GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astC in Collimonas arenae Ter10

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_128083232.1 CAter10_RS21330 4-aminobutyrate--2-oxoglutarate transaminase

Query= reanno::pseudo1_N1B4:Pf1N1B4_3440
         (406 letters)



>NCBI__GCF_001584165.1:WP_128083232.1
          Length = 420

 Score =  226 bits (577), Expect = 7e-64
 Identities = 151/408 (37%), Positives = 210/408 (51%), Gaps = 33/408 (8%)

Query: 26  FIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAHPALVAALTEQANKLWHVS-NVFTNE 84
           F       S +WD  GR  IDFA GIAV   GH HP LVAA+ EQ  K  H +  +    
Sbjct: 19  FYASHALNSEIWDVEGRRFIDFAAGIAVLNTGHRHPKLVAAIQEQLGKFTHTAYQIVPYG 78

Query: 85  PALRLAHKLVDAT---FAERVFFCNSGAEANEAAFKLARRVAHDRFGTEKYEIVAALNSF 141
             + LA ++   T    A++  F ++GAEA E A K+AR        T +  ++A   +F
Sbjct: 79  SYVELAERINAVTPGDHAKKTTFFSTGAEAVENAVKIARAA------TGRSAVIAFSGAF 132

Query: 142 HGRTLFTVNVGGQS-KYSDGFGPKITGITHVPY----------NDLAAL----KAAVSDK 186
           HGRT+  + + G+   Y  GFGP    + HVP+          N LAAL    KA V  K
Sbjct: 133 HGRTMMGMALTGKVVPYKVGFGPFPAEVYHVPFPVELHGVSIENSLAALQSLFKADVDPK 192

Query: 187 -TCAVVLEPIQGEGGVLPAELSYLQGARELCDAHNALLVFDEVQTGMGRSGKLFAYQHYG 245
              A++LEP+QGEGG   A  +++Q  R+LCD H  LLV DEVQTG  R+GKLFA +H G
Sbjct: 193 RVAAIILEPVQGEGGFYAAPPAFMQALRKLCDEHGILLVVDEVQTGFARTGKLFAVEHSG 252

Query: 246 VTPDILTSAKSLGGGFPIAAMLTTEDLAKHLVVGTHGTTYGGNPLACAVAEAVIDVINTP 305
           V PD++T AKSL GG P++A+    ++      G  G TY GNPLA A A AV+DVI   
Sbjct: 253 VIPDLMTMAKSLAGGMPLSAVCGRAEIMDAAAPGGLGGTYAGNPLAVASALAVLDVIEEE 312

Query: 306 EVLNGVNAKHDKFKTRLEQIGEKYGLFTEVRGLGLLLGCVLSDAWKGK-----AKDIFNA 360
           +++   N    + K  LE +        ++RGLG ++    +     +      K +   
Sbjct: 313 KLVERANVLGGRLKQVLEGLRADVPQIADIRGLGAMVAVEFTQPGSKQPDADFTKKVQAE 372

Query: 361 AEREGLMILQAG--PDVIRFAPSLVVEDADIDAGLDRFERAAAKLTQA 406
           A + GL++L  G   + IRF   L +EDA +D  L    +A   +  A
Sbjct: 373 ALKNGLLLLSCGVYSNAIRFLFPLTIEDALMDEALAILSKAMRTVAAA 420


Lambda     K      H
   0.320    0.136    0.400 

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: 427
Number of extensions: 19
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: 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 24 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