GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astC in Shewanella loihica PV-4

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate 5209240 Shew_1718 adenosylmethionine-8-amino-7-oxononanoate aminotransferase (RefSeq)

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



>FitnessBrowser__PV4:5209240
          Length = 446

 Score =  159 bits (403), Expect = 1e-43
 Identities = 120/347 (34%), Positives = 172/347 (49%), Gaps = 31/347 (8%)

Query: 15  MPVYAPAAFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAGKFWHT 74
           +PVY       V  EG  L    G+  ID          G+ HP +++A+ +Q     H 
Sbjct: 27  LPVYGV-----VSAEGCELILDDGRRLIDGTSSWWACVHGYGHPYILEAMQKQLSTLSHV 81

Query: 75  G-NGYTNEPVLRLAKQLIDATFAD--RVFFCNSGAEANEAALKLARKYAHDRFGSEKSGI 131
              G T+   + ++K+L+  T  +  +VF  +SG+ A E A+K+A +Y   R    K  I
Sbjct: 82  MFGGITHPSAIAVSKKLLAMTSDNLTKVFLADSGSIAVEVAMKMALQYWQGRGAPSKQRI 141

Query: 132 VAFKNAFHGRTLFTVSAG----------GQPAYSQDFAPLP--PQIQHAIYNDLDSAKAL 179
           +  K+ +HG T   +S            G+    Q FAP P  P  +  I +DL++ +AL
Sbjct: 142 LTVKHGYHGDTFAAMSVCDPEGGMHTMFGEAVTQQLFAPAPKTPFGETLIADDLEAMEAL 201

Query: 180 ID---DNTCAVIVEP-MQGEGGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGEL 235
           ++       AVI+EP MQG G +    AD+L+GLR LCD +  LLI DE+ TG GRTG+L
Sbjct: 202 LNAHHQTIAAVIIEPIMQGAGAMHFYSADYLKGLRALCDRYKVLLILDEIATGFGRTGKL 261

Query: 236 YAYMHYGVTPDLLSTAKALGGGF-PIGALLASERCA-----SVMTVGTHGTTYGGNPLAC 289
           +AY H G+  D+L   KAL GG+  + A L S+  A     S   V  HG T+ GNPLAC
Sbjct: 262 FAYQHAGIEADILCLGKALTGGYISLAATLCSDEVALGISDSPSGVFMHGPTFMGNPLAC 321

Query: 290 AVAGEVFATINTREVLNGVKQRHQWFCERLNAINARYGLFKEIRGLG 336
           A A      IN  +    V    Q   + L   +A  G+ K +R LG
Sbjct: 322 AAASASLDLINQHQWPEQVAAIEQQMKQELATASAIEGV-KAVRCLG 367


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: 414
Number of extensions: 22
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: 406
Length of database: 446
Length adjustment: 32
Effective length of query: 374
Effective length of database: 414
Effective search space:   154836
Effective search space used:   154836
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 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