GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patA in Rhodanobacter denitrificans FW104-10B01

Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate WP_027490801.1 LRK54_RS04500 acetyl ornithine aminotransferase family protein

Query= BRENDA::P42588
         (459 letters)



>NCBI__GCF_021560695.1:WP_027490801.1
          Length = 444

 Score =  240 bits (612), Expect = 8e-68
 Identities = 158/405 (39%), Positives = 225/405 (55%), Gaps = 39/405 (9%)

Query: 78  DTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAMLAKTLAALT 137
           D  G  F+D + G  +   GH +P VV AVQ+  AK    S +        L + LAA+ 
Sbjct: 52  DVDGNRFLDFMAGIAVCATGHAHPQVVKAVQDAAAKFLHISSDYWHEEMTGLGERLAAVA 111

Query: 138 P-GKLKYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATSGAFHGKSLGALSATA-KST 195
           P G    SF C SGTE+VE ALKLA+      G+  FI   G FHG++ G+LS T+ K T
Sbjct: 112 PLGAPAMSFICQSGTEAVEGALKLARYVT---GRPRFIGFLGGFHGRTFGSLSFTSSKYT 168

Query: 196 FRKPFMPLLPGFRHVPFGN---------------IEAMRTALNECKKTGDDVAAVILEPI 240
            +K F P L G  HVP+ N               ++ +R  L +      +VAA+++EP+
Sbjct: 169 QQKGFSPTLAGVTHVPYPNPYRPLFAGDDQGAAVLDYIRM-LFQRSVPPSEVAAILIEPM 227

Query: 241 QGEGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAK 300
           QGEGG + PP G+L  +R LCDE G L+I DEVQ+G+GRTG+MFACEH  VQPDI+  AK
Sbjct: 228 QGEGGYLTPPDGFLAGLRALCDEHGILLIFDEVQSGIGRTGRMFACEHWGVQPDIITSAK 287

Query: 301 ALGGGVMPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAE 360
            LG G +PIGA IA + + S        H  T+GGNP+ CAAA AT++ L+   L   A 
Sbjct: 288 GLGSG-LPIGAVIAKKSIMSQW--KRGAHGNTYGGNPVTCAAANATLD-LVRGGLMDNAA 343

Query: 361 QKGDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFAS---EMFRQRVLVAG 417
           + GD  +   R+L R+YP  + E RGKG+ + +E ++++     A+   E   QR    G
Sbjct: 344 RVGDHFMARLRELQRDYP-CIGEVRGKGLWIGMELIEDDGKKTPATALCEAVVQRAFHNG 402

Query: 418 TL---NNAKTIRIEPPLTLTIEQCELVIKAARKALAAMRVSVEEA 459
            L       T+R  PPL +++ + +       +A+A +R S+++A
Sbjct: 403 LLLLSCGTSTVRFMPPLNVSVGEVD-------EAIALLRSSLDQA 440


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: 493
Number of extensions: 32
Number of successful extensions: 10
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: 444
Length adjustment: 33
Effective length of query: 426
Effective length of database: 411
Effective search space:   175086
Effective search space used:   175086
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 Apr 09 2024. 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