GapMind for catabolism of small carbon sources

 

Aligments for a candidate for patA in Pseudomonas fluorescens FW300-N2E3

Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate AO353_15040 AO353_15040 aminotransferase

Query= BRENDA::Q9I6J2
         (456 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_15040 AO353_15040
           aminotransferase
          Length = 456

 Score =  494 bits (1271), Expect = e-144
 Identities = 229/449 (51%), Positives = 329/449 (73%), Gaps = 4/449 (0%)

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

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

Query: 126 ANDTVLRMVRHYWATKGQPQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDFPIPGIVH 185
           AN+ ++R VR YW   G+P+KKV+IGRWNGYHGST+A  +LGGMK +HE G   IP I H
Sbjct: 123 ANEVLIRTVRRYWTILGKPEKKVMIGRWNGYHGSTLAATALGGMKFMHEMGGM-IPDIAH 181

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

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

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

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

Query: 423 MIISPPLVIDPSQIDELITLARKCLDQTA 451
           MI++P L+    ++DEL+    + +D+TA
Sbjct: 422 MIMAPALIATREEVDELVGKTLRAVDRTA 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: 686
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: 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 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