GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patA in Williamsia sterculiae CPCC 203464

Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate WP_076476008.1 BW971_RS02060 4-aminobutyrate--2-oxoglutarate transaminase

Query= BRENDA::P42588
         (459 letters)



>NCBI__GCF_900156495.1:WP_076476008.1
          Length = 452

 Score =  178 bits (451), Expect = 4e-49
 Identities = 134/388 (34%), Positives = 199/388 (51%), Gaps = 39/388 (10%)

Query: 76  LVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAMLA--KTL 133
           +VD  G   ID   G  +  VG  NP V  AV  Q A    H+  ++ P    +A  + L
Sbjct: 55  IVDVDGNSLIDLGSGIAVTGVGASNPAVADAVAAQ-AHHFTHTCFMVTPYEGYVAVAEKL 113

Query: 134 AALTPGKL-KYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATSGAFHGKSLGALSATA 192
             LTPG   K S   NSG E+VE A+K+A+      G+   +A   A+HG++   ++ TA
Sbjct: 114 NELTPGDHEKRSVLFNSGAEAVENAVKVARL---ATGRDAIVAFDHAYHGRTNLTMALTA 170

Query: 193 KST-FRKPFMPLLPGFRHVPFG----------NIEAMRTALNECKKT--GDDVAAVILEP 239
           K+  ++  F P  P    +P             + A + A+ + +    G+ VA +++EP
Sbjct: 171 KTQPYKYNFGPFAPEIYRMPMSYPYRDDLGTDGVSAAKRAIRQIETQIGGEAVAGLLIEP 230

Query: 240 IQGEGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLA 299
           IQGEGG I+P PG+LT + +   + G + I DEVQ G  RTG  FA E E + PDI+  A
Sbjct: 231 IQGEGGFIVPAPGFLTTLAEWARDNGVVFIADEVQAGFCRTGTWFASEAEGIVPDIVTTA 290

Query: 300 KALGGGVMPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQA 359
           K + GG MP+ A     ++   +  +P     T+GGNP+ACAAALATI  + E +L A+A
Sbjct: 291 KGIAGG-MPLSAITGRADLLDKV--HPGGLGGTYGGNPVACAAALATIAEMEELDLNARA 347

Query: 360 EQKGDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRV------ 413
               ++ L   R LA +  D++ + RG+G ++AIE V  E G +  +    ++V      
Sbjct: 348 HHIEEIALPRLRTLADDL-DVIGDVRGRGAMLAIEIV--EPGTDTPAPALAKKVAAAALE 404

Query: 414 -----LVAGTLNNAKTIRIEPPLTLTIE 436
                LV GT  N   IR+ PPL +  E
Sbjct: 405 AGVVILVTGTFGN--VIRLLPPLVIDDE 430


Lambda     K      H
   0.320    0.135    0.393 

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: 516
Number of extensions: 28
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: 459
Length of database: 452
Length adjustment: 33
Effective length of query: 426
Effective length of database: 419
Effective search space:   178494
Effective search space used:   178494
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: 51 (24.3 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