GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD'B in Clostridium acetobutylicum ATCC 824

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_010965684.1 CA_RS12260 aspartate aminotransferase family protein

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



>NCBI__GCF_000008765.1:WP_010965684.1
          Length = 387

 Score =  347 bits (890), Expect = e-100
 Identities = 179/373 (47%), Positives = 240/373 (64%), Gaps = 5/373 (1%)

Query: 27  RGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAGKFWHTGNGYTNEPVLRL 86
           +GEG++L+D+ G EYIDF  G+AVN LGH +P +VKA+ EQ+ K  H  N Y NE  + L
Sbjct: 19  KGEGTKLYDKDGNEYIDFVSGVAVNCLGHCNPSIVKAIEEQSSKLMHVSNYYWNENAMEL 78

Query: 87  AKQLIDATFADRVFFCNSGAEANEAALKLARKYAHDRFGSEKSGIVAFKNAFHGRTLFTV 146
            + L   +  D+VF CNSG EA EA LKLARKYA       K  I+   N+FHGRT+  +
Sbjct: 79  TEILCKNSEFDKVFMCNSGTEAIEAGLKLARKYALLHGDENKKEIIYMDNSFHGRTMGAL 138

Query: 147 SAGGQPAYSQDFAPLPPQIQHAIYNDLDSAKALIDDNTCAVIVEPMQGEGGVVPADADFL 206
           S  GQP Y + F PL   ++   +NDLD  K  I   T AVIVEP+QGEGG++PA  ++L
Sbjct: 139 SVTGQPKYQESFKPLIGAVKSVKFNDLDDIKQKISSKTAAVIVEPIQGEGGIIPAKKEYL 198

Query: 207 RGLRELCDAHNALLIFDEVQTGVGRTGELYAYMHYGVTPDLLSTAKALGGGFPIGALLAS 266
           + LR+LCD +NALLIFDEVQ G+GR G L+AY  + V PD++  AKALGGGFPIGA+LA 
Sbjct: 199 KLLRDLCDENNALLIFDEVQCGMGRVGSLFAYQKFEVVPDIVCIAKALGGGFPIGAMLAK 258

Query: 267 ERCASVMTVGTHGTTYGGNPLACAVAGEVFATINTREVLN-GVKQRHQWFCERLNAINAR 325
           E  AS    G HG TYGGNPLACAVA  V   +  ++V+   V ++ ++  ++L  +  +
Sbjct: 259 ESVASSFVPGDHGNTYGGNPLACAVAIAVLKELVDKKVVEINVNEKSKYLFDKLMTLKEK 318

Query: 326 YGLFKEIRGLGLLIGCVLKDEYAGKAKAISNQAAEEGLMILIAGANVVRFAPALIISEDE 385
           Y +  ++RG+GLLIG     E A   K I N+  E  L+++ AG NVVRF P L +S +E
Sbjct: 319 YKVINDVRGMGLLIGV----EVACDVKKIINKCFESKLLLITAGKNVVRFLPPLNVSFEE 374

Query: 386 VNSGLDRFELACK 398
           ++  L  FE + K
Sbjct: 375 IDKALGIFEESIK 387


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: 437
Number of extensions: 15
Number of successful extensions: 3
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: 387
Length adjustment: 31
Effective length of query: 375
Effective length of database: 356
Effective search space:   133500
Effective search space used:   133500
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 Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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