GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Methylocapsa aurea KYG

Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate WP_036264374.1 DL86_RS17780 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA

Query= BRENDA::P23883
         (495 letters)



>NCBI__GCF_000746085.1:WP_036264374.1
          Length = 1033

 Score =  154 bits (389), Expect = 1e-41
 Identities = 142/481 (29%), Positives = 221/481 (45%), Gaps = 24/481 (4%)

Query: 30   AAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPAKRKAVLNK 89
            AA E        P+  + +  +       +  AM  ARG F+   WS +    R A L++
Sbjct: 550  AAREGAARAIASPIDGSSIGLVREAAPGLLQEAMREARGGFKI--WSRTPVGLRAACLDR 607

Query: 90   LADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAI---RWYAEAIDKVYGEVATTS 146
             A  +EA A     L  ++ GK    +L D I     AI   R+YA+   + +   A   
Sbjct: 608  AAQELEAQAPRWLHLLQIEAGK----TLEDAIGEWREAIDFCRYYAQEARRRFASPAPMP 663

Query: 147  --SHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSAIRLA 204
              + E   +     GV   I PWNFPL +   ++  ALAAGNSV+ KP+E++PL A +  
Sbjct: 664  GPTGEDNRLFCHGRGVFVCISPWNFPLSIFLGQIAAALAAGNSVLAKPAEQTPLIAAQAV 723

Query: 205  GLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKD--AGDSNMK 262
             L   AG+P  VL+++ G G + G AL   + +  +A TGS  T  ++ +   A    + 
Sbjct: 724  SLLYRAGVPASVLHLLPGDG-DVGAALVALDGVAGVAITGSMDTATKINRSLAAKSGPIA 782

Query: 263  RVWLEAGGKSANIVFADCPDL-QQAASATAAGIFYNQGQVCIAGTRLLLEESIADEFLAL 321
            ++  E GG   N + AD   L +Q      A  F + GQ C A   L L+E +AD  +A+
Sbjct: 783  QLIAETGG--VNAMIADATALPEQVCDDVVASAFRSAGQRCSALRLLCLQEDVADRMIAM 840

Query: 322  LKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDGRNAGLAAAIGP 381
            +K  A+    G P      +G +ID A   S+ + I +  +   +   GR    A   G 
Sbjct: 841  IKGAARELLVGDPRALGVHVGPVIDLAAKRSLEAHIEDMRACAIVHYAGRAPSTAPPRGF 900

Query: 382  TIFVDVDPNASLS--REEIFGPVLVVTRFTSEEQA--LQLANDSQYGLGAAVWTRDLSRA 437
             +   +   +S+S  R E FGP+L V R+ + E    L     + +GL   V +R  +  
Sbjct: 901  YLAPHIFELSSVSDLRREAFGPILHVARYKASELGGLLDSIEAAGFGLTLGVHSRIDAVI 960

Query: 438  HRMSRRLKAGSVFVNNYNDGDM--TVPFGGYKQSGNG-RDKSLHALEKFTELKTIWISLE 494
              +  R  AG+ +VN    G +  T PFGG+  SG G +    H L++F   +T+ I+  
Sbjct: 961  DEIVERRLAGNCYVNRNMIGAVVGTQPFGGFGLSGTGPKAGGPHYLDRFCVEQTVTINTA 1020

Query: 495  A 495
            A
Sbjct: 1021 A 1021


Lambda     K      H
   0.317    0.133    0.389 

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: 961
Number of extensions: 41
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: 495
Length of database: 1033
Length adjustment: 39
Effective length of query: 456
Effective length of database: 994
Effective search space:   453264
Effective search space used:   453264
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 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