GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astC in Cupriavidus basilensis 4G11

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate RR42_RS26240 RR42_RS26240 4-aminobutyrate aminotransferase

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



>FitnessBrowser__Cup4G11:RR42_RS26240
          Length = 420

 Score =  226 bits (575), Expect = 1e-63
 Identities = 150/403 (37%), Positives = 210/403 (52%), Gaps = 38/403 (9%)

Query: 23  FIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAGKFWHTGNGYTNEP 82
           F   R E S LWD +G  YIDFA GIAV   GH HPRLV+A+  Q  +F HT   Y   P
Sbjct: 24  FYAERAENSELWDVEGNRYIDFAAGIAVLNTGHRHPRLVQAMQAQMERFTHTA--YQIVP 81

Query: 83  V---LRLAKQL---IDATFADRVFFCNSGAEANEAALKLARKYAHDRFGSEKSGIVAFKN 136
               + LA+++       FA +  F  +GAEA E A+K+AR        + + G++AF  
Sbjct: 82  YASYIELAEKINARAPGAFAKKTAFFTTGAEAVENAIKIARA------ATGRPGVIAFSG 135

Query: 137 AFHGRTLFTVSAGGQPA-YSQDFAPLPPQIQHAIY-------NDLDSAKAL-------ID 181
            FHGRT+  ++  G+   Y   F P P  + HA Y       +  DS  AL       +D
Sbjct: 136 GFHGRTMMGMALTGKVVPYKVGFGPFPGDVFHAPYPYGLHGVSVQDSINALHQLFKADVD 195

Query: 182 DN-TCAVIVEPMQGEGGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGELYAYMH 240
                A+I EP+QGEGG   A A+F+R LR +CD H  LL+ DEVQTG GRTG+L+A  H
Sbjct: 196 PKRVAAIIFEPVQGEGGFNVAPAEFVRALRAICDEHGILLVADEVQTGFGRTGKLFAMEH 255

Query: 241 YGVTPDLLSTAKALGGGFPIGALLASERCASVMTVGTHGTTYGGNPLACAVAGEVFATIN 300
           Y VTPDL + AK+L GG P+ A+            G  G TY GNPLA A A  V   + 
Sbjct: 256 YDVTPDLTTMAKSLAGGMPLSAVCGRAEIMDAPAPGGLGGTYAGNPLAVASALAVLDVLE 315

Query: 301 TREVLNGVKQRHQWFCERLNAINARYGLFKEIRGLGLLIGCVLKDEYAGK-----AKAIS 355
           + +++       Q   ++L+ + +R     E+RG+G +I    + +  G+      + + 
Sbjct: 316 SEKLIERGAALGQRLQDKLDGLKSRVPEIGEVRGVGAMIAVEFR-KADGRPDPEFTRQVQ 374

Query: 356 NQAAEEGLMILIAG--ANVVRFAPALIISEDEVNSGLDRFELA 396
           ++A E GL++L  G   NVVRF   L I +  ++ GL   E A
Sbjct: 375 DRALERGLLLLSCGVYGNVVRFLFPLTIPDAVMDEGLGILEAA 417


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: 423
Number of extensions: 20
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: 420
Length adjustment: 31
Effective length of query: 375
Effective length of database: 389
Effective search space:   145875
Effective search space used:   145875
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.

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