GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astC in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_068170823.1 HTA01S_RS10480 4-aminobutyrate--2-oxoglutarate transaminase

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



>NCBI__GCF_001592305.1:WP_068170823.1
          Length = 428

 Score =  213 bits (543), Expect = 7e-60
 Identities = 139/400 (34%), Positives = 199/400 (49%), Gaps = 34/400 (8%)

Query: 29  EGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAGKFWHTGNGYTNEPV---LR 85
           + + LWD +G+ +IDFAGGIAV   GH HP++  A+  Q  +F H+   Y   P    + 
Sbjct: 37  KNAELWDIEGRRFIDFAGGIAVLNTGHVHPKVQAAIAAQLQRFTHSC--YQVVPYAEYVS 94

Query: 86  LAKQL---IDATFADRVFFCNSGAEANEAALKLARKYAHDRFGSEKSGIVAFKNAFHGRT 142
           LA+++   +      +  F ++GAEA E A+K+AR        + +SG++AF  AFHGR+
Sbjct: 95  LAERINAIVPIEGKAKTAFFSTGAEAIENAIKIARS------STGRSGVIAFGGAFHGRS 148

Query: 143 LFTVSAGGQ-PAYSQDFAPLPPQIQHAIYN----DLDSAKALID---------DNTCAVI 188
           LF VS  G+   Y   F P PP+I H  +      LD  K  +D             A++
Sbjct: 149 LFAVSLTGKVQPYKAGFGPFPPEIYHVPFPAEGASLDETKRAMDHVFKCDIEPSRVAAIV 208

Query: 189 VEPMQGEGGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGELYAYMHYGVTPDLL 248
            EP+QGEGG  P   D +  LR LCD H  LLI DEVQTG  RTG ++A  HYGV+PDL+
Sbjct: 209 FEPVQGEGGFNPIQKDAVLWLRALCDQHGILLIADEVQTGFARTGRMFAMEHYGVSPDLM 268

Query: 249 STAKALGGGFPIGALLASERCASVMTVGTHGTTYGGNPLACAVAGEVFATINTREVLNGV 308
           + AK++ GG  + A+            G  G TY GNPLA A +  V   +   ++    
Sbjct: 269 TMAKSMAGGTTLSAVSGKAAIMDGPAPGGLGGTYAGNPLAIAASHAVLDVMAEEKLPERA 328

Query: 309 KQRHQWFCERLNAINARYGLFKEIRGLGLLIGCVLKDEY----AGKAKAISNQAAEEGLM 364
           ++        L A  A+Y    E+RGLG ++ C   D      A   K +   A + GL+
Sbjct: 329 QRLGDQLVAHLRAAKAKYPRIGEVRGLGAMVACEFVDAAGAPDADTTKQVQAAALKRGLL 388

Query: 365 ILIAG--ANVVRFAPALIISEDEVNSGLDRFELACKRFLA 402
           +L  G   NV+R+   L I +      L   + A    LA
Sbjct: 389 LLTCGVYGNVIRYLFPLTIEDSVFAEALGVLDAAMAETLA 428


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: 465
Number of extensions: 21
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: 428
Length adjustment: 31
Effective length of query: 375
Effective length of database: 397
Effective search space:   148875
Effective search space used:   148875
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 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