GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ARO8 in Oceanisphaera arctica V1-41

Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_104485224.1 UN63_RS02645 aspartate/tyrosine/aromatic aminotransferase

Query= BRENDA::A0A140ND68
         (396 letters)



>NCBI__GCF_002936955.1:WP_104485224.1
          Length = 396

 Score =  529 bits (1363), Expect = e-155
 Identities = 251/396 (63%), Positives = 311/396 (78%)

Query: 1   MFENITAAPADPILGLADLFRADERPGKINLGIGVYKDETGKTPVLTSVKKAEQYLLENE 60
           MFE +TAAPADPILGL D FR D R  KINLG+G+YKDE G+TPVL  VKKAE  L++ +
Sbjct: 1   MFEKVTAAPADPILGLTDAFRKDPRTDKINLGVGIYKDEAGQTPVLRCVKKAEARLVQEQ 60

Query: 61  TTKNYLGIDGIPEFGRCTQELLFGKGSALINDKRARTAQTPGGTGALRVAADFLAKNTSV 120
           TTKNYL I+GI  +GR  Q+LLFG  S++I  +RARTAQ PGGTGALR+A +F+A+    
Sbjct: 61  TTKNYLSIEGIEAYGRVVQQLLFGADSSIIASQRARTAQAPGGTGALRIAGEFIARQLET 120

Query: 121 KRVWVSNPSWPNHKSVFNSAGLEVREYAYYDAENHTLDFDALINSLNEAQAGDVVLFHGC 180
             +W+SNP+W NH++VF +AGLEV+EY YY+A+   LDFDA++  L  A+AGDVVL HGC
Sbjct: 121 NTIWISNPTWANHRAVFTAAGLEVKEYGYYNADAKDLDFDAMLADLAHAKAGDVVLLHGC 180

Query: 181 CHNPTGIDPTLEQWQTLAQLSVEKGWLPLFDFAYQGFARGLEEDAEGLRAFAAMHKELIV 240
           CHNPTGIDPT  QW+ LA+LS EKGWLPLFDFAYQGFA+G+EEDA GLR FA  + EL++
Sbjct: 181 CHNPTGIDPTEAQWEQLAKLSAEKGWLPLFDFAYQGFAKGIEEDAYGLRVFAEHNIELLI 240

Query: 241 ASSYSKNFGLYNERVGACTLVAADSETVDRAFSQMKAAIRANYSNPPAHGASVVATILSN 300
           ASS+SKNFGLYNERVGA TLVA D +T + +FSQ+K  IRANYSNPP+HGA+VVA I ++
Sbjct: 241 ASSFSKNFGLYNERVGAFTLVAKDVDTANTSFSQVKGIIRANYSNPPSHGANVVAIIAND 300

Query: 301 DALRAIWEQELTDMRQRIQRMRQLFVNTLQEKGANRDFSFIIKQNGMFSFSGLTKEQVLR 360
             L   W  EL +MR RIQ MR LFV  L  +G N+DFSFI +QNGMFSFSGL KEQV R
Sbjct: 301 PELYQDWLAELAEMRDRIQEMRTLFVEKLSSRGVNKDFSFIARQNGMFSFSGLNKEQVAR 360

Query: 361 LREEFGVYAVASGRVNVAGMTPDNMAPLCEAIVAVL 396
           L++EFG+Y V SGR++VAG+T  N+  LC+A+ A++
Sbjct: 361 LKDEFGIYIVGSGRISVAGITKSNIDALCDALAAIV 396


Lambda     K      H
   0.318    0.134    0.392 

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: 485
Number of extensions: 16
Number of successful extensions: 1
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: 396
Length of database: 396
Length adjustment: 31
Effective length of query: 365
Effective length of database: 365
Effective search space:   133225
Effective search space used:   133225
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: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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:

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