GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lysN in Collimonas arenae Ter10

Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate WP_128083232.1 CAter10_RS21330 4-aminobutyrate--2-oxoglutarate transaminase

Query= reanno::Putida:PP_4108
         (416 letters)



>NCBI__GCF_001584165.1:WP_128083232.1
          Length = 420

 Score =  347 bits (890), Expect = e-100
 Identities = 185/410 (45%), Positives = 253/410 (61%), Gaps = 11/410 (2%)

Query: 8   QSIAIVHPITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHY 67
           + + ++     SH  N+E+WD +G+R+IDF  GI VLN GH +P +V AIQ Q  + TH 
Sbjct: 11  RGVGVMCDFYASHALNSEIWDVEGRRFIDFAAGIAVLNTGHRHPKLVAAIQEQLGKFTHT 70

Query: 68  AFNAAPHGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGATGKRAIIAFDG 127
           A+   P+G Y+ L E+++   P  +       ++GAEA ENA+K+AR ATG+ A+IAF G
Sbjct: 71  AYQIVPYGSYVELAERINAVTPGDHAKKTTFFSTGAEAVENAVKIARAATGRSAVIAFSG 130

Query: 128 GFHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELA 187
            FHGRT+  + L GKV PYK   G  P  VYH+P+P    GV+ E +L A+  LF  ++ 
Sbjct: 131 AFHGRTMMGMALTGKVVPYKVGFGPFPAEVYHVPFPVELHGVSIENSLAALQSLFKADVD 190

Query: 188 VEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPR 247
            + VAA I EPVQGEGGF A  PAF QALR+ CDE GIL+++DE+Q+GF RTG+ FA   
Sbjct: 191 PKRVAAIILEPVQGEGGFYAAPPAFMQALRKLCDEHGILLVVDEVQTGFARTGKLFAVEH 250

Query: 248 LGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMT 307
            G+ PDL+ +AKS+AGGMPL AV GR E+M A   GGLGGTY+GNP++ A+ALA L  + 
Sbjct: 251 SGVIPDLMTMAKSLAGGMPLSAVCGRAEIMDAAAPGGLGGTYAGNPLAVASALAVLDVIE 310

Query: 308 DENLA----TWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQ 363
           +E L       G R +Q +    E  +A    P I  + G+GAM  +EF         A 
Sbjct: 311 EEKLVERANVLGGRLKQVL----EGLRAD--VPQIADIRGLGAMVAVEFTQPGSKQPDAD 364

Query: 364 LAKVMEA-ARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCL 412
             K ++A A   GLLL+  G   + IR L PLTIE  +++E L IL + +
Sbjct: 365 FTKKVQAEALKNGLLLLSCGVYSNAIRFLFPLTIEDALMDEALAILSKAM 414


Lambda     K      H
   0.320    0.137    0.402 

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: 508
Number of extensions: 21
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: 416
Length of database: 420
Length adjustment: 32
Effective length of query: 384
Effective length of database: 388
Effective search space:   148992
Effective search space used:   148992
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.

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