GapMind for catabolism of small carbon sources

 

Aligments for a candidate for astC in Echinicola vietnamensis KMM 6221, DSM 17526

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate Echvi_0577 Echvi_0577 ornithine aminotransferase

Query= reanno::Koxy:BWI76_RS11670
         (406 letters)



>lcl|FitnessBrowser__Cola:Echvi_0577 Echvi_0577 ornithine
           aminotransferase
          Length = 413

 Score =  228 bits (582), Expect = 2e-64
 Identities = 130/389 (33%), Positives = 204/389 (52%), Gaps = 6/389 (1%)

Query: 18  YAPAAFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAGKFWHTGNG 77
           Y P   +  RGEG  +WD +G++Y DF    +    GH HPR+++ L +QAG    T   
Sbjct: 23  YHPLPVVLSRGEGVFMWDVEGEKYYDFLSSYSAVNQGHCHPRILQTLIDQAGTLTLTSRA 82

Query: 78  YTNEPVLRLAKQLIDATFADRVFFCNSGAEANEAALKLARKYAHDRFG--SEKSGIVAFK 135
           + N+ +    K L +    D+V   N+GAE  E A+K+ARK+ +++ G    +  I+  K
Sbjct: 83  FHNDVLGPFEKFLTEYFGYDKVLPMNTGAEGVETAIKIARKWGYEKKGIPENEGTIIVAK 142

Query: 136 NAFHGRTLFTVSAGGQPAYSQDFAPLPPQIQHAIYNDLDSAKALIDD--NTCAVIVEPMQ 193
           N FHGRT   +S        ++F P  P      ++D+D+ K ++    N    +VEP+Q
Sbjct: 143 NNFHGRTTTVISFSNDETARKNFGPYTPGFVTIPHDDIDALKDVLSQSKNIIGYLVEPIQ 202

Query: 194 GEGGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGELYAYMHYGVTPDLLSTAKA 253
           GE GV      +L+ +  +C  H  L + DE+QTG+ RTG+L A  H GV PD+L   KA
Sbjct: 203 GEAGVYVPKEGYLKEVAAVCKDHGVLFMADEIQTGIARTGKLLACDHEGVKPDMLILGKA 262

Query: 254 LGGGF-PIGALLASERCASVMTVGTHGTTYGGNPLACAVAGEVFATINTREVLNGVKQRH 312
           + GGF P+ A+LA +    V+  G HG+T+GGNPL   VA      +   ++     +  
Sbjct: 263 ISGGFYPVSAVLADDHIMEVIQPGQHGSTFGGNPLGAKVAMTALNVVKDEKLAENADKLG 322

Query: 313 QWFCERLNAINARYGLFKEIRGLGLLIGCVLKD-EYAGKAKAISNQAAEEGLMILIAGAN 371
           + F ER+  +  +  L + +RG GLL   V+ D E +  A  +     E GL+      N
Sbjct: 323 KLFRERIQQLVDKSDLVELVRGKGLLNAIVINDTEDSDTAWRLCLALKENGLLAKPTHGN 382

Query: 372 VVRFAPALIISEDEVNSGLDRFELACKRF 400
           ++RFAP L+I+E++++   D  E   + F
Sbjct: 383 IIRFAPPLVITEEQLHDCCDIIEKTIQNF 411


Lambda     K      H
   0.321    0.137    0.412 

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: 417
Number of extensions: 25
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: 406
Length of database: 413
Length adjustment: 31
Effective length of query: 375
Effective length of database: 382
Effective search space:   143250
Effective search space used:   143250
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: 50 (23.9 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, 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