GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patA in Sinorhizobium fredii NGR234

Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate WP_015886749.1 NGR_RS03045 aspartate aminotransferase family protein

Query= BRENDA::Q9I6J2
         (456 letters)



>NCBI__GCF_000018545.1:WP_015886749.1
          Length = 458

 Score =  325 bits (834), Expect = 1e-93
 Identities = 177/440 (40%), Positives = 250/440 (56%), Gaps = 7/440 (1%)

Query: 16  LSRDHHLPPFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCVNVGYGREELV 75
           L R H + P   Y+   + G R++  A+G  + D+ G +++D  AGLWCVN GYG E +V
Sbjct: 9   LDRAHLIHPVASYRGHEKLGVRVLASAKGATVTDASGRQLIDGFAGLWCVNAGYGHESIV 68

Query: 76  QAATRQMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEANDTVLRMVR 135
           +AATRQMRELP+   +F     P + LA  +A+ AP  ++HVFFT  GS+A D+ +R +R
Sbjct: 69  EAATRQMRELPYATGYFGLGSEPAIRLASELAERAPGNLDHVFFTLGGSDAVDSTIRFIR 128

Query: 136 HYWATKGQPQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDFPIPGIVHIAQPYWYGEG 195
           +YW  +G+PQ+   I    GYHGS+  G  L  + A H     P      I   Y Y   
Sbjct: 129 YYWIGRGEPQRDQFISVEQGYHGSSTVGAGLTALPAFHAGFGIPFDWQHKIPSHYAYRNP 188

Query: 196 GDMSPDEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYWPKIREILAKY 255
               P      +   L +K+ E+G E VAAF AEPIQG+GGV+VPP  +   +R++  + 
Sbjct: 189 VGDDPQAIIDASLAALRQKVEEIGPERVAAFYAEPIQGSGGVLVPPKGWMKAMRQLCQEL 248

Query: 256 DILFIADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVEVLNQ 315
            ILF+ADEVI GFGRTG  F        PD M +AKGLTSGY+PMG V + D I + +  
Sbjct: 249 GILFVADEVITGFGRTGPLFACHEDEIVPDFMTVAKGLTSGYVPMGAVFMGDHIYQTIAD 308

Query: 316 ---GGEFYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQELADHPLV 372
               G   HG+TYS HPV+AAV LE +++   E +    KA     L    + L DHPLV
Sbjct: 309 SAGAGAVGHGYTYSAHPVSAAVGLEVLKLYENELLDNGRKA--GARLMAGLESLKDHPLV 366

Query: 373 GEARGVGMVAALELVKNKKTRERFTDKG-VGMLCREHCFRNGLIMRAVGDTMI-ISPPLV 430
           G+ RG GM+AA+ELV +K+ +     K        +  + NGL++RA  + ++  +PPL 
Sbjct: 367 GDVRGRGMLAAVELVVDKEKKTPLPAKAEPARRIFDRAWENGLVIRAFANGVLGYAPPLC 426

Query: 431 IDPSQIDELITLARKCLDQT 450
              ++ID ++   RK LD+T
Sbjct: 427 CTEAEIDGIVERTRKVLDET 446


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: 627
Number of extensions: 29
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: 456
Length of database: 458
Length adjustment: 33
Effective length of query: 423
Effective length of database: 425
Effective search space:   179775
Effective search space used:   179775
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