TQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQ-ELLDPLRAMLAKTLAALT 137
           + G++ +D   G    N GH    +  AV  Q+A+       ++  PL   LA+ LAA++
Sbjct: 40  SDGRQVLDGTAGLWCCNAGHGRREISEAVSKQIARMDFAPTFQMGHPLPFELAEKLAAIS 99

Query: 138 PGKLKYSFFCNSGTESVEAALKLAKAYQSPRGKFT---FIATSGAFHGKSLGALSATAKS 194
           P  L   FF NSG+ES + ALK+A AYQ   G+ +    I    A+HG   G +S    +
Sbjct: 100 PEGLNRVFFTNSGSESADTALKIALAYQRAIGQGSRTRLIGRELAYHGVGFGGMSVGGMA 159

Query: 195 TFRKPFMPLLPGFRHVPFGNIEAMRTALNE-----------------CKKTGDDVAAVIL 237
             R+ F P+LPG  H+P   ++  R A ++                      +++AAVI+
Sbjct: 160 NNRRAFGPMLPGVDHLPH-TLDLQRNAFSKGLPQHGVERADELERLVTLHGAENIAAVIV 218

Query: 238 EPIQGEGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILC 297
           EP+ G  GVILPP GYL  +R++  + G L+I DEV TG GR G+ FA +   V PDIL 
Sbjct: 219 EPMSGSAGVILPPVGYLQRLREITAKHGILLIFDEVITGFGRVGEAFAAQRWGVTPDILT 278

Query: 298 LAKALGGGVMPIGATIATEEVFSVLFDNP-----FLHTTTFGGNPLACAAALATINVLLE 352
            AK L  G +P+GA    + ++      P     F H  T+ G+P+ACAAALAT  +  +
Sbjct: 279 CAKGLTNGAIPMGAVFVADRLYDAFMQGPESVIEFFHGYTYSGHPVACAAALATQQIYQQ 338

Query: 353 QNLPAQAEQKGDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVDN-----EIGYNFASE 407
           +NL  +A        +    L R+ P+++ + R  G++  I+F  +     + GY    E
Sbjct: 339 ENLFQKAIDLEPYWQEALFSL-RDLPNVI-DIRTVGLVAGIQFAAHADGVGKRGYEVFRE 396

Query: 408 MFRQRVLVAGTLNNAKTIRIEPPLTLTIEQCEL 440
            F   +LV     +  TI + P   L +E+ E+
Sbjct: 397 CFENGLLVRA---SGDTIALSP--ALIVEKAEI 424


Lambda     K      H
   0.320    0.135    0.393 

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: 419
Number of extensions: 29
Number of successful extensions: 5
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: 459
Length of database: 439
Length adjustment: 33
Effective length of query: 426
Effective length of database: 406
Effective search space:   172956
Effective search space used:   172956
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 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