GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Caulo:CCNA_03245
          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 (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