GapMind for catabolism of small carbon sources

 

Aligments for a candidate for patA in Caulobacter crescentus NA1000

Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate CCNA_03245 CCNA_03245 beta alanine-pyruvate transaminase

Query= BRENDA::Q9I6J2
         (456 letters)



>lcl|FitnessBrowser__Caulo:CCNA_03245 CCNA_03245 beta
           alanine-pyruvate transaminase
          Length = 442

 Score =  262 bits (669), Expect = 2e-74
 Identities = 150/433 (34%), Positives = 232/433 (53%), Gaps = 17/433 (3%)

Query: 24  PFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCVNVGYGREELVQAATRQMR 83
           PFT  ++  ++  R+++ A G++    E  ++LDA +GLWCVN G+ R ++ +A  +Q  
Sbjct: 18  PFTPNRRF-KRHPRMLSSASGMWYRTPESREVLDATSGLWCVNAGHDRPKIREAIQKQAA 76

Query: 84  ELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEANDTVLRMVRHYWATKGQ 143
           E+  Y   F   HP   + A  +A + P+G++ +FFT SGSE+ DT L++   Y   +G+
Sbjct: 77  EMD-YAPCFNMGHPLAFQFASRLAQITPKGLDRIFFTNSGSESVDTALKIALAYHRARGK 135

Query: 144 PQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDFPIPGIVHIAQPYWYGEGGDM---SP 200
             K  +IGR  GYHG    G+S+GG+          + G+ H+  P+ +G  G+      
Sbjct: 136 GTKTRLIGRERGYHGVGFGGISVGGIPKNRMYFGSLLTGVDHL--PHTHGLPGNTCAKGQ 193

Query: 201 DEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYWPKIREILAKYDILFI 260
            E G   A+ LE+ +      N+AA I EP+ G+ GV++PP  Y  ++R I  K+DIL I
Sbjct: 194 PENGAHLADDLERIVALHDASNIAAVIVEPVAGSTGVLIPPKGYLERLRAICDKHDILLI 253

Query: 261 ADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVEVLNQGG--- 317
            DEVI GFGR G  F ++ +G  PDL+ +AKGLT+  +P G V    +I + +  G    
Sbjct: 254 FDEVITGFGRVGAPFAAERFGVTPDLICMAKGLTNAAVPCGAVAASGKIYDAMMDGADAP 313

Query: 318 -EFYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQELADHPLVGEAR 376
            E +HG+TYS HP+A A  L  +   RE+ +  +  A    Y Q     LAD   V + R
Sbjct: 314 IELFHGYTYSAHPLACAAGLATLETYREDDLFARA-AGLEGYWQDAMHSLADARHVVDVR 372

Query: 377 GVGMVAALELVKNKKTRERFTDKGVGMLCREHCFRNGLIMRAVGDTMIISPPLVIDPSQI 436
            +G+VA +EL                M   E CF  GL++R  GD + +SPPL+++   I
Sbjct: 373 NLGLVAGIELEPRPG-----APTARAMEVFETCFDEGLLIRVTGDIIALSPPLILEKDHI 427

Query: 437 DELITLARKCLDQ 449
           D ++   R+ L Q
Sbjct: 428 DRMVETIRRVLGQ 440


Lambda     K      H
   0.320    0.138    0.425 

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: 554
Number of extensions: 31
Number of successful extensions: 6
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: 456
Length of database: 442
Length adjustment: 33
Effective length of query: 423
Effective length of database: 409
Effective search space:   173007
Effective search space used:   173007
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 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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