GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patA in Halomonas xinjiangensis TRM 0175

Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate WP_043527315.1 JH15_RS04225 4-aminobutyrate--2-oxoglutarate transaminase

Query= BRENDA::P42588
         (459 letters)



>NCBI__GCF_000759345.1:WP_043527315.1
          Length = 432

 Score =  197 bits (502), Expect = 4e-55
 Identities = 144/430 (33%), Positives = 226/430 (52%), Gaps = 39/430 (9%)

Query: 54  RKSVTAGGDYGAVEWQAGSLNTLV-DTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLA 112
           ++ V  G    A ++   + N L+ D  G   ID  GG G+ N+GHR+P VV AV+ QL 
Sbjct: 11  QRYVANGAASPATQFADRAENALIWDADGNRLIDFAGGIGVLNIGHRHPKVVEAVKAQLD 70

Query: 113 KQPLHSQELLDPLRAML--AKTLAALTP--GKLKYSFFCNSGTESVEAALKLAKAYQSPR 168
           K  +H+ + + P    +  A+ L+ +TP  G  K     NSG E++E A+K+A+A     
Sbjct: 71  KV-MHTCQTVMPYEGYVKVAEKLSQITPVRGHAKV-MLANSGAEALENAVKVARA---AT 125

Query: 169 GKFTFIATSGAFHGKSLGALSATAKSTFRKPFMPLLPG--FRH---VPFGNI---EAMRT 220
           GK   I   G +HG++   ++   K          +PG  FR    VP+  +   EA+R 
Sbjct: 126 GKNNVICFDGGYHGRTFMTMAMNGKVAPYATDFGSMPGNVFRAPYPVPYHGVSEDEALRG 185

Query: 221 ALNECKKTGD--DVAAVILEPIQGEGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMG 278
                K   +  D AA++LEP+ GEGG    P  +L A+R +CDE G L+I+DEVQ+G G
Sbjct: 186 LKMALKTDANPKDTAAIVLEPVLGEGGFYAAPASFLKAIRDICDEHGILLIIDEVQSGFG 245

Query: 279 RTGKMFACEHENVQPDILCLAKALGGGVMPIGATIATEEVFSVLFDNPFLHTTTFGGNPL 338
           RTGKMFA EH  V+PDI+C+AK++  G MPI A + T++V      N      T+ G+P+
Sbjct: 246 RTGKMFAIEHSGVEPDIICMAKSMADG-MPISAVVGTDKVMDASGGNSL--GGTYTGSPV 302

Query: 339 ACAAALATINVLLEQNLPAQAEQKGDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVDN 398
           +CAA LA + V  E+ +  +++  GD L   F Q  +++ D V   R  G + A + V +
Sbjct: 303 SCAATLAVLEVFEEEKILEKSQALGDKLAKRFSQWEQDF-DCVDNGRNLGAMAAFDLVSD 361

Query: 399 EIGYNFASEM-------FRQRVLV---AGTLNNAKTIRIEPPLTL---TIEQCELVIKAA 445
           +  +   +++        R++ LV    G   N  TIR   P+T+    +E+   V+++A
Sbjct: 362 KAQHTPDADLAGALCKRAREKGLVLLSCGLYGN--TIRFLMPVTIEDDILEEGLGVVESA 419

Query: 446 RKALAAMRVS 455
            K L   + +
Sbjct: 420 LKELVGNKAA 429


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: 433
Number of extensions: 19
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: 459
Length of database: 432
Length adjustment: 32
Effective length of query: 427
Effective length of database: 400
Effective search space:   170800
Effective search space used:   170800
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