GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patA in Pseudomonas fluorescens GW456-L13

Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate PfGW456L13_1398 Omega-amino acid--pyruvate aminotransferase (EC 2.6.1.18)

Query= BRENDA::Q9I6J2
         (456 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1398
          Length = 456

 Score =  493 bits (1268), Expect = e-144
 Identities = 230/449 (51%), Positives = 324/449 (72%), Gaps = 4/449 (0%)

Query: 6   TNAKTREWQALSRDHHLPPFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCV 65
           T   TR++QA    HH+  F D K LN++G R++ + E +++WD++G + LD M+GLWC 
Sbjct: 3   TPRDTRDYQAADAAHHIHAFVDQKALNDEGPRVMVRGERLHLWDNDGRRYLDGMSGLWCT 62

Query: 66  NVGYGREELVQAATRQMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSE 125
           N+GYGR++L  AA+RQ+ +LP+YN+FF T HP V+EL++ +  + P   +H  +T SGSE
Sbjct: 63  NLGYGRKDLAAAASRQLEQLPYYNMFFHTTHPQVIELSELLFSLLPAHYSHAIYTNSGSE 122

Query: 126 ANDTVLRMVRHYWATKGQPQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDFPIPGIVH 185
           AN+ ++R VR YW   G+P+KK++IGRWNGYHGST+A  +LGGMK +HE G   IP I H
Sbjct: 123 ANEVLIRTVRRYWQVLGKPEKKIMIGRWNGYHGSTLAATALGGMKFMHEMGGM-IPDIEH 181

Query: 186 IAQPYWYGEGGDMSPDEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYW 245
           I +PY++   G+++P EFG+ AA+QLE KILE+G + VA FIAEP QGAGG+I PP++YW
Sbjct: 182 IDEPYFFAHEGNLTPAEFGLRAAQQLEAKILELGADKVAGFIAEPFQGAGGMIFPPESYW 241

Query: 246 PKIREILAKYDILFIADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVV 305
           P+I+ I  KYD+L  ADEVI GFGRTGEWF  +Y+G  PD + IAKGLTSGYIPMGG+++
Sbjct: 242 PEIQRICRKYDVLLCADEVIGGFGRTGEWFAHEYFGFEPDTLSIAKGLTSGYIPMGGLIL 301

Query: 306 RDEIVEVL-NQGGEFYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQ 364
             ++  VL  QGG F HG TYSGHPVAAAVA+ N++ LR+E ++ +VK +  PYLQ+  +
Sbjct: 302 SKKMASVLVEQGGVFAHGLTYSGHPVAAAVAIANLKALRDEGVVTRVKDDIGPYLQQCLR 361

Query: 365 EL-ADHPLVGEARGVGMVAALELVKNKKTRERFTDKG-VGMLCREHCFRNGLIMRAVGDT 422
           E+   HPLVG+ +G GMVAAL+L ++K +R+RF ++  +   CR   F  G+I+R+    
Sbjct: 362 EVFGKHPLVGDIQGTGMVAALQLAEDKTSRKRFANENDIAWRCRTIGFEEGVIIRSTLGR 421

Query: 423 MIISPPLVIDPSQIDELITLARKCLDQTA 451
           MI++P L+    +IDELI    K +D+TA
Sbjct: 422 MIMAPALIASREEIDELIAKTLKAVDRTA 450


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: 676
Number of extensions: 37
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: 456
Length adjustment: 33
Effective length of query: 423
Effective length of database: 423
Effective search space:   178929
Effective search space used:   178929
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